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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 : parrello 1.61 #
7 : olson 1.30 # The SEED Toolkit is free software. You can redistribute
8 :     # it and/or modify it under the terms of the SEED Toolkit
9 : parrello 1.61 # Public License.
10 : olson 1.30 #
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 1.72 @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);
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 : parrello 1.47 use Cwd;
28 : parrello 1.12 use FIG_Config;
29 : parrello 1.9 use PageBuilder;
30 : parrello 1.21 use Digest::MD5;
31 : parrello 1.36 use File::Basename;
32 : parrello 1.37 use File::Path;
33 : parrello 1.48 use File::stat;
34 : parrello 1.59 use LWP::UserAgent;
35 : parrello 1.64 use Time::HiRes 'gettimeofday';
36 : parrello 1.65 use URI::Escape;
37 : olson 1.1
38 :     =head1 Tracing and Debugging Helpers
39 :    
40 : parrello 1.72 =head2 Tracing
41 : olson 1.1
42 :     This package provides simple tracing for debugging and reporting purposes. To use it simply call the
43 : parrello 1.72 L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
44 :     L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
45 :     each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
46 :     level is less than or equal to the setup trace level and whose category is activated will
47 : parrello 1.2 be written. Thus, a higher trace level on a message indicates that the message
48 : parrello 1.72 is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
49 :     appear.
50 : olson 1.1
51 : parrello 1.72 =head3 Putting Trace Messages in Your Code
52 :    
53 :     To generate a trace message, use the following syntax.
54 :    
55 :     Trace($message) if T(errors => 4);
56 : olson 1.1
57 : parrello 1.2 This statement will produce a trace message if the trace level is 4 or more and the C<errors>
58 : parrello 1.72 category is active. There is a special category C<main> that is always active, so
59 : olson 1.1
60 : parrello 1.72 Trace($message) if T(main => 4);
61 : olson 1.1
62 :     will trace if the trace level is 4 or more.
63 :    
64 :     If the category name is the same as the package name, all you need is the number. So, if the
65 :     following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
66 :     active and the trace level is 2 or more.
67 :    
68 : parrello 1.72 Trace($message) if T(2);
69 :    
70 :     In scripts, where no package name is available, the category defaults to C<main>.
71 :    
72 :     =head3 Custom Tracing
73 :    
74 :     Many programs have customized tracing configured using the L</TSetup> method. This is no longer
75 :     the preferred method, but a knowledge of how custom tracing works can make the more modern
76 :     L</Emergency Tracing> easier to understand.
77 : olson 1.1
78 : parrello 1.72 To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
79 :     a list of category names, and a destination. The trace level and list of category names are
80 : olson 1.1 specified as a space-delimited string. Thus
81 :    
82 : parrello 1.72 TSetup('3 errors Sprout ERDB', 'TEXT');
83 : olson 1.1
84 : parrello 1.7 sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
85 : parrello 1.72 specifies that messages should be sent to the standard output.
86 : parrello 1.12
87 :     To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
88 :     level 3 and writes the output to the standard error output. This sort of thing might be
89 :     useful in a CGI environment.
90 :    
91 : parrello 1.72 TSetup('3 *', 'WARN');
92 : olson 1.1
93 : parrello 1.72 In addition standard error and file output for trace messages, you can specify that the trace messages
94 : olson 1.1 be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
95 :     is useful if you are building a web page. Instead of having the trace messages interspersed with
96 :     the page output, they can be gathered together and displayed at the end of the page. This makes
97 :     it easier to debug page formatting problems.
98 :    
99 : parrello 1.72 Finally, you can specify that all trace messages be emitted to a file, or the standard output and
100 :     a file at the same time. To trace to a file, specify the filename with an output character in front
101 :     of it.
102 :    
103 :     TSetup('4 SQL', ">$fileName");
104 :    
105 :     To trace to the standard output and a file at the same time, put a C<+> in front of the angle
106 :     bracket.
107 :    
108 :     TSetup('3 *', "+>$fileName");
109 : parrello 1.4
110 : olson 1.1 The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
111 :     Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
112 :     Thus, debugging information is available and easily retrieved even when the application is
113 :     being used out in the field.
114 :    
115 : parrello 1.72 =head3 Trace Levels
116 :    
117 : parrello 1.10 There is no hard and fast rule on how to use trace levels. The following is therefore only
118 :     a suggestion.
119 :    
120 :     =over 4
121 :    
122 : parrello 1.32 =item Error 0
123 : parrello 1.10
124 :     Message indicates an error that may lead to incorrect results or that has stopped the
125 :     application entirely.
126 :    
127 : parrello 1.32 =item Warning 1
128 : parrello 1.10
129 :     Message indicates something that is unexpected but that probably did not interfere
130 :     with program execution.
131 :    
132 : parrello 1.32 =item Notice 2
133 : parrello 1.10
134 :     Message indicates the beginning or end of a major task.
135 :    
136 : parrello 1.32 =item Information 3
137 : parrello 1.10
138 :     Message indicates a subtask. In the FIG system, a subtask generally relates to a single
139 :     genome. This would be a big loop that is not expected to execute more than 500 times or so.
140 :    
141 : parrello 1.32 =item Detail 4
142 : parrello 1.10
143 :     Message indicates a low-level loop iteration.
144 :    
145 :     =back
146 :    
147 : parrello 1.69 The format of trace messages is important because some utilities analyze trace files.
148 : parrello 1.72 There are three fields-- the time stamp, the category name, and the text.
149 :     The time stamp is between square brackets and the category name between angle brackets.
150 :     After the category name there is a colon (C<:>) followed by the message text.
151 :     If the square brackets or angle brackets are missing, then the trace management
152 :     utilities assume that they are encountering a set of pre-formatted lines.
153 :    
154 :     Note, however, that this formatting is done automatically by the tracing functions. You
155 :     only need to know about it if you want to parse a trace file.
156 :    
157 :     =head3 Emergency Tracing
158 :    
159 :     Sometimes, you need a way for tracing to happen automatically without putting parameters
160 :     in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
161 :     from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.
162 :     Emergency tracing requires you specify a tracing key. For command-line tools, the key is
163 :     taken from the C<TRACING> environment variable. For web services, the key is taken from
164 :     a cookie. Either way, the key tells the tracing facility who you are, so that you control
165 :     the tracing in your environment without stepping on other users.
166 :    
167 :     The key can be anything you want. If you don't have a key, the C<SetPassword> page will
168 :     generate one for you.
169 :    
170 :     You can activate and de-activate emergency tracing from the debugging control panel, as
171 :     well as display the trace file itself.
172 :    
173 :     To enable emergency tracing in your code, call
174 :    
175 :     ETracing($cgi)
176 :    
177 :     from a web script and
178 :    
179 :     ETracing()
180 :    
181 :     from a command-line script.
182 :    
183 :     The web script will look for the tracing key in the cookies, and the command-line
184 :     script will look for it in the C<TRACING> environment variable. If you are
185 :     using the L</StandardScript> or L</StandardSetup> methods, emergency tracing
186 :     will be configured automatically.
187 :    
188 :     =head3 Debugging Control Panel
189 :    
190 :     The debugging control panel provides several tools to assist in development of
191 :     SEED and Sprout software. You access the debugging control panel from the URL
192 :     C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,
193 :     for example, the panel access point for the development NMPDR system is
194 :     C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to
195 :     find out what the password is. From this page, you can also specify a tracing
196 :     key. If you don't specify a key, one will be generated for you.
197 :    
198 :     =head4 Emergency Tracing Form
199 :    
200 :     At the bottom of the debugging control panel is a form that allows you to
201 :     specify a trace level and tracing categories. Special and common categories
202 :     are listed with check boxes. You can hold your mouse over a check box to see
203 :     what its category does. In general, however, a category name is the same as
204 :     the name of the package in which the trace message occurs.
205 :    
206 :     Additional categories can be entered in an input box, delimited by spaces or commas.
207 :    
208 :     The B<Activate> button turns on Emergency tracing at the level you specify with the
209 :     specified categories active. The B<Terminate> button turns tracing off. The
210 :     B<Show File> button displays the current contents of the trace file. The tracing
211 :     form at the bottom of the control panel is designed for emergency tracing, so it
212 :     will only affect programs that call L</ETracing>, L</StandardScript>,
213 :     or L</StandardSetup>.
214 :    
215 :     =head4 Script Form
216 :    
217 :     The top form of the debugging control panel allows you to enter a tiny script and
218 :     have the output generated in a formatted table. Certain object variables are
219 :     predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),
220 :     and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.
221 :    
222 :     The last line of the script must be a scalar, but it can be a reference to a hash,
223 :     a list, a list of lists, and various other combinations. If you select the appropriate
224 :     data type in the dropdown box, the output will be formatted accordingly. The form
225 :     also has controls for specifying tracing. These controls override any emergency
226 :     tracing in effect.
227 :    
228 :     =head4 Database Query Forms
229 :    
230 :     The forms between the script form and the emergency tracing form allow you to
231 :     make queries against the database. The FIG query form allows simple queries against
232 :     a single FIG table. The Sprout query form uses the B<GetAll> method to do a
233 :     multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>
234 :     package, and it takes five parameters.
235 :    
236 :     GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
237 :    
238 :     Each of the five parameters corresponds to a text box on the query form:
239 :    
240 :     =over 4
241 :    
242 :     =item Objects
243 :    
244 :     Comma-separated list containing the names of the entity and relationship objects to be retrieved.
245 :    
246 :     =item Filter
247 :    
248 :     WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
249 :     be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
250 :     B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a
251 :     field, I<objectName> is the name of the entity or relationship object containing the field, and
252 :     I<number> is the 1-based position of the object in the object list. Any parameters
253 :     specified in the filter clause should be specified in the B<Params> field.
254 :     The fields in a filter clause can come from primary entity relations,
255 :     relationship relations, or secondary entity relations; however, all of the
256 :     entities and relationships involved must be included in the list of object names.
257 :    
258 :     =item Params
259 :    
260 :     List of the parameters to be substituted in for the parameters marks in the filter clause. This
261 :     is a comma-separated list without any quoting or escaping.
262 :    
263 :     =item fields
264 :    
265 :     Comma-separated list of the fields to be returned in each element of the list returned. Fields
266 :     are specified in the same manner as in the filter clause.
267 :    
268 :     =item count
269 :    
270 :     Maximum number of records to return. If omitted or 0, all available records will be returned.
271 :    
272 :     =back
273 :    
274 :     B<GetAll> automatically joins together the entities and relationships listed in the object
275 :     names. This simplifies the coding of the filter clause, but it means that some queries are
276 :     not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation
277 :     that has yet to be addressed.
278 : parrello 1.69
279 : olson 1.1 =cut
280 : parrello 1.2
281 : olson 1.1 # Declare the configuration variables.
282 :    
283 : parrello 1.12 my $Destination = "NONE"; # Description of where to send the trace output.
284 :     my $TeeFlag = 0; # TRUE if output is going to a file and to the
285 :     # standard output
286 : parrello 1.3 my %Categories = ( main => 1 );
287 : parrello 1.12 # hash of active category names
288 :     my $TraceLevel = 0; # trace level; a higher trace level produces more
289 :     # messages
290 :     my @Queue = (); # queued list of trace messages.
291 : parrello 1.7 my $LastCategory = "main"; # name of the last category interrogated
292 : parrello 1.11 my $SetupCount = 0; # number of times TSetup called
293 : parrello 1.12 my $AllTrace = 0; # TRUE if we are tracing all categories.
294 : olson 1.1
295 :     =head2 Public Methods
296 :    
297 :     =head3 TSetup
298 :    
299 :     C<< TSetup($categoryList, $target); >>
300 :    
301 :     This method is used to specify the trace options. The options are stored as package data
302 :     and interrogated by the L</Trace> and L</T> methods.
303 :    
304 :     =over 4
305 :    
306 :     =item categoryList
307 :    
308 :     A string specifying the trace level and the categories to be traced, separated by spaces.
309 :     The trace level must come first.
310 :    
311 :     =item target
312 :    
313 :     The destination for the trace output. To send the trace output to a file, specify the file
314 :     name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
315 : parrello 1.10 to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
316 :     symbol with a C<+> to echo output to a file AND to the standard output. In addition to
317 :     sending the trace messages to a file, you can specify a special destination. C<HTML> will
318 :     cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
319 : parrello 1.5 will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
320 : parrello 1.9 messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
321 : parrello 1.6 messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
322 : parrello 1.9 cause trace messages to be emitted as warnings using the B<warn> directive. C<NONE> will
323 : parrello 1.6 cause tracing to be suppressed.
324 : olson 1.1
325 :     =back
326 :    
327 :     =cut
328 :    
329 :     sub TSetup {
330 : parrello 1.12 # Get the parameters.
331 :     my ($categoryList, $target) = @_;
332 :     # Parse the category list.
333 :     my @categoryData = split /\s+/, $categoryList;
334 :     # Extract the trace level.
335 :     $TraceLevel = shift @categoryData;
336 :     # Presume category-based tracing until we learn otherwise.
337 :     $AllTrace = 0;
338 :     # Build the category hash. Note that if we find a "*", we turn on non-category
339 : parrello 1.33 # tracing. We must also clear away any pre-existing data.
340 : parrello 1.34 %Categories = ( main => 1 );
341 : parrello 1.12 for my $category (@categoryData) {
342 :     if ($category eq '*') {
343 :     $AllTrace = 1;
344 :     } else {
345 : parrello 1.13 $Categories{lc $category} = 1;
346 : parrello 1.12 }
347 :     }
348 :     # Now we need to process the destination information. The most important special
349 :     # cases are the single ">", which requires we clear the file first, and the
350 :     # "+" prefix which indicates a double echo.
351 :     if ($target =~ m/^\+?>>?/) {
352 :     if ($target =~ m/^\+/) {
353 :     $TeeFlag = 1;
354 :     $target = substr($target, 1);
355 :     }
356 :     if ($target =~ m/^>[^>]/) {
357 :     open TRACEFILE, $target;
358 : parrello 1.69 print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";
359 : parrello 1.12 close TRACEFILE;
360 :     $Destination = ">$target";
361 :     } else {
362 :     $Destination = $target;
363 :     }
364 :     } else {
365 :     $Destination = uc($target);
366 :     }
367 :     # Increment the setup counter.
368 :     $SetupCount++;
369 : parrello 1.11 }
370 :    
371 : parrello 1.31 =head3 StandardSetup
372 :    
373 : parrello 1.36 C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>
374 : parrello 1.31
375 :     This method performs standard command-line parsing and tracing setup. The return
376 :     values are a hash of the command-line options and a list of the positional
377 :     parameters. Tracing is automatically set up and the command-line options are
378 :     validated.
379 :    
380 :     This is a complex method that does a lot of grunt work. The parameters can
381 :     be more easily understood, however, once they are examined individually.
382 :    
383 :     The I<categories> parameter is the most obtuse. It is a reference to a list of
384 :     special-purpose tracing categories. Most tracing categories are PERL package
385 :     names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
386 :     B<ERDB>, and B<SproutLoad> packages, you would specify the categories
387 :    
388 :     ["Sprout", "SproutLoad", "ERDB"]
389 :    
390 :     This would cause trace messages in the specified three packages to appear in
391 : parrello 1.69 the output. There are two special tracing categories that are automatically
392 : parrello 1.31 handled by this method. In other words, if you used L</TSetup> you would need
393 :     to include these categories manually, but if you use this method they are turned
394 :     on automatically.
395 :    
396 :     =over 4
397 :    
398 :     =item SQL
399 :    
400 :     Traces SQL commands and activity.
401 :    
402 :     =item Tracer
403 :    
404 :     Traces error messages and call stacks.
405 :    
406 :     =back
407 :    
408 :     C<SQL> is only turned on if the C<-sql> option is specified in the command line.
409 :     The trace level is specified using the C<-trace> command-line option. For example,
410 :     the following command line for C<TransactFeatures> turns on SQL tracing and runs
411 :     all tracing at level 3.
412 :    
413 :     TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
414 :    
415 :     Standard tracing is output to the standard output and echoed to the file
416 : parrello 1.38 C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
417 :     process ID. You can also specify the C<user> parameter to put a user ID
418 :     instead of a process ID in the trace file name. So, for example
419 : parrello 1.31
420 : parrello 1.35 The default trace level is 2. To get all messages, specify a trace level of 4.
421 :     For a genome-by-genome update, use 3.
422 : parrello 1.31
423 : parrello 1.38 TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
424 :    
425 :     would send the trace output to C<traceBruce.log> in the temporary directory.
426 :    
427 : parrello 1.31 The I<options> parameter is a reference to a hash containing the command-line
428 : parrello 1.36 options, their default values, and an explanation of what they mean. Command-line
429 :     options may be in the form of switches or keywords. In the case of a switch, the
430 :     option value is 1 if it is specified and 0 if it is not specified. In the case
431 :     of a keyword, the value is separated from the option name by an equal sign. You
432 :     can see this last in the command-line example above.
433 : parrello 1.31
434 : parrello 1.42 You can specify a different default trace level by setting C<$options->{trace}>
435 :     prior to calling this method.
436 :    
437 : parrello 1.31 An example at this point would help. Consider, for example, the command-line utility
438 :     C<TransactFeatures>. It accepts a list of positional parameters plus the options
439 :     C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
440 :     the following code.
441 :    
442 :     my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
443 : parrello 1.36 { safe => [0, "use database transactions"],
444 :     noAlias => [0, "do not expect aliases in CHANGE transactions"],
445 :     start => [' ', "start with this genome"],
446 :     tblFiles => [0, "output TBL files containing the corrected IDs"] },
447 :     "command transactionDirectory IDfile",
448 :     @ARGV);
449 : parrello 1.31
450 :    
451 :     The call to C<ParseCommand> specifies the default values for the options and
452 :     stores the actual options in a hash that is returned as C<$options>. The
453 : parrello 1.61 positional parameters are returned in C<@parameters>.
454 : parrello 1.31
455 :     The following is a sample command line for C<TransactFeatures>.
456 :    
457 :     TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
458 :    
459 :     In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
460 :     parameters, and would find themselves in I<@parameters> after executing the
461 :     above code fragment. The tracing would be set to level 2, and the categories
462 : parrello 1.69 would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
463 : parrello 1.31 and C<DocUtils> was included because it came in within the first parameter
464 :     to this method. The I<$options> hash would be
465 :    
466 :     { trace => 2, sql => 0, safe => 0,
467 :     noAlias => 1, start => ' ', tblFiles => 0 }
468 :    
469 :     Use of C<StandardSetup> in this way provides a simple way of performing
470 :     standard tracing setup and command-line parsing. Note that the caller is
471 :     not even aware of the command-line switches C<-trace> and C<-sql>, which
472 :     are used by this method to control the tracing. If additional tracing features
473 :     need to be added in the future, they can be processed by this method without
474 :     upsetting the command-line utilities.
475 :    
476 : parrello 1.42 If the C<background> option is specified on the command line, then the
477 :     standard and error outputs will be directed to files in the temporary
478 :     directory, using the same suffix as the trace file. So, if the command
479 :     line specified
480 :    
481 :     -user=Bruce -background
482 :    
483 :     then the trace output would go to C<traceBruce.log>, the standard output to
484 :     C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
485 :     simplify starting a command in the background.
486 :    
487 : parrello 1.72 The user name is also used as the tracing key for L</Emergency Tracing>.
488 :     Specifying a value of C<E> for the trace level causes emergency tracing to
489 :     be used instead of custom tracing. If the user name is not specified,
490 :     the tracing key is taken from the C<Tracing> environment variable. If there
491 :     is no value for that variable, the tracing key will be computed from the PID.
492 :    
493 : parrello 1.36 Finally, if the special option C<-h> is specified, the option names will
494 :     be traced at level 0 and the program will exit without processing.
495 :     This provides a limited help capability. For example, if the user enters
496 :    
497 :     TransactFeatures -h
498 :    
499 :     he would see the following output.
500 :    
501 :     TransactFeatures [options] command transactionDirectory IDfile
502 : parrello 1.72 -trace tracing level (default E)
503 : parrello 1.36 -sql trace SQL commands
504 :     -safe use database transactions
505 :     -noAlias do not expect aliases in CHANGE transactions
506 :     -start start with this genome
507 :     -tblFiles output TBL files containing the corrected IDs
508 :    
509 : parrello 1.44 The caller has the option of modifying the tracing scheme by placing a value
510 :     for C<trace> in the incoming options hash. The default value can be overridden,
511 :     or the tracing to the standard output can be turned off by suffixing a minus
512 : parrello 1.61 sign to the trace level. So, for example,
513 : parrello 1.44
514 :     { trace => [0, "tracing level (default 0)"],
515 :     ...
516 :    
517 : parrello 1.72 would set the default trace level to 0 instead of E, while
518 : parrello 1.44
519 :     { trace => ["2-", "tracing level (default 2)"],
520 :     ...
521 :    
522 : parrello 1.72 would set the default to 2, but trace only to the log file, not to the
523 : parrello 1.44 standard output.
524 :    
525 : parrello 1.31 The parameters to this method are as follows.
526 :    
527 :     =over 4
528 :    
529 :     =item categories
530 :    
531 :     Reference to a list of tracing category names. These should be names of
532 :     packages whose internal workings will need to be debugged to get the
533 :     command working.
534 :    
535 :     =item options
536 :    
537 :     Reference to a hash containing the legal options for the current command mapped
538 : parrello 1.36 to their default values and descriptions. The user can override the defaults
539 :     by specifying the options as command-line switches prefixed by a hyphen.
540 :     Tracing-related options may be added to this hash. If the C<-h> option is
541 :     specified on the command line, the option descriptions will be used to
542 : parrello 1.44 explain the options. To turn off tracing to the standard output, add a
543 :     minus sign to the value for C<trace> (see above).
544 : parrello 1.36
545 :     =item parmHelp
546 :    
547 :     A string that vaguely describes the positional parameters. This is used
548 :     if the user specifies the C<-h> option.
549 : parrello 1.31
550 : parrello 1.44 =item argv
551 : parrello 1.31
552 :     List of command line parameters, including the option switches, which must
553 :     precede the positional parameters and be prefixed by a hyphen.
554 :    
555 :     =item RETURN
556 :    
557 :     Returns a list. The first element of the list is the reference to a hash that
558 :     maps the command-line option switches to their values. These will either be the
559 :     default values or overrides specified on the command line. The remaining
560 :     elements of the list are the position parameters, in order.
561 :    
562 :     =back
563 :    
564 :     =cut
565 :    
566 :     sub StandardSetup {
567 :     # Get the parameters.
568 : parrello 1.36 my ($categories, $options, $parmHelp, @argv) = @_;
569 : parrello 1.72 # Get the default tracing key.
570 :     my $tkey = EmergencyKey();
571 : parrello 1.31 # Add the tracing options.
572 : parrello 1.41 if (! exists $options->{trace}) {
573 : parrello 1.72 $options->{trace} = ['E', "tracing level (E for emergency tracing)"];
574 : parrello 1.41 }
575 : parrello 1.36 $options->{sql} = [0, "turn on SQL tracing"];
576 :     $options->{h} = [0, "display command-line options"];
577 : parrello 1.72 $options->{user} = [$tkey, "tracing key"];
578 : parrello 1.42 $options->{background} = [0, "spool standard and error output"];
579 : parrello 1.36 # Create a parsing hash from the options hash. The parsing hash
580 :     # contains the default values rather than the default value
581 :     # and the description. While we're at it, we'll memorize the
582 :     # length of the longest option name.
583 :     my $longestName = 0;
584 :     my %parseOptions = ();
585 :     for my $key (keys %{$options}) {
586 :     if (length $key > $longestName) {
587 :     $longestName = length $key;
588 :     }
589 :     $parseOptions{$key} = $options->{$key}->[0];
590 :     }
591 : parrello 1.31 # Parse the command line.
592 : parrello 1.36 my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
593 : parrello 1.42 # Get the logfile suffix.
594 :     my $suffix = $retOptions->{user};
595 :     # Check for background mode.
596 :     if ($retOptions->{background}) {
597 :     my $outFileName = "$FIG_Config::temp/out$suffix.log";
598 :     my $errFileName = "$FIG_Config::temp/err$suffix.log";
599 :     open STDOUT, ">$outFileName";
600 :     open STDERR, ">$errFileName";
601 :     }
602 : parrello 1.72 # Now we want to set up tracing. First, we need to know if the user
603 :     # wants emergency tracing.
604 :     if ($retOptions->{trace} eq 'E') {
605 :     ETracing($retOptions->{user});
606 : parrello 1.44 } else {
607 : parrello 1.72 # Here the tracing is controlled from the command line.
608 :     my @cats = @{$categories};
609 :     if ($retOptions->{sql}) {
610 :     push @cats, "SQL";
611 :     }
612 :     # Add the default categories.
613 :     push @cats, "Tracer";
614 :     # Next, we create the category string by joining the categories.
615 :     my $cats = join(" ", @cats);
616 :     # Check to determine whether or not the caller wants to turn off tracing
617 :     # to the standard output.
618 :     my $traceLevel = $retOptions->{trace};
619 :     my $textOKFlag = 1;
620 :     if ($traceLevel =~ /^(.)-/) {
621 :     $traceLevel = $1;
622 :     $textOKFlag = 0;
623 :     }
624 :     # Now we set up the trace mode.
625 :     my $traceMode;
626 :     # Verify that we can open a file in the FIG temporary directory.
627 :     my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
628 :     if (open TESTTRACE, ">$traceFileName") {
629 :     # Here we can trace to a file.
630 :     $traceMode = ">$traceFileName";
631 :     if ($textOKFlag) {
632 :     # Echo to standard output if the text-OK flag is set.
633 :     $traceMode = "+$traceMode";
634 :     }
635 :     # Close the test file.
636 :     close TESTTRACE;
637 : parrello 1.44 } else {
638 : parrello 1.72 # Here we can't trace to a file. We trace to the standard output if it's
639 :     # okay, and the error log otherwise.
640 :     if ($textOKFlag) {
641 :     $traceMode = "TEXT";
642 :     } else {
643 :     $traceMode = "WARN";
644 :     }
645 : parrello 1.44 }
646 : parrello 1.72 # Now set up the tracing.
647 :     TSetup("$traceLevel $cats", $traceMode);
648 : parrello 1.40 }
649 : parrello 1.36 # Check for the "h" option. If it is specified, dump the command-line
650 :     # options and exit the program.
651 :     if ($retOptions->{h}) {
652 :     $0 =~ m#[/\\](\w+)(\.pl)?$#i;
653 : parrello 1.69 print "$1 [options] $parmHelp\n";
654 : parrello 1.36 for my $key (sort keys %{$options}) {
655 :     my $name = Pad($key, $longestName, 0, ' ');
656 :     my $desc = $options->{$key}->[1];
657 :     if ($options->{$key}->[0]) {
658 :     $desc .= " (default " . $options->{$key}->[0] . ")";
659 :     }
660 : parrello 1.69 print " $name $desc\n";
661 : parrello 1.36 }
662 :     exit(0);
663 :     }
664 : parrello 1.31 # Return the parsed parameters.
665 :     return ($retOptions, @retParameters);
666 :     }
667 :    
668 : parrello 1.11 =head3 Setups
669 :    
670 :     C<< my $count = Tracer::Setups(); >>
671 :    
672 :     Return the number of times L</TSetup> has been called.
673 :    
674 :     This method allows for the creation of conditional tracing setups where, for example, we
675 :     may want to set up tracing if nobody else has done it before us.
676 :    
677 :     =cut
678 :    
679 :     sub Setups {
680 : parrello 1.12 return $SetupCount;
681 : olson 1.1 }
682 :    
683 : parrello 1.10 =head3 Open
684 :    
685 :     C<< my $handle = Open($fileHandle, $fileSpec, $message); >>
686 :    
687 : parrello 1.11 Open a file.
688 : parrello 1.10
689 :     The I<$fileSpec> is essentially the second argument of the PERL C<open>
690 :     function. The mode is specified using Unix-like shell information. So, for
691 :     example,
692 :    
693 : parrello 1.12 Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
694 : parrello 1.10
695 :     would open for output appended to the specified file, and
696 :    
697 : parrello 1.12 Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
698 : parrello 1.10
699 :     would open a pipe that sorts the records written and removes duplicates. Note
700 : parrello 1.11 the use of file handle syntax in the Open call. To use anonymous file handles,
701 :     code as follows.
702 : parrello 1.10
703 : parrello 1.12 my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
704 : parrello 1.10
705 : parrello 1.11 The I<$message> parameter is used if the open fails. If it is set to C<0>, then
706 :     the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
707 :     failed open will throw an exception and the third parameter will be used to construct
708 :     an error message. If the parameter is omitted, a standard message is constructed
709 :     using the file spec.
710 : parrello 1.10
711 : parrello 1.12 Could not open "/usr/spool/news/twitlog"
712 : parrello 1.10
713 :     Note that the mode characters are automatically cleaned from the file name.
714 :     The actual error message from the file system will be captured and appended to the
715 :     message in any case.
716 :    
717 : parrello 1.12 Could not open "/usr/spool/news/twitlog": file not found.
718 : parrello 1.10
719 :     In some versions of PERL the only error message we get is a number, which
720 :     corresponds to the C++ C<errno> value.
721 :    
722 : parrello 1.12 Could not open "/usr/spool/news/twitlog": 6.
723 : parrello 1.10
724 :     =over 4
725 :    
726 :     =item fileHandle
727 :    
728 :     File handle. If this parameter is C<undef>, a file handle will be generated
729 :     and returned as the value of this method.
730 :    
731 :     =item fileSpec
732 :    
733 :     File name and mode, as per the PERL C<open> function.
734 :    
735 :     =item message (optional)
736 :    
737 :     Error message to use if the open fails. If omitted, a standard error message
738 :     will be generated. In either case, the error information from the file system
739 : parrello 1.11 is appended to the message. To specify a conditional open that does not throw
740 :     an error if it fails, use C<0>.
741 : parrello 1.10
742 :     =item RETURN
743 :    
744 : parrello 1.11 Returns the name of the file handle assigned to the file, or C<undef> if the
745 :     open failed.
746 : parrello 1.10
747 :     =back
748 :    
749 :     =cut
750 :    
751 :     sub Open {
752 : parrello 1.12 # Get the parameters.
753 :     my ($fileHandle, $fileSpec, $message) = @_;
754 :     # Attempt to open the file.
755 :     my $rv = open $fileHandle, $fileSpec;
756 :     # If the open failed, generate an error message.
757 :     if (! $rv) {
758 :     # Save the system error message.
759 :     my $sysMessage = $!;
760 :     # See if we need a default message.
761 :     if (!$message) {
762 :     # Clean any obvious mode characters and leading spaces from the
763 :     # filename.
764 :     my ($fileName) = FindNamePart($fileSpec);
765 :     $message = "Could not open \"$fileName\"";
766 :     }
767 :     # Terminate with an error using the supplied message and the
768 :     # error message from the file system.
769 :     Confess("$message: $!");
770 :     }
771 :     # Return the file handle.
772 :     return $fileHandle;
773 : parrello 1.10 }
774 :    
775 : parrello 1.11 =head3 FindNamePart
776 :    
777 :     C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>
778 :    
779 :     Extract the portion of a file specification that contains the file name.
780 :    
781 :     A file specification is the string passed to an C<open> call. It specifies the file
782 :     mode and name. In a truly complex situation, it can specify a pipe sequence. This
783 :     method assumes that the file name is whatever follows the first angle bracket
784 :     sequence. So, for example, in the following strings the file name is
785 :     C</usr/fig/myfile.txt>.
786 :    
787 :     >>/usr/fig/myfile.txt
788 :     </usr/fig/myfile.txt
789 :     | sort -u > /usr/fig/myfile.txt
790 :    
791 :     If the method cannot find a file name using its normal methods, it will return the
792 :     whole incoming string.
793 :    
794 :     =over 4
795 :    
796 :     =item fileSpec
797 :    
798 :     File specification string from which the file name is to be extracted.
799 :    
800 :     =item RETURN
801 :    
802 :     Returns a three-element list. The first element contains the file name portion of
803 :     the specified string, or the whole string if a file name cannot be found via normal
804 :     methods. The second element contains the start position of the file name portion and
805 :     the third element contains the length.
806 :    
807 :     =back
808 :    
809 :     =cut
810 :     #: Return Type $;
811 :     sub FindNamePart {
812 :     # Get the parameters.
813 :     my ($fileSpec) = @_;
814 : parrello 1.12 # Default to the whole input string.
815 :     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
816 : parrello 1.11 # Parse out the file name if we can.
817 : parrello 1.12 if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
818 :     $retVal = $2;
819 :     $len = length $retVal;
820 :     $pos = (length $fileSpec) - (length $3) - $len;
821 :     }
822 : parrello 1.11 # Return the result.
823 :     return ($retVal, $pos, $len);
824 :     }
825 :    
826 :     =head3 OpenDir
827 :    
828 : parrello 1.31 C<< my @files = OpenDir($dirName, $filtered, $flag); >>
829 : parrello 1.11
830 :     Open a directory and return all the file names. This function essentially performs
831 :     the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
832 : parrello 1.31 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
833 : parrello 1.33 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
834 :     filtered out of the return list. If the directory does not open and I<$flag> is not
835 :     set, an exception is thrown. So, for example,
836 : parrello 1.11
837 : parrello 1.12 my @files = OpenDir("/Volumes/fig/contigs", 1);
838 : parrello 1.29
839 : parrello 1.11 is effectively the same as
840 :    
841 : parrello 1.12 opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
842 : parrello 1.33 my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
843 : parrello 1.11
844 :     Similarly, the following code
845 :    
846 : parrello 1.31 my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
847 : parrello 1.29
848 : parrello 1.11 Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
849 : parrello 1.31 automatically returns an empty list if the directory fails to open.
850 : parrello 1.11
851 :     =over 4
852 :    
853 :     =item dirName
854 :    
855 :     Name of the directory to open.
856 :    
857 :     =item filtered
858 :    
859 :     TRUE if files whose names begin with a period (C<.>) should be automatically removed
860 :     from the list, else FALSE.
861 :    
862 : parrello 1.31 =item flag
863 :    
864 :     TRUE if a failure to open is okay, else FALSE
865 :    
866 : parrello 1.11 =back
867 :    
868 :     =cut
869 :     #: Return Type @;
870 :     sub OpenDir {
871 :     # Get the parameters.
872 : parrello 1.31 my ($dirName, $filtered, $flag) = @_;
873 : parrello 1.11 # Declare the return variable.
874 : parrello 1.31 my @retVal = ();
875 : parrello 1.12 # Open the directory.
876 :     if (opendir(my $dirHandle, $dirName)) {
877 :     # The directory opened successfully. Get the appropriate list according to the
878 :     # strictures of the filter parameter.
879 :     if ($filtered) {
880 : parrello 1.33 @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
881 : parrello 1.12 } else {
882 :     @retVal = readdir $dirHandle;
883 :     }
884 : parrello 1.31 } elsif (! $flag) {
885 :     # Here the directory would not open and it's considered an error.
886 : parrello 1.12 Confess("Could not open directory $dirName.");
887 :     }
888 : parrello 1.11 # Return the result.
889 :     return @retVal;
890 :     }
891 :    
892 : parrello 1.6 =head3 SetLevel
893 :    
894 :     C<< Tracer::SetLevel($newLevel); >>
895 :    
896 :     Modify the trace level. A higher trace level will cause more messages to appear.
897 :    
898 :     =over 4
899 :    
900 :     =item newLevel
901 :    
902 :     Proposed new trace level.
903 :    
904 :     =back
905 :    
906 :     =cut
907 :    
908 :     sub SetLevel {
909 :     $TraceLevel = $_[0];
910 :     }
911 :    
912 : olson 1.1 =head3 Now
913 :    
914 :     C<< my $string = Tracer::Now(); >>
915 :    
916 :     Return a displayable time stamp containing the local time.
917 :    
918 :     =cut
919 :    
920 :     sub Now {
921 : parrello 1.12 my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
922 :     my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
923 :     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
924 :     return $retVal;
925 : olson 1.1 }
926 :    
927 :     # Pad a number to 2 digits.
928 :     sub _p2 {
929 : parrello 1.12 my ($value) = @_;
930 :     $value = "0$value" if ($value < 10);
931 :     return $value;
932 : olson 1.1 }
933 :    
934 :     =head3 LogErrors
935 :    
936 :     C<< Tracer::LogErrors($fileName); >>
937 :    
938 :     Route the standard error output to a log file.
939 :    
940 :     =over 4
941 :    
942 :     =item fileName
943 :    
944 :     Name of the file to receive the error output.
945 :    
946 :     =back
947 :    
948 :     =cut
949 :    
950 :     sub LogErrors {
951 : parrello 1.12 # Get the file name.
952 :     my ($fileName) = @_;
953 :     # Open the file as the standard error output.
954 :     open STDERR, '>', $fileName;
955 : olson 1.1 }
956 :    
957 : parrello 1.5 =head3 ReadOptions
958 :    
959 :     C<< my %options = Tracer::ReadOptions($fileName); >>
960 :    
961 :     Read a set of options from a file. Each option is encoded in a line of text that has the
962 :     format
963 :    
964 :     I<optionName>C<=>I<optionValue>C<; >I<comment>
965 :    
966 :     The option name must consist entirely of letters, digits, and the punctuation characters
967 : parrello 1.9 C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
968 :     character is a semi-colon will be ignored. The return hash will map each option name to
969 : parrello 1.5 the corresponding option value.
970 :    
971 :     =over 4
972 :    
973 :     =item fileName
974 :    
975 :     Name of the file containing the option data.
976 :    
977 :     =item RETURN
978 :    
979 :     Returns a hash mapping the option names specified in the file to their corresponding option
980 :     value.
981 :    
982 :     =back
983 :    
984 :     =cut
985 :    
986 :     sub ReadOptions {
987 : parrello 1.12 # Get the parameters.
988 :     my ($fileName) = @_;
989 :     # Open the file.
990 :     (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
991 :     # Count the number of records read.
992 :     my ($records, $comments) = 0;
993 :     # Create the return hash.
994 :     my %retVal = ();
995 :     # Loop through the file, accumulating key-value pairs.
996 :     while (my $line = <CONFIGFILE>) {
997 :     # Denote we've read a line.
998 :     $records++;
999 :     # Determine the line type.
1000 :     if ($line =~ /^\s*[\n\r]/) {
1001 :     # A blank line is a comment.
1002 :     $comments++;
1003 :     } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1004 :     # Here we have an option assignment.
1005 :     retVal{$1} = $2;
1006 :     } elsif ($line =~ /^\s*;/) {
1007 :     # Here we have a text comment.
1008 :     $comments++;
1009 :     } else {
1010 :     # Here we have an invalid line.
1011 :     Trace("Invalid option statement in record $records.") if T(0);
1012 :     }
1013 :     }
1014 :     # Return the hash created.
1015 :     return %retVal;
1016 : parrello 1.5 }
1017 :    
1018 : olson 1.1 =head3 GetOptions
1019 :    
1020 :     C<< Tracer::GetOptions(\%defaults, \%options); >>
1021 :    
1022 :     Merge a specified set of options into a table of defaults. This method takes two hash references
1023 :     as input and uses the data from the second to update the first. If the second does not exist,
1024 :     there will be no effect. An error will be thrown if one of the entries in the second hash does not
1025 :     exist in the first.
1026 :    
1027 :     Consider the following example.
1028 :    
1029 :     C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>
1030 :    
1031 :     In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1032 :     B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1033 :     B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1034 :     the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1035 :     will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1036 :    
1037 :     C<< {databaseType => 'Oracle'} >>
1038 :    
1039 :     an error will occur because the B<databaseType> option does not exist.
1040 :    
1041 :     =over 4
1042 :    
1043 :     =item defaults
1044 :    
1045 :     Table of default option values.
1046 :    
1047 :     =item options
1048 :    
1049 :     Table of overrides, if any.
1050 :    
1051 :     =item RETURN
1052 :    
1053 :     Returns a reference to the default table passed in as the first parameter.
1054 :    
1055 :     =back
1056 :    
1057 :     =cut
1058 :    
1059 :     sub GetOptions {
1060 : parrello 1.12 # Get the parameters.
1061 :     my ($defaults, $options) = @_;
1062 :     # Check for overrides.
1063 :     if ($options) {
1064 :     # Loop through the overrides.
1065 :     while (my ($option, $setting) = each %{$options}) {
1066 :     # Insure this override exists.
1067 :     if (!exists $defaults->{$option}) {
1068 :     croak "Unrecognized option $option encountered.";
1069 :     } else {
1070 :     # Apply the override.
1071 :     $defaults->{$option} = $setting;
1072 :     }
1073 :     }
1074 :     }
1075 :     # Return the merged table.
1076 :     return $defaults;
1077 : olson 1.1 }
1078 :    
1079 :     =head3 MergeOptions
1080 :    
1081 :     C<< Tracer::MergeOptions(\%table, \%defaults); >>
1082 :    
1083 :     Merge default values into a hash table. This method looks at the key-value pairs in the
1084 :     second (default) hash, and if a matching key is not found in the first hash, the default
1085 :     pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1086 :     checking and no return value.
1087 :    
1088 :     =over 4
1089 :    
1090 :     =item table
1091 :    
1092 :     Hash table to be updated with the default values.
1093 :    
1094 :     =item defaults
1095 :    
1096 :     Default values to be merged into the first hash table if they are not already present.
1097 :    
1098 :     =back
1099 :    
1100 :     =cut
1101 :    
1102 :     sub MergeOptions {
1103 : parrello 1.12 # Get the parameters.
1104 :     my ($table, $defaults) = @_;
1105 :     # Loop through the defaults.
1106 :     while (my ($key, $value) = each %{$defaults}) {
1107 :     if (!exists $table->{$key}) {
1108 :     $table->{$key} = $value;
1109 :     }
1110 :     }
1111 : olson 1.1 }
1112 :    
1113 :     =head3 Trace
1114 :    
1115 :     C<< Trace($message); >>
1116 :    
1117 :     Write a trace message to the target location specified in L</TSetup>. If there has not been
1118 :     any prior call to B<TSetup>.
1119 :    
1120 :     =over 4
1121 :    
1122 :     =item message
1123 :    
1124 :     Message to write.
1125 :    
1126 :     =back
1127 :    
1128 :     =cut
1129 :    
1130 :     sub Trace {
1131 : parrello 1.12 # Get the parameters.
1132 :     my ($message) = @_;
1133 :     # Get the timestamp.
1134 :     my $timeStamp = Now();
1135 :     # Format the message. Note we strip off any line terminators at the end.
1136 : parrello 1.69 my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);
1137 : parrello 1.12 # Process according to the destination.
1138 :     if ($Destination eq "TEXT") {
1139 :     # Write the message to the standard output.
1140 :     print "$formatted\n";
1141 :     } elsif ($Destination eq "ERROR") {
1142 :     # Write the message to the error output.
1143 :     print STDERR "$formatted\n";
1144 :     } elsif ($Destination eq "QUEUE") {
1145 :     # Push the message into the queue.
1146 :     push @Queue, "$formatted";
1147 :     } elsif ($Destination eq "HTML") {
1148 :     # Convert the message to HTML and write it to the standard output.
1149 :     my $escapedMessage = CGI::escapeHTML($message);
1150 :     print "<p>$formatted</p>\n";
1151 : parrello 1.4 } elsif ($Destination eq "WARN") {
1152 :     # Emit the message as a warning.
1153 :     warn $message;
1154 : parrello 1.12 } elsif ($Destination =~ m/^>>/) {
1155 :     # Write the trace message to an output file.
1156 : parrello 1.14 (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
1157 : parrello 1.12 print TRACING "$formatted\n";
1158 :     close TRACING;
1159 :     # If the Tee flag is on, echo it to the standard output.
1160 :     if ($TeeFlag) {
1161 :     print "$formatted\n";
1162 :     }
1163 :     }
1164 : olson 1.1 }
1165 :    
1166 :     =head3 T
1167 :    
1168 : parrello 1.2 C<< my $switch = T($category, $traceLevel); >>
1169 : olson 1.1
1170 : parrello 1.12 or
1171 : parrello 1.2
1172 : olson 1.1 C<< my $switch = T($traceLevel); >>
1173 :    
1174 :     Return TRUE if the trace level is at or above a specified value and the specified category
1175 :     is active, else FALSE. If no category is specified, the caller's package name is used.
1176 :    
1177 :     =over 4
1178 :    
1179 :     =item category
1180 :    
1181 :     Category to which the message belongs. If not specified, the caller's package name is
1182 :     used.
1183 :    
1184 :     =item traceLevel
1185 :    
1186 :     Relevant tracing level.
1187 :    
1188 :     =item RETURN
1189 :    
1190 :     TRUE if a message at the specified trace level would appear in the trace, else FALSE.
1191 :    
1192 :     =back
1193 :    
1194 :     =cut
1195 :    
1196 :     sub T {
1197 : parrello 1.12 # Declare the return variable.
1198 :     my $retVal = 0;
1199 :     # Only proceed if tracing is turned on.
1200 :     if ($Destination ne "NONE") {
1201 :     # Get the parameters.
1202 :     my ($category, $traceLevel) = @_;
1203 :     if (!defined $traceLevel) {
1204 :     # Here we have no category, so we need to get the calling package.
1205 :     # The calling package is normally the first parameter. If it is
1206 :     # omitted, the first parameter will be the tracelevel. So, the
1207 :     # first thing we do is shift the so-called category into the
1208 :     # $traceLevel variable where it belongs.
1209 :     $traceLevel = $category;
1210 :     my ($package, $fileName, $line) = caller;
1211 : parrello 1.3 # If there is no calling package, we default to "main".
1212 : parrello 1.12 if (!$package) {
1213 : parrello 1.3 $category = "main";
1214 : parrello 1.12 } else {
1215 :     $category = $package;
1216 :     }
1217 :     }
1218 : parrello 1.7 # Save the category name.
1219 :     $LastCategory = $category;
1220 : parrello 1.13 # Convert it to lower case before we hash it.
1221 :     $category = lc $category;
1222 : parrello 1.12 # Use the category and tracelevel to compute the result.
1223 : parrello 1.36 if (ref $traceLevel) {
1224 :     Confess("Bad trace level.");
1225 :     } elsif (ref $TraceLevel) {
1226 :     Confess("Bad trace config.");
1227 :     }
1228 : parrello 1.12 $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
1229 : parrello 1.3 }
1230 : parrello 1.12 # Return the computed result.
1231 : parrello 1.3 return $retVal;
1232 : olson 1.1 }
1233 :    
1234 :     =head3 ParseCommand
1235 :    
1236 :     C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>
1237 :    
1238 :     Parse a command line consisting of a list of parameters. The initial parameters may be option
1239 : parrello 1.2 specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1240 :     off and merged into a table of default options. The remainder of the command line is
1241 : olson 1.1 returned as a list of positional arguments. For example, consider the following invocation.
1242 :    
1243 :     C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>
1244 :    
1245 :     In this case, the list @words will be treated as a command line. There are two options available,
1246 :     B<errors> and B<logFile>. If @words has the following format
1247 :    
1248 :     C<< -logFile=error.log apple orange rutabaga >>
1249 :    
1250 :     then at the end of the invocation, C<$options> will be
1251 :    
1252 :     C<< { errors => 0, logFile => 'error.log' } >>
1253 :    
1254 :     and C<@arguments> will contain
1255 :    
1256 :     C<< apple orange rutabaga >>
1257 :    
1258 : parrello 1.2 The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1259 : olson 1.1 support for quote characters.
1260 :    
1261 :     =over 4
1262 :    
1263 :     =item optionTable
1264 :    
1265 :     Table of default options.
1266 :    
1267 :     =item inputList
1268 :    
1269 :     List of words on the command line.
1270 :    
1271 :     =item RETURN
1272 :    
1273 :     Returns a reference to the option table and a list of the positional arguments.
1274 :    
1275 :     =back
1276 :    
1277 :     =cut
1278 :    
1279 :     sub ParseCommand {
1280 : parrello 1.12 # Get the parameters.
1281 :     my ($optionTable, @inputList) = @_;
1282 :     # Process any options in the input list.
1283 :     my %overrides = ();
1284 :     while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {
1285 :     # Get the current option.
1286 :     my $arg = shift @inputList;
1287 :     # Pull out the option name.
1288 :     $arg =~ /^-([^=]*)/g;
1289 :     my $name = $1;
1290 :     # Check for an option value.
1291 :     if ($arg =~ /\G=(.*)$/g) {
1292 :     # Here we have a value for the option.
1293 :     $overrides{$name} = UnEscape($1);
1294 :     } else {
1295 :     # Here there is no value, so we use 1.
1296 :     $overrides{$name} = 1;
1297 :     }
1298 :     }
1299 :     # Merge the options into the defaults.
1300 :     GetOptions($optionTable, \%overrides);
1301 :     # Translate the remaining parameters.
1302 :     my @retVal = ();
1303 :     for my $inputParm (@inputList) {
1304 :     push @retVal, UnEscape($inputParm);
1305 :     }
1306 :     # Return the results.
1307 :     return ($optionTable, @retVal);
1308 : olson 1.1 }
1309 :    
1310 : parrello 1.9 =head3 Escape
1311 :    
1312 :     C<< my $codedString = Tracer::Escape($realString); >>
1313 :    
1314 : parrello 1.25 Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines
1315 : parrello 1.28 replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
1316 :     result is to reverse the effect of L</UnEscape>.
1317 : parrello 1.9
1318 :     =over 4
1319 :    
1320 :     =item realString
1321 :    
1322 :     String to escape.
1323 :    
1324 :     =item RETURN
1325 :    
1326 :     Escaped equivalent of the real string.
1327 :    
1328 :     =back
1329 :    
1330 :     =cut
1331 :    
1332 :     sub Escape {
1333 : parrello 1.12 # Get the parameter.
1334 :     my ($realString) = @_;
1335 :     # Initialize the return variable.
1336 :     my $retVal = "";
1337 :     # Loop through the parameter string, looking for sequences to escape.
1338 :     while (length $realString > 0) {
1339 :     # Look for the first sequence to escape.
1340 : parrello 1.27 if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1341 : parrello 1.12 # Here we found it. The text preceding the sequence is in $1. The sequence
1342 :     # itself is in $2. First, move the clear text to the return variable.
1343 :     $retVal .= $1;
1344 : parrello 1.14 # Strip the processed section off the real string.
1345 :     $realString = substr $realString, (length $2) + (length $1);
1346 : parrello 1.28 # Get the matched character.
1347 : parrello 1.12 my $char = $2;
1348 : parrello 1.28 # If we have a CR, we are done.
1349 :     if ($char ne "\r") {
1350 :     # It's not a CR, so encode the escape sequence.
1351 :     $char =~ tr/\t\n/tn/;
1352 :     $retVal .= "\\" . $char;
1353 :     }
1354 : parrello 1.12 } else {
1355 :     # Here there are no more escape sequences. The rest of the string is
1356 :     # transferred unmodified.
1357 :     $retVal .= $realString;
1358 :     $realString = "";
1359 :     }
1360 :     }
1361 :     # Return the result.
1362 :     return $retVal;
1363 : parrello 1.9 }
1364 :    
1365 : olson 1.1 =head3 UnEscape
1366 :    
1367 :     C<< my $realString = Tracer::UnEscape($codedString); >>
1368 :    
1369 : parrello 1.25 Replace escape sequences with their actual equivalents. C<\t> will be replaced by
1370 : parrello 1.28 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
1371 :     be deleted.
1372 : olson 1.1
1373 :     =over 4
1374 :    
1375 :     =item codedString
1376 :    
1377 :     String to un-escape.
1378 :    
1379 :     =item RETURN
1380 :    
1381 :     Returns a copy of the original string with the escape sequences converted to their actual
1382 :     values.
1383 :    
1384 :     =back
1385 :    
1386 :     =cut
1387 :    
1388 :     sub UnEscape {
1389 : parrello 1.12 # Get the parameter.
1390 :     my ($codedString) = @_;
1391 :     # Initialize the return variable.
1392 :     my $retVal = "";
1393 :     # Only proceed if the incoming string is nonempty.
1394 :     if (defined $codedString) {
1395 :     # Loop through the parameter string, looking for escape sequences. We can't do
1396 : parrello 1.25 # translating because it causes problems with the escaped slash. ("\\t" becomes
1397 :     # "\<tab>" no matter what we do.)
1398 : parrello 1.12 while (length $codedString > 0) {
1399 :     # Look for the first escape sequence.
1400 : parrello 1.27 if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
1401 : parrello 1.12 # Here we found it. The text preceding the sequence is in $1. The sequence
1402 :     # itself is in $2. First, move the clear text to the return variable.
1403 :     $retVal .= $1;
1404 :     $codedString = substr $codedString, (2 + length $1);
1405 : parrello 1.28 # Get the escape value.
1406 : parrello 1.12 my $char = $2;
1407 : parrello 1.28 # If we have a "\r", we are done.
1408 :     if ($char ne 'r') {
1409 :     # Here it's not an 'r', so we convert it.
1410 :     $char =~ tr/\\tn/\\\t\n/;
1411 :     $retVal .= $char;
1412 :     }
1413 : parrello 1.12 } else {
1414 :     # Here there are no more escape sequences. The rest of the string is
1415 :     # transferred unmodified.
1416 :     $retVal .= $codedString;
1417 :     $codedString = "";
1418 :     }
1419 :     }
1420 :     }
1421 :     # Return the result.
1422 :     return $retVal;
1423 : olson 1.1 }
1424 :    
1425 :     =head3 ParseRecord
1426 :    
1427 :     C<< my @fields = Tracer::ParseRecord($line); >>
1428 :    
1429 :     Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1430 :     and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1431 :     These will automatically be converted.
1432 :    
1433 :     =over 4
1434 :    
1435 :     =item line
1436 :    
1437 :     Line of data containing the tab-delimited fields.
1438 :    
1439 :     =item RETURN
1440 :    
1441 :     Returns a list of the fields found in the data line.
1442 :    
1443 :     =back
1444 :    
1445 :     =cut
1446 :    
1447 :     sub ParseRecord {
1448 : parrello 1.12 # Get the parameter.
1449 :     my ($line) = @_;
1450 :     # Remove the trailing new-line, if any.
1451 :     chomp $line;
1452 :     # Split the line read into pieces using the tab character.
1453 :     my @retVal = split /\t/, $line;
1454 :     # Trim and fix the escapes in each piece.
1455 :     for my $value (@retVal) {
1456 :     # Trim leading whitespace.
1457 :     $value =~ s/^\s+//;
1458 :     # Trim trailing whitespace.
1459 :     $value =~ s/\s+$//;
1460 :     # Delete the carriage returns.
1461 :     $value =~ s/\r//g;
1462 :     # Convert the escapes into their real values.
1463 :     $value =~ s/\\t/"\t"/ge;
1464 :     $value =~ s/\\n/"\n"/ge;
1465 :     }
1466 :     # Return the result.
1467 :     return @retVal;
1468 : olson 1.1 }
1469 :    
1470 :     =head3 Merge
1471 :    
1472 :     C<< my @mergedList = Tracer::Merge(@inputList); >>
1473 :    
1474 :     Sort a list of strings and remove duplicates.
1475 :    
1476 :     =over 4
1477 :    
1478 :     =item inputList
1479 :    
1480 :     List of scalars to sort and merge.
1481 :    
1482 :     =item RETURN
1483 :    
1484 :     Returns a list containing the same elements sorted in ascending order with duplicates
1485 :     removed.
1486 :    
1487 :     =back
1488 :    
1489 :     =cut
1490 :    
1491 :     sub Merge {
1492 : parrello 1.12 # Get the input list in sort order.
1493 :     my @inputList = sort @_;
1494 :     # Only proceed if the list has at least two elements.
1495 :     if (@inputList > 1) {
1496 :     # Now we want to move through the list splicing out duplicates.
1497 :     my $i = 0;
1498 :     while ($i < @inputList) {
1499 :     # Get the current entry.
1500 :     my $thisEntry = $inputList[$i];
1501 :     # Find out how many elements duplicate the current entry.
1502 :     my $j = $i + 1;
1503 :     my $dup1 = $i + 1;
1504 :     while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
1505 :     # If the number is nonzero, splice out the duplicates found.
1506 :     if ($j > $dup1) {
1507 :     splice @inputList, $dup1, $j - $dup1;
1508 :     }
1509 :     # Now the element at position $dup1 is different from the element before it
1510 :     # at position $i. We push $i forward one position and start again.
1511 :     $i++;
1512 :     }
1513 :     }
1514 :     # Return the merged list.
1515 :     return @inputList;
1516 : olson 1.1 }
1517 :    
1518 : parrello 1.54 =head3 Percent
1519 :    
1520 :     C<< my $percent = Tracer::Percent($number, $base); >>
1521 :    
1522 :     Returns the percent of the base represented by the given number. If the base
1523 :     is zero, returns zero.
1524 :    
1525 :     =over 4
1526 :    
1527 :     =item number
1528 :    
1529 :     Percent numerator.
1530 :    
1531 :     =item base
1532 :    
1533 :     Percent base.
1534 :    
1535 :     =item RETURN
1536 :    
1537 :     Returns the percentage of the base represented by the numerator.
1538 :    
1539 :     =back
1540 :    
1541 :     =cut
1542 :    
1543 :     sub Percent {
1544 :     # Get the parameters.
1545 :     my ($number, $base) = @_;
1546 :     # Declare the return variable.
1547 :     my $retVal = 0;
1548 :     # Compute the percent.
1549 :     if ($base != 0) {
1550 :     $retVal = $number * 100 / $base;
1551 :     }
1552 :     # Return the result.
1553 :     return $retVal;
1554 :     }
1555 :    
1556 : olson 1.1 =head3 GetFile
1557 :    
1558 : parrello 1.6 C<< my @fileContents = Tracer::GetFile($fileName); >>
1559 : olson 1.1
1560 : parrello 1.35 or
1561 :    
1562 :     C<< my $fileContents = Tracer::GetFile($fileName); >>
1563 :    
1564 :     Return the entire contents of a file. In list context, line-ends are removed and
1565 :     each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1566 : olson 1.1
1567 :     =over 4
1568 :    
1569 :     =item fileName
1570 :    
1571 :     Name of the file to read.
1572 :    
1573 :     =item RETURN
1574 :    
1575 : parrello 1.6 In a list context, returns the entire file as a list with the line terminators removed.
1576 : parrello 1.39 In a scalar context, returns the entire file as a string. If an error occurs opening
1577 :     the file, an empty list will be returned.
1578 : olson 1.1
1579 :     =back
1580 :    
1581 :     =cut
1582 :    
1583 :     sub GetFile {
1584 : parrello 1.12 # Get the parameters.
1585 :     my ($fileName) = @_;
1586 :     # Declare the return variable.
1587 :     my @retVal = ();
1588 :     # Open the file for input.
1589 : parrello 1.60 my $handle = Open(undef, "<$fileName");
1590 :     # Read the whole file into the return variable, stripping off any terminator
1591 :     # characters.
1592 :     my $lineCount = 0;
1593 :     while (my $line = <$handle>) {
1594 :     $lineCount++;
1595 :     $line = Strip($line);
1596 :     push @retVal, $line;
1597 :     }
1598 :     # Close it.
1599 :     close $handle;
1600 :     my $actualLines = @retVal;
1601 : parrello 1.12 # Return the file's contents in the desired format.
1602 : parrello 1.9 if (wantarray) {
1603 : parrello 1.12 return @retVal;
1604 : parrello 1.6 } else {
1605 :     return join "\n", @retVal;
1606 :     }
1607 : olson 1.1 }
1608 :    
1609 : parrello 1.60 =head3 PutFile
1610 :    
1611 :     C<< Tracer::PutFile($fileName, \@lines); >>
1612 :    
1613 :     Write out a file from a list of lines of text.
1614 :    
1615 :     =over 4
1616 :    
1617 :     =item fileName
1618 :    
1619 :     Name of the output file.
1620 :    
1621 :     =item lines
1622 :    
1623 :     Reference to a list of text lines. The lines will be written to the file in order, with trailing
1624 : parrello 1.66 new-line characters. Alternatively, may be a string, in which case the string will be written without
1625 :     modification.
1626 : parrello 1.60
1627 :     =back
1628 :    
1629 :     =cut
1630 :    
1631 :     sub PutFile {
1632 :     # Get the parameters.
1633 :     my ($fileName, $lines) = @_;
1634 :     # Open the output file.
1635 :     my $handle = Open(undef, ">$fileName");
1636 : parrello 1.66 if (ref $lines ne 'ARRAY') {
1637 :     # Here we have a scalar, so we write it raw.
1638 :     print $handle $lines;
1639 :     } else {
1640 :     # Write the lines one at a time.
1641 :     for my $line (@{$lines}) {
1642 :     print $handle "$line\n";
1643 :     }
1644 : parrello 1.60 }
1645 :     # Close the output file.
1646 :     close $handle;
1647 :     }
1648 :    
1649 : olson 1.1 =head3 QTrace
1650 :    
1651 :     C<< my $data = QTrace($format); >>
1652 :    
1653 :     Return the queued trace data in the specified format.
1654 :    
1655 :     =over 4
1656 :    
1657 :     =item format
1658 :    
1659 :     C<html> to format the data as an HTML list, C<text> to format it as straight text.
1660 :    
1661 :     =back
1662 :    
1663 :     =cut
1664 :    
1665 :     sub QTrace {
1666 : parrello 1.12 # Get the parameter.
1667 :     my ($format) = @_;
1668 :     # Create the return variable.
1669 :     my $retVal = "";
1670 : parrello 1.14 # Only proceed if there is an actual queue.
1671 :     if (@Queue) {
1672 :     # Process according to the format.
1673 :     if ($format =~ m/^HTML$/i) {
1674 :     # Convert the queue into an HTML list.
1675 :     $retVal = "<ul>\n";
1676 :     for my $line (@Queue) {
1677 :     my $escapedLine = CGI::escapeHTML($line);
1678 :     $retVal .= "<li>$escapedLine</li>\n";
1679 :     }
1680 :     $retVal .= "</ul>\n";
1681 :     } elsif ($format =~ m/^TEXT$/i) {
1682 :     # Convert the queue into a list of text lines.
1683 :     $retVal = join("\n", @Queue) . "\n";
1684 :     }
1685 :     # Clear the queue.
1686 :     @Queue = ();
1687 : parrello 1.12 }
1688 :     # Return the formatted list.
1689 :     return $retVal;
1690 : olson 1.1 }
1691 :    
1692 :     =head3 Confess
1693 :    
1694 :     C<< Confess($message); >>
1695 :    
1696 : parrello 1.22 Trace the call stack and abort the program with the specified message. When used with
1697 : parrello 1.9 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
1698 : parrello 1.6 So, for example
1699 : olson 1.1
1700 : parrello 1.6 C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
1701 : olson 1.1
1702 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
1703 :    
1704 :     =over 4
1705 :    
1706 :     =item message
1707 :    
1708 :     Message to include in the trace.
1709 :    
1710 :     =back
1711 :    
1712 :     =cut
1713 :    
1714 :     sub Confess {
1715 : parrello 1.12 # Get the parameters.
1716 :     my ($message) = @_;
1717 :     # Trace the call stack.
1718 : parrello 1.22 Cluck($message);
1719 : parrello 1.12 # Abort the program.
1720 :     croak(">>> $message");
1721 : olson 1.1 }
1722 :    
1723 : parrello 1.6 =head3 Assert
1724 :    
1725 :     C<< Assert($condition1, $condition2, ... $conditionN); >>
1726 :    
1727 :     Return TRUE if all the conditions are true. This method can be used in conjunction with
1728 : parrello 1.29 the OR operator and the L</Confess> method as a debugging assert.
1729 : parrello 1.6 So, for example
1730 :    
1731 :     C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
1732 :    
1733 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
1734 :    
1735 :     =cut
1736 :     sub Assert {
1737 :     my $retVal = 1;
1738 :     LOOP: for my $condition (@_) {
1739 :     if (! $condition) {
1740 :     $retVal = 0;
1741 :     last LOOP;
1742 :     }
1743 :     }
1744 :     return $retVal;
1745 :     }
1746 :    
1747 : olson 1.1 =head3 Cluck
1748 :    
1749 :     C<< Cluck($message); >>
1750 :    
1751 :     Trace the call stack. Note that for best results, you should qualify the call with a
1752 :     trace condition. For example,
1753 :    
1754 :     C<< Cluck("Starting record parse.") if T(3); >>
1755 :    
1756 :     will only trace the stack if the trace level for the package is 3 or more.
1757 :    
1758 :     =over 4
1759 :    
1760 :     =item message
1761 :    
1762 :     Message to include in the trace.
1763 :    
1764 :     =back
1765 :    
1766 :     =cut
1767 :    
1768 :     sub Cluck {
1769 : parrello 1.12 # Get the parameters.
1770 :     my ($message) = @_;
1771 : parrello 1.5 # Trace what's happening.
1772 :     Trace("Stack trace for event: $message");
1773 : parrello 1.12 my $confession = longmess($message);
1774 :     # Convert the confession to a series of trace messages. Note we skip any
1775 : parrello 1.5 # messages relating to calls into Tracer.
1776 : parrello 1.12 for my $line (split /\s*\n/, $confession) {
1777 :     Trace($line) if ($line !~ /Tracer\.pm/);
1778 :     }
1779 : olson 1.1 }
1780 :    
1781 : parrello 1.5 =head3 Min
1782 :    
1783 :     C<< my $min = Min($value1, $value2, ... $valueN); >>
1784 :    
1785 :     Return the minimum argument. The arguments are treated as numbers.
1786 :    
1787 :     =over 4
1788 :    
1789 :     =item $value1, $value2, ... $valueN
1790 :    
1791 :     List of numbers to compare.
1792 :    
1793 :     =item RETURN
1794 :    
1795 :     Returns the lowest number in the list.
1796 :    
1797 :     =back
1798 :    
1799 :     =cut
1800 :    
1801 :     sub Min {
1802 : parrello 1.12 # Get the parameters. Note that we prime the return value with the first parameter.
1803 :     my ($retVal, @values) = @_;
1804 :     # Loop through the remaining parameters, looking for the lowest.
1805 :     for my $value (@values) {
1806 :     if ($value < $retVal) {
1807 :     $retVal = $value;
1808 :     }
1809 :     }
1810 :     # Return the minimum found.
1811 :     return $retVal;
1812 : parrello 1.5 }
1813 :    
1814 :     =head3 Max
1815 :    
1816 :     C<< my $max = Max($value1, $value2, ... $valueN); >>
1817 :    
1818 :     Return the maximum argument. The arguments are treated as numbers.
1819 :    
1820 :     =over 4
1821 :    
1822 :     =item $value1, $value2, ... $valueN
1823 :    
1824 :     List of numbers to compare.
1825 :    
1826 :     =item RETURN
1827 :    
1828 :     Returns the highest number in the list.
1829 :    
1830 :     =back
1831 :    
1832 :     =cut
1833 :    
1834 :     sub Max {
1835 : parrello 1.12 # Get the parameters. Note that we prime the return value with the first parameter.
1836 :     my ($retVal, @values) = @_;
1837 :     # Loop through the remaining parameters, looking for the highest.
1838 :     for my $value (@values) {
1839 :     if ($value > $retVal) {
1840 :     $retVal = $value;
1841 :     }
1842 :     }
1843 :     # Return the maximum found.
1844 :     return $retVal;
1845 : parrello 1.5 }
1846 :    
1847 :     =head3 AddToListMap
1848 :    
1849 : parrello 1.53 C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>
1850 : parrello 1.5
1851 :     Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list
1852 :     is created for the key. Otherwise, the new value is pushed onto the list.
1853 :    
1854 :     =over 4
1855 :    
1856 :     =item hash
1857 :    
1858 :     Reference to the target hash.
1859 :    
1860 :     =item key
1861 :    
1862 :     Key for which the value is to be added.
1863 :    
1864 : parrello 1.53 =item value1, value2, ... valueN
1865 : parrello 1.5
1866 : parrello 1.53 List of values to add to the key's value list.
1867 : parrello 1.5
1868 :     =back
1869 :    
1870 :     =cut
1871 :    
1872 :     sub AddToListMap {
1873 :     # Get the parameters.
1874 : parrello 1.53 my ($hash, $key, @values) = @_;
1875 : parrello 1.5 # Process according to whether or not the key already has a value.
1876 :     if (! exists $hash->{$key}) {
1877 : parrello 1.53 $hash->{$key} = [@values];
1878 : parrello 1.5 } else {
1879 : parrello 1.53 push @{$hash->{$key}}, @values;
1880 : parrello 1.5 }
1881 :     }
1882 : olson 1.1
1883 : parrello 1.7 =head3 DebugMode
1884 :    
1885 :     C<< if (Tracer::DebugMode) { ...code... } >>
1886 :    
1887 : parrello 1.69 Return TRUE if debug mode has been turned on, else abort.
1888 : parrello 1.7
1889 :     Certain CGI scripts are too dangerous to exist in the production
1890 :     environment. This method provides a simple way to prevent them
1891 : parrello 1.21 from working unless they are explicitly turned on by creating a password
1892 :     cookie via the B<SetPassword> script. If debugging mode
1893 : parrello 1.69 is not turned on, an error will occur.
1894 : parrello 1.7
1895 :     =cut
1896 :    
1897 :     sub DebugMode {
1898 : parrello 1.12 # Declare the return variable.
1899 : parrello 1.21 my $retVal = 0;
1900 : parrello 1.12 # Check the debug configuration.
1901 : parrello 1.21 my $password = CGI::cookie("DebugMode");
1902 :     my $encrypted = Digest::MD5::md5_hex($password);
1903 :     if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1904 : parrello 1.12 $retVal = 1;
1905 :     } else {
1906 : parrello 1.69 # Here debug mode is off, so we generate an error.
1907 :     Confess("Cannot use this facility without logging in.");
1908 : parrello 1.12 }
1909 :     # Return the determination indicator.
1910 : parrello 1.18 return $retVal;
1911 : parrello 1.9 }
1912 :    
1913 :     =head3 Strip
1914 :    
1915 :     C<< my $string = Tracer::Strip($line); >>
1916 :    
1917 :     Strip all line terminators off a string. This is necessary when dealing with files
1918 :     that may have been transferred back and forth several times among different
1919 :     operating environments.
1920 :    
1921 :     =over 4
1922 :    
1923 :     =item line
1924 :    
1925 :     Line of text to be stripped.
1926 :    
1927 :     =item RETURN
1928 :    
1929 :     The same line of text with all the line-ending characters chopped from the end.
1930 :    
1931 :     =back
1932 :    
1933 :     =cut
1934 :    
1935 :     sub Strip {
1936 : parrello 1.12 # Get a copy of the parameter string.
1937 :     my ($string) = @_;
1938 : parrello 1.29 my $retVal = (defined $string ? $string : "");
1939 : parrello 1.9 # Strip the line terminator characters.
1940 :     $retVal =~ s/(\r|\n)+$//g;
1941 : parrello 1.12 # Return the result.
1942 :     return $retVal;
1943 : parrello 1.9 }
1944 :    
1945 :     =head3 Pad
1946 :    
1947 :     C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>
1948 :    
1949 :     Pad a string to a specified length. The pad character will be a
1950 :     space, and the padding will be on the right side unless specified
1951 :     in the third parameter.
1952 :    
1953 :     =over 4
1954 :    
1955 :     =item string
1956 :    
1957 :     String to be padded.
1958 :    
1959 :     =item len
1960 :    
1961 :     Desired length of the padded string.
1962 :    
1963 :     =item left (optional)
1964 :    
1965 :     TRUE if the string is to be left-padded; otherwise it will be padded on the right.
1966 :    
1967 :     =item padChar (optional)
1968 :    
1969 : parrello 1.22 Character to use for padding. The default is a space.
1970 :    
1971 : parrello 1.9 =item RETURN
1972 :    
1973 : parrello 1.22 Returns a copy of the original string with the pad character added to the
1974 :     specified end so that it achieves the desired length.
1975 : parrello 1.9
1976 :     =back
1977 :    
1978 :     =cut
1979 :    
1980 :     sub Pad {
1981 : parrello 1.12 # Get the parameters.
1982 :     my ($string, $len, $left, $padChar) = @_;
1983 :     # Compute the padding character.
1984 :     if (! defined $padChar) {
1985 :     $padChar = " ";
1986 :     }
1987 :     # Compute the number of spaces needed.
1988 :     my $needed = $len - length $string;
1989 :     # Copy the string into the return variable.
1990 :     my $retVal = $string;
1991 :     # Only proceed if padding is needed.
1992 :     if ($needed > 0) {
1993 :     # Create the pad string.
1994 :     my $pad = $padChar x $needed;
1995 :     # Affix it to the return value.
1996 :     if ($left) {
1997 :     $retVal = $pad . $retVal;
1998 :     } else {
1999 :     $retVal .= $pad;
2000 :     }
2001 :     }
2002 :     # Return the result.
2003 :     return $retVal;
2004 : parrello 1.7 }
2005 :    
2006 : parrello 1.29 =head3 EOF
2007 :    
2008 :     This is a constant that is lexically greater than any useful string.
2009 :    
2010 :     =cut
2011 :    
2012 :     sub EOF {
2013 :     return "\xFF\xFF\xFF\xFF\xFF";
2014 :     }
2015 :    
2016 : parrello 1.15 =head3 TICK
2017 :    
2018 :     C<< my @results = TICK($commandString); >>
2019 :    
2020 :     Perform a back-tick operation on a command. If this is a Windows environment, any leading
2021 :     dot-slash (C<./> will be removed. So, for example, if you were doing
2022 :    
2023 :     `./protein.cgi`
2024 :    
2025 :     from inside a CGI script, it would work fine in Unix, but would issue an error message
2026 :     in Windows complaining that C<'.'> is not a valid command. If instead you code
2027 :    
2028 :     TICK("./protein.cgi")
2029 :    
2030 :     it will work correctly in both environments.
2031 :    
2032 :     =over 4
2033 :    
2034 :     =item commandString
2035 :    
2036 :     The command string to pass to the system.
2037 :    
2038 :     =item RETURN
2039 :    
2040 :     Returns the standard output from the specified command, as a list.
2041 :    
2042 :     =back
2043 :    
2044 :     =cut
2045 :     #: Return Type @;
2046 :     sub TICK {
2047 :     # Get the parameters.
2048 :     my ($commandString) = @_;
2049 :     # Chop off the dot-slash if this is Windows.
2050 :     if ($FIG_Config::win_mode) {
2051 :     $commandString =~ s!^\./!!;
2052 :     }
2053 :     # Activate the command and return the result.
2054 :     return `$commandString`;
2055 :     }
2056 :    
2057 : parrello 1.35 =head3 ScriptSetup
2058 :    
2059 : parrello 1.69 C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>
2060 : parrello 1.35
2061 :     Perform standard tracing and debugging setup for scripts. The value returned is
2062 :     the CGI object followed by a pre-built variable hash.
2063 :    
2064 : parrello 1.72 The C<Trace> form parameter is used to determine whether or not tracing is active and
2065 : parrello 1.69 which trace modules (other than C<Tracer> itself) should be turned on. Specifying
2066 : parrello 1.35 the C<CGI> trace module will trace parameter and environment information. Parameters are
2067 : parrello 1.69 traced at level 3 and environment variables at level 4. To trace to a file instead of to
2068 :     the web page, set C<TF> to 1. At the end of the script, the client should call
2069 :     L</ScriptFinish> to output the web page.
2070 :    
2071 :     In some situations, it is not practical to invoke tracing via form parameters. For this
2072 : parrello 1.72 situation, you can turn on emergency tracing from the debugging control panel.
2073 :     Tracing will then be turned on automatically for all programs that use the L</ETracing>
2074 :     method, which includes every program that uses this method or L</StandardSetup>.
2075 : parrello 1.69
2076 :     =over 4
2077 :    
2078 :     =item noTrace (optional)
2079 :    
2080 :     If specified, tracing will be suppressed. This is useful if the script wants to set up
2081 :     tracing manually.
2082 :    
2083 :     =item RETURN
2084 :    
2085 :     Returns a two-element list consisting of a CGI query object and a variable hash for
2086 :     the output page.
2087 :    
2088 :     =back
2089 : parrello 1.35
2090 :     =cut
2091 :    
2092 :     sub ScriptSetup {
2093 : parrello 1.69 # Get the parameters.
2094 :     my ($noTrace) = @_;
2095 : parrello 1.35 # Get the CGI query object.
2096 : parrello 1.69 my $cgi = CGI->new();
2097 :     # Set up tracing if it's not suppressed.
2098 : parrello 1.72 ETracing($cgi) unless $noTrace;
2099 : parrello 1.69 # Create the variable hash.
2100 :     my $varHash = { results => '' };
2101 :     # Return the query object and variable hash.
2102 :     return ($cgi, $varHash);
2103 :     }
2104 :    
2105 : parrello 1.72 =head3 ETracing
2106 : parrello 1.69
2107 : parrello 1.72 C<< ETracing($parameter); >>
2108 : parrello 1.69
2109 : parrello 1.72 Set up emergency tracing. Emergency tracing is tracing that is turned
2110 :     on automatically for any program that calls this method. The emergency
2111 :     tracing parameters are stored in a a file identified by a tracing key.
2112 :     If this method is called with a CGI object, then the tracing key is
2113 :     taken from a cookie. If it is called with no parameters, then the tracing
2114 :     key is taken from an environment variable. If it is called with a string,
2115 :     the tracing key is that string.
2116 : parrello 1.69
2117 :     =over 4
2118 :    
2119 : parrello 1.72 =item parameter
2120 : parrello 1.69
2121 : parrello 1.72 A parameter from which the tracing key is computed. If it is a scalar,
2122 :     that scalar is used as the tracing key. If it is a CGI object, the
2123 :     tracing key is taken from the C<IP> cookie. If it is omitted, the
2124 :     tracing key is taken from the C<TRACING> environment variable. If it
2125 :     is a CGI object and emergency tracing is not on, the C<Trace> and
2126 :     C<TF> parameters will be used to determine the type of tracing.
2127 : parrello 1.69
2128 :     =back
2129 :    
2130 :     =cut
2131 :    
2132 : parrello 1.72 sub ETracing {
2133 :     # Get the parameter.
2134 :     my ($parameter) = @_;
2135 :     # Check for CGI mode.
2136 :     my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
2137 : parrello 1.69 # Default to no tracing except errors.
2138 :     my ($tracing, $dest) = ("0", "WARN");
2139 :     # Check for emergency tracing.
2140 : parrello 1.72 my $tkey = EmergencyKey($parameter);
2141 :     my $emergencyFile = EmergencyFileName($tkey);
2142 : parrello 1.69 if (-e $emergencyFile) {
2143 :     # We have the file. Read in the data.
2144 :     my @tracing = GetFile($emergencyFile);
2145 :     # Pull off the time limit.
2146 :     my $expire = shift @tracing;
2147 :     # Convert it to seconds.
2148 :     $expire *= 3600;
2149 :     # Check the file data.
2150 :     my $stat = stat($emergencyFile);
2151 :     my ($now) = gettimeofday;
2152 :     if ($now - $stat->mtime > $expire) {
2153 :     # Delete the expired file.
2154 :     unlink $emergencyFile;
2155 :     } else {
2156 :     # Emergency tracing is on. Pull off the destination and
2157 :     # the trace level;
2158 :     $dest = shift @tracing;
2159 :     my $level = shift @tracing;
2160 :     # Convert the destination to a real tracing destination.
2161 :     # temp directory.
2162 : parrello 1.72 $dest = EmergencyTracingDest($tkey, $dest);
2163 : parrello 1.69 # Insure Tracer is specified.
2164 :     my %moduleHash = map { $_ => 1 } @tracing;
2165 :     $moduleHash{Tracer} = 1;
2166 :     # Set the trace parameter.
2167 :     $tracing = join(" ", $level, sort keys %moduleHash);
2168 : parrello 1.72 }
2169 :     } elsif (defined $cgi) {
2170 :     # There's no emergency tracing, but we have a CGI object, so check
2171 :     # for tracing from the form parameters.
2172 :     if ($cgi->param('Trace')) {
2173 :     # Here the user has requested tracing via a form.
2174 :     $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
2175 :     $tracing = $cgi->param('Trace') . " Tracer";
2176 :     }
2177 :     }
2178 : parrello 1.69 # Setup the tracing we've determined from all the stuff above.
2179 :     TSetup($tracing, $dest);
2180 : parrello 1.72 # If we're a web script, trace the parameter and environment data.
2181 :     if (defined $cgi) {
2182 :     TraceParms($cgi);
2183 :     }
2184 : parrello 1.69 }
2185 :    
2186 :     =head3 EmergencyFileName
2187 :    
2188 : parrello 1.72 C<< my $fileName = Tracer::EmergencyFileName($tkey); >>
2189 : parrello 1.69
2190 :     Return the emergency tracing file name. This is the file that specifies
2191 :     the tracing information.
2192 :    
2193 :     =over 4
2194 :    
2195 : parrello 1.72 =item tkey
2196 : parrello 1.69
2197 : parrello 1.72 Tracing key for the current program.
2198 : parrello 1.69
2199 :     =item RETURN
2200 :    
2201 :     Returns the name of the file to contain the emergency tracing information.
2202 :    
2203 :     =back
2204 :    
2205 :     =cut
2206 :    
2207 :     sub EmergencyFileName {
2208 :     # Get the parameters.
2209 : parrello 1.72 my ($tkey) = @_;
2210 : parrello 1.69 # Compute the emergency tracing file name.
2211 : parrello 1.72 return "$FIG_Config::temp/Emergency$tkey.txt";
2212 : parrello 1.69 }
2213 :    
2214 :     =head3 EmergencyFileTarget
2215 :    
2216 : parrello 1.72 C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>
2217 : parrello 1.69
2218 :     Return the emergency tracing target file name. This is the file that receives
2219 :     the tracing output for file-based tracing.
2220 :    
2221 :     =over 4
2222 :    
2223 : parrello 1.72 =item tkey
2224 : parrello 1.69
2225 : parrello 1.72 Tracing key for the current program.
2226 : parrello 1.69
2227 :     =item RETURN
2228 :    
2229 : parrello 1.72 Returns the name of the file to contain the trace output.
2230 : parrello 1.69
2231 :     =back
2232 :    
2233 :     =cut
2234 :    
2235 :     sub EmergencyFileTarget {
2236 :     # Get the parameters.
2237 : parrello 1.72 my ($tkey) = @_;
2238 : parrello 1.69 # Compute the emergency tracing file name.
2239 : parrello 1.72 return "$FIG_Config::temp/trace$tkey.log";
2240 : parrello 1.69 }
2241 :    
2242 :     =head3 EmergencyTracingDest
2243 :    
2244 : parrello 1.72 C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>
2245 : parrello 1.69
2246 :     This method converts an emergency tracing destination to a real
2247 :     tracing destination. The main difference is that if the
2248 :     destination is C<FILE> or C<APPEND>, we convert it to file
2249 :     output.
2250 :    
2251 :     =over 4
2252 :    
2253 : parrello 1.72 =item tkey
2254 : parrello 1.69
2255 : parrello 1.72 Tracing key for this environment.
2256 : parrello 1.69
2257 :     =item myDest
2258 :    
2259 :     Destination from the emergency tracing file.
2260 :    
2261 :     =item RETURN
2262 :    
2263 :     Returns a destination that can be passed into L</TSetup>.
2264 :    
2265 :     =back
2266 :    
2267 :     =cut
2268 :    
2269 :     sub EmergencyTracingDest {
2270 :     # Get the parameters.
2271 : parrello 1.72 my ($tkey, $myDest) = @_;
2272 : parrello 1.69 # Declare the return variable.
2273 :     my $retVal;
2274 :     # Process according to the destination value.
2275 :     if ($myDest eq 'FILE') {
2276 : parrello 1.72 $retVal = ">" . EmergencyFileTarget($tkey);
2277 : parrello 1.69 } elsif ($myDest eq 'APPEND') {
2278 : parrello 1.72 $retVal = ">>" . EmergencyFileTarget($tkey);
2279 : parrello 1.35 } else {
2280 : parrello 1.69 $retVal = $myDest;
2281 : parrello 1.35 }
2282 : parrello 1.69 # Return the result.
2283 :     return $retVal;
2284 :     }
2285 :    
2286 :     =head3 Emergency
2287 :    
2288 : parrello 1.72 C<< Emergency($key, $hours, $dest, $level, @modules); >>
2289 : parrello 1.69
2290 :     Turn on emergency tracing. This method can only be invoked over the web and is
2291 :     should not be called if debug mode is off. The caller specifies the duration of the
2292 :     emergency in hours, the desired tracing destination, the trace level,
2293 : parrello 1.72 and a list of the trace modules to activate. For the length of the duration, when a
2294 :     program in an environment with the specified tracing key active invokes a Sprout
2295 :     CGI script, tracing will be turned on automatically. See L</TSetup> for more
2296 :     about tracing setup and L</ETracing> for more about emergency tracing.
2297 : parrello 1.69
2298 :     =over 4
2299 :    
2300 : parrello 1.72 =item tkey
2301 : parrello 1.69
2302 : parrello 1.72 The tracing key. This is used to identify the control file and the trace file.
2303 : parrello 1.69
2304 :     =item hours
2305 :    
2306 :     Number of hours to keep emergency tracing alive.
2307 :    
2308 :     =item dest
2309 :    
2310 :     Tracing destination. If no path information is specified for a file
2311 :     destination, it is put in the FIG temporary directory.
2312 :    
2313 :     =item level
2314 :    
2315 :     Tracing level. A higher level means more trace messages.
2316 :    
2317 :     =item modules
2318 :    
2319 :     A list of the tracing modules to activate.
2320 :    
2321 :     =back
2322 :    
2323 :     =cut
2324 :    
2325 :     sub Emergency {
2326 :     # Get the parameters.
2327 : parrello 1.72 my ($tkey, $hours, $dest, $level, @modules) = @_;
2328 : parrello 1.69 # Create the emergency file.
2329 : parrello 1.72 my $specFile = EmergencyFileName($tkey);
2330 : parrello 1.69 my $outHandle = Open(undef, ">$specFile");
2331 : parrello 1.71 print $outHandle join("\n", $hours, $dest, $level, @modules, "");
2332 : parrello 1.69 }
2333 :    
2334 : parrello 1.72 =head3 EmergencyKey
2335 : parrello 1.69
2336 : parrello 1.72 C<< my $tkey = EmergencyKey($parameter); >>
2337 : parrello 1.69
2338 : parrello 1.72 Return the Key to be used for emergency tracing. This could be an IP address,
2339 :     a session ID, or a user name, depending on the environment.
2340 : parrello 1.69
2341 :     =over 4
2342 :    
2343 : parrello 1.72 =item parameter
2344 : parrello 1.69
2345 : parrello 1.72 Parameter defining the method for finding the tracing key. If it is a scalar,
2346 :     then it is presumed to be the tracing key itself. If it is a CGI object, then
2347 :     the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
2348 :     taken from the C<TRACING> environment variable.
2349 : parrello 1.69
2350 :     =item RETURN
2351 :    
2352 : parrello 1.72 Returns the key to be used for labels in emergency tracing.
2353 : parrello 1.69
2354 :     =back
2355 :    
2356 :     =cut
2357 :    
2358 : parrello 1.72 sub EmergencyKey {
2359 : parrello 1.69 # Get the parameters.
2360 : parrello 1.72 my ($parameter) = @_;
2361 :     # Declare the return variable.
2362 :     my $retVal;
2363 :     # Determine the parameter type.
2364 :     if (! defined $parameter) {
2365 :     # Here we're supposed to check the environment.
2366 :     $retVal = $ENV{TRACING};
2367 :     } else {
2368 :     my $ptype = ref $parameter;
2369 :     if ($ptype eq 'CGI') {
2370 :     # Here we were invoked from a web page. Look for a cookie.
2371 :     $retVal = $parameter->cookie('IP');
2372 :     } elsif (! $ptype) {
2373 :     # Here the key was passed in.
2374 :     $retVal = $parameter;
2375 :     }
2376 :     }
2377 :     # If no luck finding a key, use the PID.
2378 :     if (! defined $retVal) {
2379 :     $retVal = $$;
2380 :     }
2381 : parrello 1.69 # Return the result.
2382 : parrello 1.70 return $retVal;
2383 : parrello 1.35 }
2384 :    
2385 : parrello 1.69
2386 : parrello 1.65 =head3 TraceParms
2387 :    
2388 : parrello 1.69 C<< Tracer::TraceParms($cgi); >>
2389 : parrello 1.65
2390 :     Trace the CGI parameters at trace level CGI => 3 and the environment variables
2391 :     at level CGI => 4.
2392 :    
2393 :     =over 4
2394 :    
2395 : parrello 1.69 =item cgi
2396 : parrello 1.65
2397 :     CGI query object containing the parameters to trace.
2398 :    
2399 :     =back
2400 :    
2401 :     =cut
2402 :    
2403 :     sub TraceParms {
2404 :     # Get the parameters.
2405 : parrello 1.69 my ($cgi) = @_;
2406 : parrello 1.65 if (T(CGI => 3)) {
2407 :     # Here we want to trace the parameter data.
2408 : parrello 1.69 my @names = $cgi->param;
2409 : parrello 1.65 for my $parmName (sort @names) {
2410 : parrello 1.68 # Note we skip the Trace parameters, which are for our use only.
2411 :     if ($parmName ne 'Trace' && $parmName ne 'TF') {
2412 : parrello 1.69 my @values = $cgi->param($parmName);
2413 : parrello 1.65 Trace("CGI: $parmName = " . join(", ", @values));
2414 :     }
2415 :     }
2416 : parrello 1.67 # Display the request method.
2417 : parrello 1.69 my $method = $cgi->request_method();
2418 : parrello 1.67 Trace("Method: $method");
2419 : parrello 1.65 }
2420 :     if (T(CGI => 4)) {
2421 :     # Here we want the environment data too.
2422 :     for my $envName (sort keys %ENV) {
2423 :     Trace("ENV: $envName = $ENV{$envName}");
2424 :     }
2425 :     }
2426 :     }
2427 :    
2428 : parrello 1.35 =head3 ScriptFinish
2429 :    
2430 :     C<< ScriptFinish($webData, $varHash); >>
2431 :    
2432 :     Output a web page at the end of a script. Either the string to be output or the
2433 :     name of a template file can be specified. If the second parameter is omitted,
2434 :     it is assumed we have a string to be output; otherwise, it is assumed we have the
2435 :     name of a template file. The template should have the variable C<DebugData>
2436 :     specified in any form that invokes a standard script. If debugging mode is turned
2437 :     on, a form field will be put in that allows the user to enter tracing data.
2438 :     Trace messages will be placed immediately before the terminal C<BODY> tag in
2439 :     the output, formatted as a list.
2440 :    
2441 :     A typical standard script would loook like the following.
2442 :    
2443 :     BEGIN {
2444 :     # Print the HTML header.
2445 :     print "CONTENT-TYPE: text/html\n\n";
2446 :     }
2447 :     use Tracer;
2448 :     use CGI;
2449 :     use FIG;
2450 :     # ... more uses ...
2451 : parrello 1.61
2452 : parrello 1.69 my ($cgi, $varHash) = ScriptSetup();
2453 : parrello 1.35 eval {
2454 : parrello 1.69 # ... get data from $cgi, put it in $varHash ...
2455 : parrello 1.35 };
2456 :     if ($@) {
2457 :     Trace("Script Error: $@") if T(0);
2458 :     }
2459 :     ScriptFinish("Html/MyTemplate.html", $varHash);
2460 :    
2461 :     The idea here is that even if the script fails, you'll see trace messages and
2462 :     useful output.
2463 :    
2464 :     =over 4
2465 :    
2466 :     =item webData
2467 :    
2468 :     A string containing either the full web page to be written to the output or the
2469 :     name of a template file from which the page is to be constructed. If the name
2470 :     of a template file is specified, then the second parameter must be present;
2471 :     otherwise, it must be absent.
2472 :    
2473 :     =item varHash (optional)
2474 :    
2475 :     If specified, then a reference to a hash mapping variable names for a template
2476 :     to their values. The template file will be read into memory, and variable markers
2477 :     will be replaced by data in this hash reference.
2478 :    
2479 : parrello 1.37 =back
2480 :    
2481 : parrello 1.35 =cut
2482 :    
2483 :     sub ScriptFinish {
2484 :     # Get the parameters.
2485 :     my ($webData, $varHash) = @_;
2486 :     # Check for a template file situation.
2487 :     my $outputString;
2488 :     if (defined $varHash) {
2489 : parrello 1.64 # Here we have a template file. We need to determine the template type.
2490 :     my $template;
2491 :     if ($FIG_Config::template_url && $webData =~ /\.php$/) {
2492 :     $template = "$FIG_Config::template_url/$webData";
2493 :     } else {
2494 :     $template = "<<$webData";
2495 :     }
2496 :     $outputString = PageBuilder::Build($template, $varHash, "Html");
2497 : parrello 1.35 } else {
2498 :     # Here the user gave us a raw string.
2499 :     $outputString = $webData;
2500 :     }
2501 :     # Check for trace messages.
2502 : parrello 1.68 if ($Destination ne "NONE" && $TraceLevel > 0) {
2503 : parrello 1.35 # We have trace messages, so we want to put them at the end of the body. This
2504 :     # is either at the end of the whole string or at the beginning of the BODY
2505 :     # end-tag.
2506 :     my $pos = length $outputString;
2507 :     if ($outputString =~ m#</body>#gi) {
2508 :     $pos = (pos $outputString) - 7;
2509 :     }
2510 : parrello 1.68 # If the trace messages were queued, we unroll them. Otherwise, we display the
2511 :     # destination.
2512 :     my $traceHtml;
2513 :     if ($Destination eq "QUEUE") {
2514 :     $traceHtml = QTrace('Html');
2515 :     } elsif ($Destination =~ /^>>(.+)$/) {
2516 :     # Here the tracing output it to a file. We code it as a hyperlink so the user
2517 :     # can copy the file name into the clipboard easily.
2518 :     my $actualDest = $1;
2519 : parrello 1.73 $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
2520 : parrello 1.68 } else {
2521 :     # Here we have one of the special destinations.
2522 :     $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
2523 :     }
2524 :     substr $outputString, $pos, 0, $traceHtml;
2525 : parrello 1.35 }
2526 :     # Write the output string.
2527 :     print $outputString;
2528 :     }
2529 :    
2530 : parrello 1.37 =head3 Insure
2531 :    
2532 :     C<< Insure($dirName); >>
2533 :    
2534 :     Insure a directory is present.
2535 :    
2536 :     =over 4
2537 :    
2538 :     =item dirName
2539 :    
2540 :     Name of the directory to check. If it does not exist, it will be created.
2541 :    
2542 :     =back
2543 :    
2544 :     =cut
2545 :    
2546 :     sub Insure {
2547 :     my ($dirName) = @_;
2548 :     if (! -d $dirName) {
2549 :     Trace("Creating $dirName directory.") if T(2);
2550 : parrello 1.43 eval { mkpath $dirName; };
2551 :     if ($@) {
2552 :     Confess("Error creating $dirName: $@");
2553 :     }
2554 :     }
2555 :     }
2556 :    
2557 :     =head3 ChDir
2558 :    
2559 :     C<< ChDir($dirName); >>
2560 :    
2561 :     Change to the specified directory.
2562 :    
2563 :     =over 4
2564 :    
2565 :     =item dirName
2566 :    
2567 :     Name of the directory to which we want to change.
2568 :    
2569 :     =back
2570 :    
2571 :     =cut
2572 :    
2573 :     sub ChDir {
2574 :     my ($dirName) = @_;
2575 :     if (! -d $dirName) {
2576 :     Confess("Cannot change to directory $dirName: no such directory.");
2577 :     } else {
2578 :     Trace("Changing to directory $dirName.") if T(4);
2579 :     my $okFlag = chdir $dirName;
2580 :     if (! $okFlag) {
2581 :     Confess("Error switching to directory $dirName.");
2582 :     }
2583 : parrello 1.37 }
2584 :     }
2585 :    
2586 : parrello 1.59 =head3 SendSMS
2587 :    
2588 :     C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>
2589 :    
2590 :     Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
2591 :     user name, password, and API ID for the relevant account in the hash reference variable
2592 :     I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
2593 :     example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
2594 :     is C<2561022>, then the FIG_Config file must contain
2595 :    
2596 :     $phone = { user => 'BruceTheHumanPet',
2597 :     password => 'silly',
2598 :     api_id => '2561022' };
2599 :    
2600 :     The original purpose of this method was to insure Bruce would be notified immediately when the
2601 :     Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
2602 :     when you call this method.
2603 :    
2604 :     The message ID will be returned if successful, and C<undef> if an error occurs.
2605 :    
2606 :     =over 4
2607 :    
2608 :     =item phoneNumber
2609 :    
2610 :     Phone number to receive the message, in international format. A United States phone number
2611 :     would be prefixed by "1". A British phone number would be prefixed by "44".
2612 :    
2613 :     =item msg
2614 :    
2615 :     Message to send to the specified phone.
2616 :    
2617 :     =item RETURN
2618 :    
2619 :     Returns the message ID if successful, and C<undef> if the message could not be sent.
2620 :    
2621 :     =back
2622 :    
2623 :     =cut
2624 :    
2625 :     sub SendSMS {
2626 :     # Get the parameters.
2627 :     my ($phoneNumber, $msg) = @_;
2628 :     # Declare the return variable. If we do not change it, C<undef> will be returned.
2629 :     my $retVal;
2630 :     # Only proceed if we have phone support.
2631 :     if (! defined $FIG_Config::phone) {
2632 :     Trace("Phone support not present in FIG_Config.") if T(1);
2633 :     } else {
2634 :     # Get the phone data.
2635 :     my $parms = $FIG_Config::phone;
2636 :     # Get the Clickatell URL.
2637 :     my $url = "http://api.clickatell.com/http/";
2638 :     # Create the user agent.
2639 :     my $ua = LWP::UserAgent->new;
2640 :     # Request a Clickatell session.
2641 :     my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
2642 :     password => $parms->{password},
2643 :     api_id => $parms->{api_id},
2644 :     to => $phoneNumber,
2645 :     text => $msg});
2646 :     # Check for an error.
2647 :     if (! $resp->is_success) {
2648 :     Trace("Alert failed.") if T(1);
2649 :     } else {
2650 :     # Get the message ID.
2651 :     my $rstring = $resp->content;
2652 :     if ($rstring =~ /^ID:\s+(.*)$/) {
2653 :     $retVal = $1;
2654 :     } else {
2655 :     Trace("Phone attempt failed with $rstring") if T(1);
2656 :     }
2657 :     }
2658 :     }
2659 :     # Return the result.
2660 :     return $retVal;
2661 :     }
2662 :    
2663 : parrello 1.55 =head3 CommaFormat
2664 :    
2665 :     C<< my $formatted = Tracer::CommaFormat($number); >>
2666 :    
2667 :     Insert commas into a number.
2668 :    
2669 :     =over 4
2670 :    
2671 :     =item number
2672 :    
2673 :     A sequence of digits.
2674 :    
2675 :     =item RETURN
2676 :    
2677 :     Returns the same digits with commas strategically inserted.
2678 :    
2679 :     =back
2680 :    
2681 :     =cut
2682 :    
2683 :     sub CommaFormat {
2684 :     # Get the parameters.
2685 :     my ($number) = @_;
2686 :     # Pad the length up to a multiple of three.
2687 :     my $padded = "$number";
2688 :     $padded = " " . $padded while length($padded) % 3 != 0;
2689 :     # This is a fancy PERL trick. The parentheses in the SPLIT pattern
2690 :     # cause the delimiters to be included in the output stream. The
2691 :     # GREP removes the empty strings in between the delimiters.
2692 :     my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
2693 :     # Clean out the spaces.
2694 :     $retVal =~ s/ //g;
2695 :     # Return the result.
2696 :     return $retVal;
2697 :     }
2698 : parrello 1.46 =head3 SetPermissions
2699 :    
2700 : parrello 1.49 C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>
2701 : parrello 1.46
2702 :     Set the permissions for a directory and all the files and folders inside it.
2703 :     In addition, the group ownership will be changed to the specified value.
2704 :    
2705 :     This method is more vulnerable than most to permission and compatability
2706 :     problems, so it does internal error recovery.
2707 :    
2708 :     =over 4
2709 :    
2710 :     =item dirName
2711 :    
2712 :     Name of the directory to process.
2713 :    
2714 :     =item group
2715 :    
2716 :     Name of the group to be assigned.
2717 :    
2718 :     =item mask
2719 :    
2720 :     Permission mask. Bits that are C<1> in this mask will be ORed into the
2721 :     permission bits of any file or directory that does not already have them
2722 :     set to 1.
2723 :    
2724 : parrello 1.49 =item otherMasks
2725 :    
2726 :     Map of search patterns to permission masks. If a directory name matches
2727 :     one of the patterns, that directory and all its members and subdirectories
2728 :     will be assigned the new pattern. For example, the following would
2729 :     assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2730 :    
2731 :     Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2732 :    
2733 :     The list is ordered, so the following would use 0777 for C<tmp1> and
2734 :     0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2735 :    
2736 :     Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2737 :     '^tmp' => 0666);
2738 :    
2739 :     Note that the pattern matches are all case-insensitive, and only directory
2740 :     names are matched, not file names.
2741 :    
2742 : parrello 1.46 =back
2743 :    
2744 :     =cut
2745 :    
2746 :     sub SetPermissions {
2747 :     # Get the parameters.
2748 : parrello 1.49 my ($dirName, $group, $mask, @otherMasks) = @_;
2749 : parrello 1.46 # Set up for error recovery.
2750 :     eval {
2751 : parrello 1.49 # Switch to the specified directory.
2752 : parrello 1.46 ChDir($dirName);
2753 :     # Get the group ID.
2754 :     my $gid = getgrnam($group);
2755 : parrello 1.50 # Get the mask for tracing.
2756 : parrello 1.51 my $traceMask = sprintf("%04o", $mask) . "($mask)";
2757 : parrello 1.50 Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(2);
2758 : parrello 1.46 my $fixCount = 0;
2759 :     my $lookCount = 0;
2760 :     # @dirs will be a stack of directories to be processed.
2761 :     my @dirs = (getcwd());
2762 :     while (scalar(@dirs) > 0) {
2763 :     # Get the current directory.
2764 :     my $dir = pop @dirs;
2765 : parrello 1.49 # Check for a match to one of the specified directory names. To do
2766 :     # that, we need to pull the individual part of the name off of the
2767 :     # whole path.
2768 :     my $simpleName = $dir;
2769 : parrello 1.57 if ($dir =~ m!/([^/]+)$!) {
2770 : parrello 1.49 $simpleName = $1;
2771 :     }
2772 : parrello 1.56 Trace("Simple directory name for $dir is $simpleName.") if T(4);
2773 : parrello 1.49 # Search for a match.
2774 :     my $match = 0;
2775 :     my $i;
2776 :     for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2777 :     my $pattern = $otherMasks[$i];
2778 :     if ($simpleName =~ /$pattern/i) {
2779 :     $match = 1;
2780 : parrello 1.46 }
2781 : parrello 1.49 }
2782 : parrello 1.52 # Check for a match. Note we use $i-1 because the loop added 2
2783 :     # before terminating due to the match.
2784 :     if ($match && $otherMasks[$i-1] != $mask) {
2785 : parrello 1.49 # This directory matches one of the incoming patterns, and it's
2786 :     # a different mask, so we process it recursively with that mask.
2787 : parrello 1.52 SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2788 : parrello 1.49 } else {
2789 :     # Here we can process normally. Get all of the non-hidden members.
2790 :     my @submems = OpenDir($dir, 1);
2791 :     for my $submem (@submems) {
2792 :     # Get the full name.
2793 :     my $thisMem = "$dir/$submem";
2794 :     Trace("Checking member $thisMem.") if T(4);
2795 :     $lookCount++;
2796 :     if ($lookCount % 1000 == 0) {
2797 : parrello 1.50 Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(3);
2798 : parrello 1.49 }
2799 :     # Fix the group.
2800 :     chown -1, $gid, $thisMem;
2801 :     # Insure this member is not a symlink.
2802 :     if (! -l $thisMem) {
2803 :     # Get its info.
2804 :     my $fileInfo = stat $thisMem;
2805 :     # Only proceed if we got the info. Otherwise, it's a hard link
2806 :     # and we want to skip it anyway.
2807 :     if ($fileInfo) {
2808 :     my $fileMode = $fileInfo->mode;
2809 : parrello 1.58 if (($fileMode & $mask) != $mask) {
2810 : parrello 1.49 # Fix this member.
2811 :     $fileMode |= $mask;
2812 :     chmod $fileMode, $thisMem;
2813 :     $fixCount++;
2814 :     }
2815 :     # If it's a subdirectory, stack it.
2816 :     if (-d $thisMem) {
2817 :     push @dirs, $thisMem;
2818 :     }
2819 : parrello 1.46 }
2820 :     }
2821 :     }
2822 :     }
2823 :     }
2824 :     Trace("$lookCount files and directories processed, $fixCount fixed.") if T(2);
2825 :     };
2826 :     # Check for an error.
2827 :     if ($@) {
2828 :     Confess("SetPermissions error: $@");
2829 :     }
2830 :     }
2831 :    
2832 : parrello 1.62 =head3 CompareLists
2833 :    
2834 :     C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>
2835 :    
2836 :     Compare two lists of tuples, and return a hash analyzing the differences. The lists
2837 :     are presumed to be sorted alphabetically by the value in the $keyIndex column.
2838 :     The return value contains a list of items that are only in the new list
2839 :     (inserted) and only in the old list (deleted).
2840 :    
2841 :     =over 4
2842 :    
2843 :     =item newList
2844 :    
2845 :     Reference to a list of new tuples.
2846 :    
2847 :     =item oldList
2848 :    
2849 :     Reference to a list of old tuples.
2850 :    
2851 :     =item keyIndex (optional)
2852 :    
2853 :     Index into each tuple of its key field. The default is 0.
2854 :    
2855 :     =item RETURN
2856 :    
2857 :     Returns a 2-tuple consisting of a reference to the list of items that are only in the new
2858 :     list (inserted) followed by a reference to the list of items that are only in the old
2859 :     list (deleted).
2860 :    
2861 :     =back
2862 :    
2863 :     =cut
2864 :    
2865 :     sub CompareLists {
2866 :     # Get the parameters.
2867 :     my ($newList, $oldList, $keyIndex) = @_;
2868 :     if (! defined $keyIndex) {
2869 :     $keyIndex = 0;
2870 :     }
2871 :     # Declare the return variables.
2872 :     my ($inserted, $deleted) = ([], []);
2873 :     # Loop through the two lists simultaneously.
2874 :     my ($newI, $oldI) = (0, 0);
2875 :     my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
2876 :     while ($newI < $newN || $oldI < $oldN) {
2877 :     # Get the current object in each list. Note that if one
2878 :     # of the lists is past the end, we'll get undef.
2879 :     my $newItem = $newList->[$newI];
2880 :     my $oldItem = $oldList->[$oldI];
2881 : parrello 1.63 if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
2882 : parrello 1.62 # The old item is not in the new list, so mark it deleted.
2883 :     push @{$deleted}, $oldItem;
2884 :     $oldI++;
2885 :     } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
2886 :     # The new item is not in the old list, so mark it inserted.
2887 :     push @{$inserted}, $newItem;
2888 :     $newI++;
2889 :     } else {
2890 :     # The item is in both lists, so push forward.
2891 :     $oldI++;
2892 :     $newI++;
2893 :     }
2894 :     }
2895 :     # Return the result.
2896 :     return ($inserted, $deleted);
2897 :     }
2898 :    
2899 : parrello 1.65 =head3 GetLine
2900 :    
2901 :     C<< my @data = Tracer::GetLine($handle); >>
2902 :    
2903 :     Read a line of data from a tab-delimited file.
2904 :    
2905 :     =over 4
2906 :    
2907 :     =item handle
2908 :    
2909 :     Open file handle from which to read.
2910 :    
2911 :     =item RETURN
2912 :    
2913 :     Returns a list of the fields in the record read. The fields are presumed to be
2914 :     tab-delimited. If we are at the end of the file, then an empty list will be
2915 :     returned. If an empty line is read, a single list item consisting of a null
2916 :     string will be returned.
2917 :    
2918 :     =back
2919 :    
2920 :     =cut
2921 :    
2922 :     sub GetLine {
2923 :     # Get the parameters.
2924 :     my ($handle) = @_;
2925 :     # Declare the return variable.
2926 :     my @retVal = ();
2927 :     # Read from the file.
2928 :     my $line = <$handle>;
2929 :     # Only proceed if we found something.
2930 :     if (defined $line) {
2931 :     # Remove the new-line.
2932 :     chomp $line;
2933 :     # If the line is empty, return a single empty string; otherwise, parse
2934 :     # it into fields.
2935 :     if ($line eq "") {
2936 :     push @retVal, "";
2937 :     } else {
2938 :     push @retVal, split /\t/,$line;
2939 :     }
2940 :     }
2941 :     # Return the result.
2942 :     return @retVal;
2943 :     }
2944 :    
2945 :     =head3 PutLine
2946 :    
2947 :     C<< Tracer::PutLine($handle, \@fields); >>
2948 :    
2949 :     Write a line of data to a tab-delimited file. The specified field values will be
2950 :     output in tab-separated form, with a trailing new-line.
2951 :    
2952 :     =over 4
2953 :    
2954 :     =item handle
2955 :    
2956 :     Output file handle.
2957 :    
2958 :     =item fields
2959 :    
2960 :     List of field values.
2961 :    
2962 :     =back
2963 :    
2964 :     =cut
2965 :    
2966 :     sub PutLine {
2967 :     # Get the parameters.
2968 :     my ($handle, $fields) = @_;
2969 :     # Write the data.
2970 :     print $handle join("\t", @{$fields}) . "\n";
2971 :     }
2972 :    
2973 :     =head3 GenerateURL
2974 :    
2975 :     C<< my $queryUrl = Tracer::GenerateURL($page, %parameters); >>
2976 :    
2977 :     Generate a GET-style URL for the specified page with the specified parameter
2978 :     names and values. The values will be URL-escaped automatically. So, for
2979 :     example
2980 :    
2981 :     Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
2982 :    
2983 :     would return
2984 :    
2985 :     form.cgi?type=1&string=%22high%20pass%22%20or%20highway
2986 :    
2987 :     =over 4
2988 :    
2989 :     =item page
2990 :    
2991 :     Page URL.
2992 :    
2993 :     =item parameters
2994 :    
2995 :     Hash mapping parameter names to parameter values.
2996 :    
2997 :     =item RETURN
2998 :    
2999 :     Returns a GET-style URL that goes to the specified page and passes in the
3000 :     specified parameters and values.
3001 :    
3002 :     =back
3003 :    
3004 :     =cut
3005 :    
3006 :     sub GenerateURL {
3007 :     # Get the parameters.
3008 :     my ($page, %parameters) = @_;
3009 :     # Prime the return variable with the page URL.
3010 :     my $retVal = $page;
3011 :     # Loop through the parameters, creating parameter elements in a list.
3012 :     my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3013 :     # If the list is nonempty, tack it on.
3014 :     if (@parmList) {
3015 :     $retVal .= "?" . join("&", @parmList);
3016 :     }
3017 :     # Return the result.
3018 :     return $retVal;
3019 :     }
3020 :    
3021 :     1;

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