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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 : parrello 1.74 use Time::Local;
38 : olson 1.1
39 :     =head1 Tracing and Debugging Helpers
40 :    
41 : parrello 1.72 =head2 Tracing
42 : olson 1.1
43 :     This package provides simple tracing for debugging and reporting purposes. To use it simply call the
44 : parrello 1.72 L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
45 :     L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
46 :     each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
47 :     level is less than or equal to the setup trace level and whose category is activated will
48 : parrello 1.2 be written. Thus, a higher trace level on a message indicates that the message
49 : parrello 1.72 is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
50 :     appear.
51 : olson 1.1
52 : parrello 1.72 =head3 Putting Trace Messages in Your Code
53 :    
54 :     To generate a trace message, use the following syntax.
55 :    
56 :     Trace($message) if T(errors => 4);
57 : olson 1.1
58 : parrello 1.2 This statement will produce a trace message if the trace level is 4 or more and the C<errors>
59 : parrello 1.72 category is active. There is a special category C<main> that is always active, so
60 : olson 1.1
61 : parrello 1.72 Trace($message) if T(main => 4);
62 : olson 1.1
63 :     will trace if the trace level is 4 or more.
64 :    
65 :     If the category name is the same as the package name, all you need is the number. So, if the
66 :     following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
67 :     active and the trace level is 2 or more.
68 :    
69 : parrello 1.72 Trace($message) if T(2);
70 :    
71 :     In scripts, where no package name is available, the category defaults to C<main>.
72 :    
73 :     =head3 Custom Tracing
74 :    
75 :     Many programs have customized tracing configured using the L</TSetup> method. This is no longer
76 :     the preferred method, but a knowledge of how custom tracing works can make the more modern
77 :     L</Emergency Tracing> easier to understand.
78 : olson 1.1
79 : parrello 1.72 To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
80 :     a list of category names, and a destination. The trace level and list of category names are
81 : olson 1.1 specified as a space-delimited string. Thus
82 :    
83 : parrello 1.72 TSetup('3 errors Sprout ERDB', 'TEXT');
84 : olson 1.1
85 : parrello 1.7 sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
86 : parrello 1.72 specifies that messages should be sent to the standard output.
87 : parrello 1.12
88 :     To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
89 :     level 3 and writes the output to the standard error output. This sort of thing might be
90 :     useful in a CGI environment.
91 :    
92 : parrello 1.72 TSetup('3 *', 'WARN');
93 : olson 1.1
94 : parrello 1.72 In addition standard error and file output for trace messages, you can specify that the trace messages
95 : olson 1.1 be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
96 :     is useful if you are building a web page. Instead of having the trace messages interspersed with
97 :     the page output, they can be gathered together and displayed at the end of the page. This makes
98 :     it easier to debug page formatting problems.
99 :    
100 : parrello 1.72 Finally, you can specify that all trace messages be emitted to a file, or the standard output and
101 :     a file at the same time. To trace to a file, specify the filename with an output character in front
102 :     of it.
103 :    
104 :     TSetup('4 SQL', ">$fileName");
105 :    
106 :     To trace to the standard output and a file at the same time, put a C<+> in front of the angle
107 :     bracket.
108 :    
109 :     TSetup('3 *', "+>$fileName");
110 : parrello 1.4
111 : olson 1.1 The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
112 :     Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
113 :     Thus, debugging information is available and easily retrieved even when the application is
114 :     being used out in the field.
115 :    
116 : parrello 1.72 =head3 Trace Levels
117 :    
118 : parrello 1.10 There is no hard and fast rule on how to use trace levels. The following is therefore only
119 :     a suggestion.
120 :    
121 :     =over 4
122 :    
123 : parrello 1.32 =item Error 0
124 : parrello 1.10
125 :     Message indicates an error that may lead to incorrect results or that has stopped the
126 :     application entirely.
127 :    
128 : parrello 1.32 =item Warning 1
129 : parrello 1.10
130 :     Message indicates something that is unexpected but that probably did not interfere
131 :     with program execution.
132 :    
133 : parrello 1.32 =item Notice 2
134 : parrello 1.10
135 :     Message indicates the beginning or end of a major task.
136 :    
137 : parrello 1.32 =item Information 3
138 : parrello 1.10
139 :     Message indicates a subtask. In the FIG system, a subtask generally relates to a single
140 :     genome. This would be a big loop that is not expected to execute more than 500 times or so.
141 :    
142 : parrello 1.32 =item Detail 4
143 : parrello 1.10
144 :     Message indicates a low-level loop iteration.
145 :    
146 :     =back
147 :    
148 : parrello 1.69 The format of trace messages is important because some utilities analyze trace files.
149 : parrello 1.72 There are three fields-- the time stamp, the category name, and the text.
150 :     The time stamp is between square brackets and the category name between angle brackets.
151 :     After the category name there is a colon (C<:>) followed by the message text.
152 :     If the square brackets or angle brackets are missing, then the trace management
153 :     utilities assume that they are encountering a set of pre-formatted lines.
154 :    
155 :     Note, however, that this formatting is done automatically by the tracing functions. You
156 :     only need to know about it if you want to parse a trace file.
157 :    
158 :     =head3 Emergency Tracing
159 :    
160 :     Sometimes, you need a way for tracing to happen automatically without putting parameters
161 :     in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
162 :     from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.
163 :     Emergency tracing requires you specify a tracing key. For command-line tools, the key is
164 :     taken from the C<TRACING> environment variable. For web services, the key is taken from
165 :     a cookie. Either way, the key tells the tracing facility who you are, so that you control
166 :     the tracing in your environment without stepping on other users.
167 :    
168 :     The key can be anything you want. If you don't have a key, the C<SetPassword> page will
169 :     generate one for you.
170 :    
171 :     You can activate and de-activate emergency tracing from the debugging control panel, as
172 :     well as display the trace file itself.
173 :    
174 :     To enable emergency tracing in your code, call
175 :    
176 :     ETracing($cgi)
177 :    
178 :     from a web script and
179 :    
180 :     ETracing()
181 :    
182 :     from a command-line script.
183 :    
184 :     The web script will look for the tracing key in the cookies, and the command-line
185 :     script will look for it in the C<TRACING> environment variable. If you are
186 :     using the L</StandardScript> or L</StandardSetup> methods, emergency tracing
187 :     will be configured automatically.
188 :    
189 : parrello 1.84 NOTE: to configure emergency tracing from the command line instead of the Debugging
190 :     Control Panel (see below), use the C<trace.pl> script.
191 :    
192 : parrello 1.72 =head3 Debugging Control Panel
193 :    
194 :     The debugging control panel provides several tools to assist in development of
195 :     SEED and Sprout software. You access the debugging control panel from the URL
196 :     C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,
197 :     for example, the panel access point for the development NMPDR system is
198 :     C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to
199 :     find out what the password is. From this page, you can also specify a tracing
200 :     key. If you don't specify a key, one will be generated for you.
201 :    
202 :     =head4 Emergency Tracing Form
203 :    
204 :     At the bottom of the debugging control panel is a form that allows you to
205 :     specify a trace level and tracing categories. Special and common categories
206 :     are listed with check boxes. You can hold your mouse over a check box to see
207 :     what its category does. In general, however, a category name is the same as
208 :     the name of the package in which the trace message occurs.
209 :    
210 :     Additional categories can be entered in an input box, delimited by spaces or commas.
211 :    
212 :     The B<Activate> button turns on Emergency tracing at the level you specify with the
213 :     specified categories active. The B<Terminate> button turns tracing off. The
214 :     B<Show File> button displays the current contents of the trace file. The tracing
215 :     form at the bottom of the control panel is designed for emergency tracing, so it
216 :     will only affect programs that call L</ETracing>, L</StandardScript>,
217 :     or L</StandardSetup>.
218 :    
219 :     =head4 Script Form
220 :    
221 :     The top form of the debugging control panel allows you to enter a tiny script and
222 :     have the output generated in a formatted table. Certain object variables are
223 :     predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),
224 :     and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.
225 :    
226 :     The last line of the script must be a scalar, but it can be a reference to a hash,
227 :     a list, a list of lists, and various other combinations. If you select the appropriate
228 :     data type in the dropdown box, the output will be formatted accordingly. The form
229 :     also has controls for specifying tracing. These controls override any emergency
230 :     tracing in effect.
231 :    
232 :     =head4 Database Query Forms
233 :    
234 :     The forms between the script form and the emergency tracing form allow you to
235 :     make queries against the database. The FIG query form allows simple queries against
236 :     a single FIG table. The Sprout query form uses the B<GetAll> method to do a
237 :     multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>
238 :     package, and it takes five parameters.
239 :    
240 :     GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
241 :    
242 :     Each of the five parameters corresponds to a text box on the query form:
243 :    
244 :     =over 4
245 :    
246 :     =item Objects
247 :    
248 :     Comma-separated list containing the names of the entity and relationship objects to be retrieved.
249 :    
250 :     =item Filter
251 :    
252 :     WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
253 :     be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
254 :     B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a
255 :     field, I<objectName> is the name of the entity or relationship object containing the field, and
256 :     I<number> is the 1-based position of the object in the object list. Any parameters
257 :     specified in the filter clause should be specified in the B<Params> field.
258 :     The fields in a filter clause can come from primary entity relations,
259 :     relationship relations, or secondary entity relations; however, all of the
260 :     entities and relationships involved must be included in the list of object names.
261 :    
262 :     =item Params
263 :    
264 :     List of the parameters to be substituted in for the parameters marks in the filter clause. This
265 :     is a comma-separated list without any quoting or escaping.
266 :    
267 :     =item fields
268 :    
269 :     Comma-separated list of the fields to be returned in each element of the list returned. Fields
270 :     are specified in the same manner as in the filter clause.
271 :    
272 :     =item count
273 :    
274 :     Maximum number of records to return. If omitted or 0, all available records will be returned.
275 :    
276 :     =back
277 :    
278 :     B<GetAll> automatically joins together the entities and relationships listed in the object
279 :     names. This simplifies the coding of the filter clause, but it means that some queries are
280 :     not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation
281 :     that has yet to be addressed.
282 : parrello 1.69
283 : olson 1.1 =cut
284 : parrello 1.2
285 : olson 1.1 # Declare the configuration variables.
286 :    
287 : parrello 1.12 my $Destination = "NONE"; # Description of where to send the trace output.
288 :     my $TeeFlag = 0; # TRUE if output is going to a file and to the
289 :     # standard output
290 : parrello 1.3 my %Categories = ( main => 1 );
291 : parrello 1.12 # hash of active category names
292 :     my $TraceLevel = 0; # trace level; a higher trace level produces more
293 :     # messages
294 :     my @Queue = (); # queued list of trace messages.
295 : parrello 1.7 my $LastCategory = "main"; # name of the last category interrogated
296 : parrello 1.11 my $SetupCount = 0; # number of times TSetup called
297 : parrello 1.12 my $AllTrace = 0; # TRUE if we are tracing all categories.
298 : olson 1.1
299 :     =head2 Public Methods
300 :    
301 :     =head3 TSetup
302 :    
303 :     C<< TSetup($categoryList, $target); >>
304 :    
305 :     This method is used to specify the trace options. The options are stored as package data
306 :     and interrogated by the L</Trace> and L</T> methods.
307 :    
308 :     =over 4
309 :    
310 :     =item categoryList
311 :    
312 :     A string specifying the trace level and the categories to be traced, separated by spaces.
313 :     The trace level must come first.
314 :    
315 :     =item target
316 :    
317 :     The destination for the trace output. To send the trace output to a file, specify the file
318 :     name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
319 : parrello 1.10 to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
320 :     symbol with a C<+> to echo output to a file AND to the standard output. In addition to
321 :     sending the trace messages to a file, you can specify a special destination. C<HTML> will
322 :     cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
323 : parrello 1.5 will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
324 : parrello 1.9 messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
325 : parrello 1.6 messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
326 : parrello 1.9 cause trace messages to be emitted as warnings using the B<warn> directive. C<NONE> will
327 : parrello 1.6 cause tracing to be suppressed.
328 : olson 1.1
329 :     =back
330 :    
331 :     =cut
332 :    
333 :     sub TSetup {
334 : parrello 1.12 # Get the parameters.
335 :     my ($categoryList, $target) = @_;
336 :     # Parse the category list.
337 :     my @categoryData = split /\s+/, $categoryList;
338 :     # Extract the trace level.
339 :     $TraceLevel = shift @categoryData;
340 :     # Presume category-based tracing until we learn otherwise.
341 :     $AllTrace = 0;
342 :     # Build the category hash. Note that if we find a "*", we turn on non-category
343 : parrello 1.33 # tracing. We must also clear away any pre-existing data.
344 : parrello 1.34 %Categories = ( main => 1 );
345 : parrello 1.12 for my $category (@categoryData) {
346 :     if ($category eq '*') {
347 :     $AllTrace = 1;
348 :     } else {
349 : parrello 1.13 $Categories{lc $category} = 1;
350 : parrello 1.12 }
351 :     }
352 :     # Now we need to process the destination information. The most important special
353 :     # cases are the single ">", which requires we clear the file first, and the
354 :     # "+" prefix which indicates a double echo.
355 :     if ($target =~ m/^\+?>>?/) {
356 :     if ($target =~ m/^\+/) {
357 :     $TeeFlag = 1;
358 :     $target = substr($target, 1);
359 :     }
360 :     if ($target =~ m/^>[^>]/) {
361 :     open TRACEFILE, $target;
362 : parrello 1.69 print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";
363 : parrello 1.12 close TRACEFILE;
364 :     $Destination = ">$target";
365 :     } else {
366 :     $Destination = $target;
367 :     }
368 :     } else {
369 :     $Destination = uc($target);
370 :     }
371 :     # Increment the setup counter.
372 :     $SetupCount++;
373 : parrello 1.11 }
374 :    
375 : parrello 1.31 =head3 StandardSetup
376 :    
377 : parrello 1.36 C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>
378 : parrello 1.31
379 :     This method performs standard command-line parsing and tracing setup. The return
380 :     values are a hash of the command-line options and a list of the positional
381 :     parameters. Tracing is automatically set up and the command-line options are
382 :     validated.
383 :    
384 :     This is a complex method that does a lot of grunt work. The parameters can
385 :     be more easily understood, however, once they are examined individually.
386 :    
387 :     The I<categories> parameter is the most obtuse. It is a reference to a list of
388 :     special-purpose tracing categories. Most tracing categories are PERL package
389 :     names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
390 :     B<ERDB>, and B<SproutLoad> packages, you would specify the categories
391 :    
392 :     ["Sprout", "SproutLoad", "ERDB"]
393 :    
394 :     This would cause trace messages in the specified three packages to appear in
395 : parrello 1.69 the output. There are two special tracing categories that are automatically
396 : parrello 1.31 handled by this method. In other words, if you used L</TSetup> you would need
397 :     to include these categories manually, but if you use this method they are turned
398 :     on automatically.
399 :    
400 :     =over 4
401 :    
402 :     =item SQL
403 :    
404 :     Traces SQL commands and activity.
405 :    
406 :     =item Tracer
407 :    
408 :     Traces error messages and call stacks.
409 :    
410 :     =back
411 :    
412 :     C<SQL> is only turned on if the C<-sql> option is specified in the command line.
413 :     The trace level is specified using the C<-trace> command-line option. For example,
414 :     the following command line for C<TransactFeatures> turns on SQL tracing and runs
415 :     all tracing at level 3.
416 :    
417 :     TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
418 :    
419 :     Standard tracing is output to the standard output and echoed to the file
420 : parrello 1.38 C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
421 :     process ID. You can also specify the C<user> parameter to put a user ID
422 :     instead of a process ID in the trace file name. So, for example
423 : parrello 1.31
424 : parrello 1.35 The default trace level is 2. To get all messages, specify a trace level of 4.
425 :     For a genome-by-genome update, use 3.
426 : parrello 1.31
427 : parrello 1.38 TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
428 :    
429 :     would send the trace output to C<traceBruce.log> in the temporary directory.
430 :    
431 : parrello 1.31 The I<options> parameter is a reference to a hash containing the command-line
432 : parrello 1.36 options, their default values, and an explanation of what they mean. Command-line
433 :     options may be in the form of switches or keywords. In the case of a switch, the
434 :     option value is 1 if it is specified and 0 if it is not specified. In the case
435 :     of a keyword, the value is separated from the option name by an equal sign. You
436 :     can see this last in the command-line example above.
437 : parrello 1.31
438 : parrello 1.42 You can specify a different default trace level by setting C<$options->{trace}>
439 :     prior to calling this method.
440 :    
441 : parrello 1.31 An example at this point would help. Consider, for example, the command-line utility
442 :     C<TransactFeatures>. It accepts a list of positional parameters plus the options
443 :     C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
444 :     the following code.
445 :    
446 :     my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
447 : parrello 1.36 { safe => [0, "use database transactions"],
448 :     noAlias => [0, "do not expect aliases in CHANGE transactions"],
449 :     start => [' ', "start with this genome"],
450 :     tblFiles => [0, "output TBL files containing the corrected IDs"] },
451 : parrello 1.84 "<command> <transactionDirectory> <IDfile>",
452 : parrello 1.36 @ARGV);
453 : parrello 1.31
454 :    
455 :     The call to C<ParseCommand> specifies the default values for the options and
456 :     stores the actual options in a hash that is returned as C<$options>. The
457 : parrello 1.61 positional parameters are returned in C<@parameters>.
458 : parrello 1.31
459 :     The following is a sample command line for C<TransactFeatures>.
460 :    
461 :     TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
462 :    
463 : parrello 1.84 Single and double hyphens are equivalent. So, you could also code the
464 :     above command as
465 :    
466 :     TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
467 :    
468 : parrello 1.31 In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
469 :     parameters, and would find themselves in I<@parameters> after executing the
470 :     above code fragment. The tracing would be set to level 2, and the categories
471 : parrello 1.69 would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
472 : parrello 1.31 and C<DocUtils> was included because it came in within the first parameter
473 :     to this method. The I<$options> hash would be
474 :    
475 :     { trace => 2, sql => 0, safe => 0,
476 :     noAlias => 1, start => ' ', tblFiles => 0 }
477 :    
478 :     Use of C<StandardSetup> in this way provides a simple way of performing
479 :     standard tracing setup and command-line parsing. Note that the caller is
480 :     not even aware of the command-line switches C<-trace> and C<-sql>, which
481 :     are used by this method to control the tracing. If additional tracing features
482 :     need to be added in the future, they can be processed by this method without
483 :     upsetting the command-line utilities.
484 :    
485 : parrello 1.42 If the C<background> option is specified on the command line, then the
486 :     standard and error outputs will be directed to files in the temporary
487 :     directory, using the same suffix as the trace file. So, if the command
488 :     line specified
489 :    
490 :     -user=Bruce -background
491 :    
492 :     then the trace output would go to C<traceBruce.log>, the standard output to
493 :     C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
494 :     simplify starting a command in the background.
495 :    
496 : parrello 1.72 The user name is also used as the tracing key for L</Emergency Tracing>.
497 :     Specifying a value of C<E> for the trace level causes emergency tracing to
498 :     be used instead of custom tracing. If the user name is not specified,
499 :     the tracing key is taken from the C<Tracing> environment variable. If there
500 :     is no value for that variable, the tracing key will be computed from the PID.
501 :    
502 : parrello 1.84 Finally, if the special option C<-help> is specified, the option
503 :     names will be traced at level 0 and the program will exit without processing.
504 : parrello 1.36 This provides a limited help capability. For example, if the user enters
505 :    
506 : parrello 1.84 TransactFeatures -help
507 : parrello 1.36
508 :     he would see the following output.
509 :    
510 : parrello 1.84 TransactFeatures [options] <command> <transactionDirectory> <IDfile>
511 : parrello 1.72 -trace tracing level (default E)
512 : parrello 1.36 -sql trace SQL commands
513 :     -safe use database transactions
514 :     -noAlias do not expect aliases in CHANGE transactions
515 :     -start start with this genome
516 :     -tblFiles output TBL files containing the corrected IDs
517 :    
518 : parrello 1.44 The caller has the option of modifying the tracing scheme by placing a value
519 :     for C<trace> in the incoming options hash. The default value can be overridden,
520 :     or the tracing to the standard output can be turned off by suffixing a minus
521 : parrello 1.61 sign to the trace level. So, for example,
522 : parrello 1.44
523 :     { trace => [0, "tracing level (default 0)"],
524 :     ...
525 :    
526 : parrello 1.72 would set the default trace level to 0 instead of E, while
527 : parrello 1.44
528 :     { trace => ["2-", "tracing level (default 2)"],
529 :     ...
530 :    
531 : parrello 1.72 would set the default to 2, but trace only to the log file, not to the
532 : parrello 1.44 standard output.
533 :    
534 : parrello 1.31 The parameters to this method are as follows.
535 :    
536 :     =over 4
537 :    
538 :     =item categories
539 :    
540 :     Reference to a list of tracing category names. These should be names of
541 :     packages whose internal workings will need to be debugged to get the
542 :     command working.
543 :    
544 :     =item options
545 :    
546 :     Reference to a hash containing the legal options for the current command mapped
547 : parrello 1.36 to their default values and descriptions. The user can override the defaults
548 :     by specifying the options as command-line switches prefixed by a hyphen.
549 :     Tracing-related options may be added to this hash. If the C<-h> option is
550 :     specified on the command line, the option descriptions will be used to
551 : parrello 1.44 explain the options. To turn off tracing to the standard output, add a
552 :     minus sign to the value for C<trace> (see above).
553 : parrello 1.36
554 :     =item parmHelp
555 :    
556 :     A string that vaguely describes the positional parameters. This is used
557 :     if the user specifies the C<-h> option.
558 : parrello 1.31
559 : parrello 1.44 =item argv
560 : parrello 1.31
561 :     List of command line parameters, including the option switches, which must
562 :     precede the positional parameters and be prefixed by a hyphen.
563 :    
564 :     =item RETURN
565 :    
566 :     Returns a list. The first element of the list is the reference to a hash that
567 :     maps the command-line option switches to their values. These will either be the
568 :     default values or overrides specified on the command line. The remaining
569 :     elements of the list are the position parameters, in order.
570 :    
571 :     =back
572 :    
573 :     =cut
574 :    
575 :     sub StandardSetup {
576 :     # Get the parameters.
577 : parrello 1.36 my ($categories, $options, $parmHelp, @argv) = @_;
578 : parrello 1.72 # Get the default tracing key.
579 :     my $tkey = EmergencyKey();
580 : parrello 1.31 # Add the tracing options.
581 : parrello 1.41 if (! exists $options->{trace}) {
582 : parrello 1.72 $options->{trace} = ['E', "tracing level (E for emergency tracing)"];
583 : parrello 1.41 }
584 : parrello 1.36 $options->{sql} = [0, "turn on SQL tracing"];
585 : parrello 1.84 $options->{help} = [0, "display command-line options"];
586 : parrello 1.72 $options->{user} = [$tkey, "tracing key"];
587 : parrello 1.42 $options->{background} = [0, "spool standard and error output"];
588 : parrello 1.36 # Create a parsing hash from the options hash. The parsing hash
589 :     # contains the default values rather than the default value
590 :     # and the description. While we're at it, we'll memorize the
591 :     # length of the longest option name.
592 :     my $longestName = 0;
593 :     my %parseOptions = ();
594 :     for my $key (keys %{$options}) {
595 :     if (length $key > $longestName) {
596 :     $longestName = length $key;
597 :     }
598 :     $parseOptions{$key} = $options->{$key}->[0];
599 :     }
600 : parrello 1.31 # Parse the command line.
601 : parrello 1.36 my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
602 : parrello 1.42 # Get the logfile suffix.
603 :     my $suffix = $retOptions->{user};
604 :     # Check for background mode.
605 :     if ($retOptions->{background}) {
606 :     my $outFileName = "$FIG_Config::temp/out$suffix.log";
607 :     my $errFileName = "$FIG_Config::temp/err$suffix.log";
608 :     open STDOUT, ">$outFileName";
609 :     open STDERR, ">$errFileName";
610 :     }
611 : parrello 1.72 # Now we want to set up tracing. First, we need to know if the user
612 :     # wants emergency tracing.
613 :     if ($retOptions->{trace} eq 'E') {
614 :     ETracing($retOptions->{user});
615 : parrello 1.44 } else {
616 : parrello 1.72 # Here the tracing is controlled from the command line.
617 :     my @cats = @{$categories};
618 :     if ($retOptions->{sql}) {
619 :     push @cats, "SQL";
620 :     }
621 :     # Add the default categories.
622 :     push @cats, "Tracer";
623 :     # Next, we create the category string by joining the categories.
624 :     my $cats = join(" ", @cats);
625 :     # Check to determine whether or not the caller wants to turn off tracing
626 :     # to the standard output.
627 :     my $traceLevel = $retOptions->{trace};
628 :     my $textOKFlag = 1;
629 :     if ($traceLevel =~ /^(.)-/) {
630 :     $traceLevel = $1;
631 :     $textOKFlag = 0;
632 :     }
633 :     # Now we set up the trace mode.
634 :     my $traceMode;
635 :     # Verify that we can open a file in the FIG temporary directory.
636 :     my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
637 :     if (open TESTTRACE, ">$traceFileName") {
638 :     # Here we can trace to a file.
639 :     $traceMode = ">$traceFileName";
640 :     if ($textOKFlag) {
641 :     # Echo to standard output if the text-OK flag is set.
642 :     $traceMode = "+$traceMode";
643 :     }
644 :     # Close the test file.
645 :     close TESTTRACE;
646 : parrello 1.44 } else {
647 : parrello 1.72 # Here we can't trace to a file. We trace to the standard output if it's
648 :     # okay, and the error log otherwise.
649 :     if ($textOKFlag) {
650 :     $traceMode = "TEXT";
651 :     } else {
652 :     $traceMode = "WARN";
653 :     }
654 : parrello 1.44 }
655 : parrello 1.72 # Now set up the tracing.
656 :     TSetup("$traceLevel $cats", $traceMode);
657 : parrello 1.40 }
658 : parrello 1.36 # Check for the "h" option. If it is specified, dump the command-line
659 :     # options and exit the program.
660 : parrello 1.84 if ($retOptions->{help}) {
661 : parrello 1.36 $0 =~ m#[/\\](\w+)(\.pl)?$#i;
662 : parrello 1.69 print "$1 [options] $parmHelp\n";
663 : parrello 1.36 for my $key (sort keys %{$options}) {
664 :     my $name = Pad($key, $longestName, 0, ' ');
665 :     my $desc = $options->{$key}->[1];
666 :     if ($options->{$key}->[0]) {
667 :     $desc .= " (default " . $options->{$key}->[0] . ")";
668 :     }
669 : parrello 1.69 print " $name $desc\n";
670 : parrello 1.36 }
671 :     exit(0);
672 :     }
673 : parrello 1.83 # Trace the options, if applicable.
674 :     if (T(3)) {
675 :     my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
676 :     Trace("Selected options: " . join(", ", sort @parms) . ".");
677 :     }
678 : parrello 1.31 # Return the parsed parameters.
679 :     return ($retOptions, @retParameters);
680 :     }
681 :    
682 : parrello 1.11 =head3 Setups
683 :    
684 :     C<< my $count = Tracer::Setups(); >>
685 :    
686 :     Return the number of times L</TSetup> has been called.
687 :    
688 :     This method allows for the creation of conditional tracing setups where, for example, we
689 :     may want to set up tracing if nobody else has done it before us.
690 :    
691 :     =cut
692 :    
693 :     sub Setups {
694 : parrello 1.12 return $SetupCount;
695 : olson 1.1 }
696 :    
697 : parrello 1.10 =head3 Open
698 :    
699 :     C<< my $handle = Open($fileHandle, $fileSpec, $message); >>
700 :    
701 : parrello 1.11 Open a file.
702 : parrello 1.10
703 :     The I<$fileSpec> is essentially the second argument of the PERL C<open>
704 :     function. The mode is specified using Unix-like shell information. So, for
705 :     example,
706 :    
707 : parrello 1.12 Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
708 : parrello 1.10
709 :     would open for output appended to the specified file, and
710 :    
711 : parrello 1.12 Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
712 : parrello 1.10
713 :     would open a pipe that sorts the records written and removes duplicates. Note
714 : parrello 1.11 the use of file handle syntax in the Open call. To use anonymous file handles,
715 :     code as follows.
716 : parrello 1.10
717 : parrello 1.12 my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
718 : parrello 1.10
719 : parrello 1.11 The I<$message> parameter is used if the open fails. If it is set to C<0>, then
720 :     the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
721 :     failed open will throw an exception and the third parameter will be used to construct
722 :     an error message. If the parameter is omitted, a standard message is constructed
723 :     using the file spec.
724 : parrello 1.10
725 : parrello 1.12 Could not open "/usr/spool/news/twitlog"
726 : parrello 1.10
727 :     Note that the mode characters are automatically cleaned from the file name.
728 :     The actual error message from the file system will be captured and appended to the
729 :     message in any case.
730 :    
731 : parrello 1.12 Could not open "/usr/spool/news/twitlog": file not found.
732 : parrello 1.10
733 :     In some versions of PERL the only error message we get is a number, which
734 :     corresponds to the C++ C<errno> value.
735 :    
736 : parrello 1.12 Could not open "/usr/spool/news/twitlog": 6.
737 : parrello 1.10
738 :     =over 4
739 :    
740 :     =item fileHandle
741 :    
742 :     File handle. If this parameter is C<undef>, a file handle will be generated
743 :     and returned as the value of this method.
744 :    
745 :     =item fileSpec
746 :    
747 :     File name and mode, as per the PERL C<open> function.
748 :    
749 :     =item message (optional)
750 :    
751 :     Error message to use if the open fails. If omitted, a standard error message
752 :     will be generated. In either case, the error information from the file system
753 : parrello 1.11 is appended to the message. To specify a conditional open that does not throw
754 :     an error if it fails, use C<0>.
755 : parrello 1.10
756 :     =item RETURN
757 :    
758 : parrello 1.11 Returns the name of the file handle assigned to the file, or C<undef> if the
759 :     open failed.
760 : parrello 1.10
761 :     =back
762 :    
763 :     =cut
764 :    
765 :     sub Open {
766 : parrello 1.12 # Get the parameters.
767 :     my ($fileHandle, $fileSpec, $message) = @_;
768 :     # Attempt to open the file.
769 :     my $rv = open $fileHandle, $fileSpec;
770 :     # If the open failed, generate an error message.
771 :     if (! $rv) {
772 :     # Save the system error message.
773 :     my $sysMessage = $!;
774 :     # See if we need a default message.
775 :     if (!$message) {
776 :     # Clean any obvious mode characters and leading spaces from the
777 :     # filename.
778 :     my ($fileName) = FindNamePart($fileSpec);
779 :     $message = "Could not open \"$fileName\"";
780 :     }
781 :     # Terminate with an error using the supplied message and the
782 :     # error message from the file system.
783 :     Confess("$message: $!");
784 :     }
785 :     # Return the file handle.
786 :     return $fileHandle;
787 : parrello 1.10 }
788 :    
789 : parrello 1.11 =head3 FindNamePart
790 :    
791 :     C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>
792 :    
793 :     Extract the portion of a file specification that contains the file name.
794 :    
795 :     A file specification is the string passed to an C<open> call. It specifies the file
796 :     mode and name. In a truly complex situation, it can specify a pipe sequence. This
797 :     method assumes that the file name is whatever follows the first angle bracket
798 :     sequence. So, for example, in the following strings the file name is
799 :     C</usr/fig/myfile.txt>.
800 :    
801 :     >>/usr/fig/myfile.txt
802 :     </usr/fig/myfile.txt
803 :     | sort -u > /usr/fig/myfile.txt
804 :    
805 :     If the method cannot find a file name using its normal methods, it will return the
806 :     whole incoming string.
807 :    
808 :     =over 4
809 :    
810 :     =item fileSpec
811 :    
812 :     File specification string from which the file name is to be extracted.
813 :    
814 :     =item RETURN
815 :    
816 :     Returns a three-element list. The first element contains the file name portion of
817 :     the specified string, or the whole string if a file name cannot be found via normal
818 :     methods. The second element contains the start position of the file name portion and
819 :     the third element contains the length.
820 :    
821 :     =back
822 :    
823 :     =cut
824 :     #: Return Type $;
825 :     sub FindNamePart {
826 :     # Get the parameters.
827 :     my ($fileSpec) = @_;
828 : parrello 1.12 # Default to the whole input string.
829 :     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
830 : parrello 1.11 # Parse out the file name if we can.
831 : parrello 1.12 if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
832 :     $retVal = $2;
833 :     $len = length $retVal;
834 :     $pos = (length $fileSpec) - (length $3) - $len;
835 :     }
836 : parrello 1.11 # Return the result.
837 :     return ($retVal, $pos, $len);
838 :     }
839 :    
840 :     =head3 OpenDir
841 :    
842 : parrello 1.31 C<< my @files = OpenDir($dirName, $filtered, $flag); >>
843 : parrello 1.11
844 :     Open a directory and return all the file names. This function essentially performs
845 :     the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
846 : parrello 1.31 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
847 : parrello 1.33 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
848 :     filtered out of the return list. If the directory does not open and I<$flag> is not
849 :     set, an exception is thrown. So, for example,
850 : parrello 1.11
851 : parrello 1.12 my @files = OpenDir("/Volumes/fig/contigs", 1);
852 : parrello 1.29
853 : parrello 1.11 is effectively the same as
854 :    
855 : parrello 1.12 opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
856 : parrello 1.33 my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
857 : parrello 1.11
858 :     Similarly, the following code
859 :    
860 : parrello 1.31 my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
861 : parrello 1.29
862 : parrello 1.11 Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
863 : parrello 1.31 automatically returns an empty list if the directory fails to open.
864 : parrello 1.11
865 :     =over 4
866 :    
867 :     =item dirName
868 :    
869 :     Name of the directory to open.
870 :    
871 :     =item filtered
872 :    
873 :     TRUE if files whose names begin with a period (C<.>) should be automatically removed
874 :     from the list, else FALSE.
875 :    
876 : parrello 1.31 =item flag
877 :    
878 :     TRUE if a failure to open is okay, else FALSE
879 :    
880 : parrello 1.11 =back
881 :    
882 :     =cut
883 :     #: Return Type @;
884 :     sub OpenDir {
885 :     # Get the parameters.
886 : parrello 1.31 my ($dirName, $filtered, $flag) = @_;
887 : parrello 1.11 # Declare the return variable.
888 : parrello 1.31 my @retVal = ();
889 : parrello 1.12 # Open the directory.
890 :     if (opendir(my $dirHandle, $dirName)) {
891 :     # The directory opened successfully. Get the appropriate list according to the
892 :     # strictures of the filter parameter.
893 :     if ($filtered) {
894 : parrello 1.33 @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
895 : parrello 1.12 } else {
896 :     @retVal = readdir $dirHandle;
897 :     }
898 : parrello 1.31 } elsif (! $flag) {
899 :     # Here the directory would not open and it's considered an error.
900 : parrello 1.12 Confess("Could not open directory $dirName.");
901 :     }
902 : parrello 1.11 # Return the result.
903 :     return @retVal;
904 :     }
905 :    
906 : parrello 1.6 =head3 SetLevel
907 :    
908 :     C<< Tracer::SetLevel($newLevel); >>
909 :    
910 :     Modify the trace level. A higher trace level will cause more messages to appear.
911 :    
912 :     =over 4
913 :    
914 :     =item newLevel
915 :    
916 :     Proposed new trace level.
917 :    
918 :     =back
919 :    
920 :     =cut
921 :    
922 :     sub SetLevel {
923 :     $TraceLevel = $_[0];
924 :     }
925 :    
926 : olson 1.1 =head3 Now
927 :    
928 :     C<< my $string = Tracer::Now(); >>
929 :    
930 :     Return a displayable time stamp containing the local time.
931 :    
932 :     =cut
933 :    
934 :     sub Now {
935 : parrello 1.12 my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
936 :     my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
937 :     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
938 :     return $retVal;
939 : olson 1.1 }
940 :    
941 :     # Pad a number to 2 digits.
942 :     sub _p2 {
943 : parrello 1.12 my ($value) = @_;
944 :     $value = "0$value" if ($value < 10);
945 :     return $value;
946 : olson 1.1 }
947 :    
948 : parrello 1.74 =head3 ParseTraceDate
949 :    
950 :     C<< my $time = Tracer::ParseTraceDate($dateString); >>
951 :    
952 :     Convert a date from the trace file into a PERL timestamp.
953 :    
954 :     =over 4
955 :    
956 :     =item dateString
957 :    
958 :     The date string from the trace file. The format of the string is determined by the
959 :     L</Now> method.
960 :    
961 :     =item RETURN
962 :    
963 :     Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
964 :     the time string is invalid.
965 :    
966 : parrello 1.78 =back
967 :    
968 : parrello 1.74 =cut
969 :    
970 :     sub ParseTraceDate {
971 :     # Get the parameters.
972 :     my ($dateString) = @_;
973 :     # Declare the return variable.
974 :     my $retVal;
975 :     # Parse the date.
976 :     if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {
977 : parrello 1.76 # Create a time object. Note we need to convert the day, month,
978 :     # and year to a different base. Years count from 1900, and
979 :     # the internal month value is relocated to January = 0.
980 :     $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);
981 : parrello 1.74 }
982 :     # Return the result.
983 :     return $retVal;
984 :     }
985 :    
986 : olson 1.1 =head3 LogErrors
987 :    
988 :     C<< Tracer::LogErrors($fileName); >>
989 :    
990 :     Route the standard error output to a log file.
991 :    
992 :     =over 4
993 :    
994 :     =item fileName
995 :    
996 :     Name of the file to receive the error output.
997 :    
998 :     =back
999 :    
1000 :     =cut
1001 :    
1002 :     sub LogErrors {
1003 : parrello 1.12 # Get the file name.
1004 :     my ($fileName) = @_;
1005 :     # Open the file as the standard error output.
1006 :     open STDERR, '>', $fileName;
1007 : olson 1.1 }
1008 :    
1009 : parrello 1.5 =head3 ReadOptions
1010 :    
1011 :     C<< my %options = Tracer::ReadOptions($fileName); >>
1012 :    
1013 :     Read a set of options from a file. Each option is encoded in a line of text that has the
1014 :     format
1015 :    
1016 :     I<optionName>C<=>I<optionValue>C<; >I<comment>
1017 :    
1018 :     The option name must consist entirely of letters, digits, and the punctuation characters
1019 : parrello 1.9 C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1020 :     character is a semi-colon will be ignored. The return hash will map each option name to
1021 : parrello 1.5 the corresponding option value.
1022 :    
1023 :     =over 4
1024 :    
1025 :     =item fileName
1026 :    
1027 :     Name of the file containing the option data.
1028 :    
1029 :     =item RETURN
1030 :    
1031 :     Returns a hash mapping the option names specified in the file to their corresponding option
1032 :     value.
1033 :    
1034 :     =back
1035 :    
1036 :     =cut
1037 :    
1038 :     sub ReadOptions {
1039 : parrello 1.12 # Get the parameters.
1040 :     my ($fileName) = @_;
1041 :     # Open the file.
1042 :     (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1043 :     # Count the number of records read.
1044 :     my ($records, $comments) = 0;
1045 :     # Create the return hash.
1046 :     my %retVal = ();
1047 :     # Loop through the file, accumulating key-value pairs.
1048 :     while (my $line = <CONFIGFILE>) {
1049 :     # Denote we've read a line.
1050 :     $records++;
1051 :     # Determine the line type.
1052 :     if ($line =~ /^\s*[\n\r]/) {
1053 :     # A blank line is a comment.
1054 :     $comments++;
1055 :     } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1056 :     # Here we have an option assignment.
1057 :     retVal{$1} = $2;
1058 :     } elsif ($line =~ /^\s*;/) {
1059 :     # Here we have a text comment.
1060 :     $comments++;
1061 :     } else {
1062 :     # Here we have an invalid line.
1063 :     Trace("Invalid option statement in record $records.") if T(0);
1064 :     }
1065 :     }
1066 :     # Return the hash created.
1067 :     return %retVal;
1068 : parrello 1.5 }
1069 :    
1070 : olson 1.1 =head3 GetOptions
1071 :    
1072 :     C<< Tracer::GetOptions(\%defaults, \%options); >>
1073 :    
1074 :     Merge a specified set of options into a table of defaults. This method takes two hash references
1075 :     as input and uses the data from the second to update the first. If the second does not exist,
1076 :     there will be no effect. An error will be thrown if one of the entries in the second hash does not
1077 :     exist in the first.
1078 :    
1079 :     Consider the following example.
1080 :    
1081 :     C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>
1082 :    
1083 :     In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1084 :     B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1085 :     B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1086 :     the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1087 :     will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1088 :    
1089 :     C<< {databaseType => 'Oracle'} >>
1090 :    
1091 :     an error will occur because the B<databaseType> option does not exist.
1092 :    
1093 :     =over 4
1094 :    
1095 :     =item defaults
1096 :    
1097 :     Table of default option values.
1098 :    
1099 :     =item options
1100 :    
1101 :     Table of overrides, if any.
1102 :    
1103 :     =item RETURN
1104 :    
1105 :     Returns a reference to the default table passed in as the first parameter.
1106 :    
1107 :     =back
1108 :    
1109 :     =cut
1110 :    
1111 :     sub GetOptions {
1112 : parrello 1.12 # Get the parameters.
1113 :     my ($defaults, $options) = @_;
1114 :     # Check for overrides.
1115 :     if ($options) {
1116 :     # Loop through the overrides.
1117 :     while (my ($option, $setting) = each %{$options}) {
1118 :     # Insure this override exists.
1119 :     if (!exists $defaults->{$option}) {
1120 :     croak "Unrecognized option $option encountered.";
1121 :     } else {
1122 :     # Apply the override.
1123 :     $defaults->{$option} = $setting;
1124 :     }
1125 :     }
1126 :     }
1127 :     # Return the merged table.
1128 :     return $defaults;
1129 : olson 1.1 }
1130 :    
1131 :     =head3 MergeOptions
1132 :    
1133 :     C<< Tracer::MergeOptions(\%table, \%defaults); >>
1134 :    
1135 :     Merge default values into a hash table. This method looks at the key-value pairs in the
1136 :     second (default) hash, and if a matching key is not found in the first hash, the default
1137 :     pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1138 :     checking and no return value.
1139 :    
1140 :     =over 4
1141 :    
1142 :     =item table
1143 :    
1144 :     Hash table to be updated with the default values.
1145 :    
1146 :     =item defaults
1147 :    
1148 :     Default values to be merged into the first hash table if they are not already present.
1149 :    
1150 :     =back
1151 :    
1152 :     =cut
1153 :    
1154 :     sub MergeOptions {
1155 : parrello 1.12 # Get the parameters.
1156 :     my ($table, $defaults) = @_;
1157 :     # Loop through the defaults.
1158 :     while (my ($key, $value) = each %{$defaults}) {
1159 :     if (!exists $table->{$key}) {
1160 :     $table->{$key} = $value;
1161 :     }
1162 :     }
1163 : olson 1.1 }
1164 :    
1165 :     =head3 Trace
1166 :    
1167 :     C<< Trace($message); >>
1168 :    
1169 :     Write a trace message to the target location specified in L</TSetup>. If there has not been
1170 :     any prior call to B<TSetup>.
1171 :    
1172 :     =over 4
1173 :    
1174 :     =item message
1175 :    
1176 :     Message to write.
1177 :    
1178 :     =back
1179 :    
1180 :     =cut
1181 :    
1182 :     sub Trace {
1183 : parrello 1.12 # Get the parameters.
1184 :     my ($message) = @_;
1185 :     # Get the timestamp.
1186 :     my $timeStamp = Now();
1187 :     # Format the message. Note we strip off any line terminators at the end.
1188 : parrello 1.69 my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);
1189 : parrello 1.12 # Process according to the destination.
1190 :     if ($Destination eq "TEXT") {
1191 :     # Write the message to the standard output.
1192 :     print "$formatted\n";
1193 :     } elsif ($Destination eq "ERROR") {
1194 :     # Write the message to the error output.
1195 :     print STDERR "$formatted\n";
1196 :     } elsif ($Destination eq "QUEUE") {
1197 :     # Push the message into the queue.
1198 :     push @Queue, "$formatted";
1199 :     } elsif ($Destination eq "HTML") {
1200 :     # Convert the message to HTML and write it to the standard output.
1201 :     my $escapedMessage = CGI::escapeHTML($message);
1202 :     print "<p>$formatted</p>\n";
1203 : parrello 1.4 } elsif ($Destination eq "WARN") {
1204 :     # Emit the message as a warning.
1205 :     warn $message;
1206 : parrello 1.12 } elsif ($Destination =~ m/^>>/) {
1207 :     # Write the trace message to an output file.
1208 : parrello 1.14 (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
1209 : parrello 1.12 print TRACING "$formatted\n";
1210 :     close TRACING;
1211 :     # If the Tee flag is on, echo it to the standard output.
1212 :     if ($TeeFlag) {
1213 :     print "$formatted\n";
1214 :     }
1215 :     }
1216 : olson 1.1 }
1217 :    
1218 :     =head3 T
1219 :    
1220 : parrello 1.2 C<< my $switch = T($category, $traceLevel); >>
1221 : olson 1.1
1222 : parrello 1.12 or
1223 : parrello 1.2
1224 : olson 1.1 C<< my $switch = T($traceLevel); >>
1225 :    
1226 :     Return TRUE if the trace level is at or above a specified value and the specified category
1227 :     is active, else FALSE. If no category is specified, the caller's package name is used.
1228 :    
1229 :     =over 4
1230 :    
1231 :     =item category
1232 :    
1233 :     Category to which the message belongs. If not specified, the caller's package name is
1234 :     used.
1235 :    
1236 :     =item traceLevel
1237 :    
1238 :     Relevant tracing level.
1239 :    
1240 :     =item RETURN
1241 :    
1242 :     TRUE if a message at the specified trace level would appear in the trace, else FALSE.
1243 :    
1244 :     =back
1245 :    
1246 :     =cut
1247 :    
1248 :     sub T {
1249 : parrello 1.12 # Declare the return variable.
1250 :     my $retVal = 0;
1251 :     # Only proceed if tracing is turned on.
1252 :     if ($Destination ne "NONE") {
1253 :     # Get the parameters.
1254 :     my ($category, $traceLevel) = @_;
1255 :     if (!defined $traceLevel) {
1256 :     # Here we have no category, so we need to get the calling package.
1257 :     # The calling package is normally the first parameter. If it is
1258 :     # omitted, the first parameter will be the tracelevel. So, the
1259 :     # first thing we do is shift the so-called category into the
1260 :     # $traceLevel variable where it belongs.
1261 :     $traceLevel = $category;
1262 :     my ($package, $fileName, $line) = caller;
1263 : parrello 1.3 # If there is no calling package, we default to "main".
1264 : parrello 1.12 if (!$package) {
1265 : parrello 1.3 $category = "main";
1266 : parrello 1.12 } else {
1267 :     $category = $package;
1268 :     }
1269 :     }
1270 : parrello 1.7 # Save the category name.
1271 :     $LastCategory = $category;
1272 : parrello 1.13 # Convert it to lower case before we hash it.
1273 :     $category = lc $category;
1274 : parrello 1.12 # Use the category and tracelevel to compute the result.
1275 : parrello 1.36 if (ref $traceLevel) {
1276 :     Confess("Bad trace level.");
1277 :     } elsif (ref $TraceLevel) {
1278 :     Confess("Bad trace config.");
1279 :     }
1280 : parrello 1.12 $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
1281 : parrello 1.3 }
1282 : parrello 1.12 # Return the computed result.
1283 : parrello 1.3 return $retVal;
1284 : olson 1.1 }
1285 :    
1286 :     =head3 ParseCommand
1287 :    
1288 :     C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>
1289 :    
1290 :     Parse a command line consisting of a list of parameters. The initial parameters may be option
1291 : parrello 1.2 specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1292 :     off and merged into a table of default options. The remainder of the command line is
1293 : olson 1.1 returned as a list of positional arguments. For example, consider the following invocation.
1294 :    
1295 :     C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>
1296 :    
1297 : parrello 1.84 In this case, the list @words will be treated as a command line and there are two options available,
1298 : olson 1.1 B<errors> and B<logFile>. If @words has the following format
1299 :    
1300 :     C<< -logFile=error.log apple orange rutabaga >>
1301 :    
1302 :     then at the end of the invocation, C<$options> will be
1303 :    
1304 :     C<< { errors => 0, logFile => 'error.log' } >>
1305 :    
1306 :     and C<@arguments> will contain
1307 :    
1308 :     C<< apple orange rutabaga >>
1309 :    
1310 : parrello 1.2 The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1311 : parrello 1.84 support for quote characters. Options can be specified with single or double hyphens.
1312 : olson 1.1
1313 :     =over 4
1314 :    
1315 :     =item optionTable
1316 :    
1317 :     Table of default options.
1318 :    
1319 :     =item inputList
1320 :    
1321 :     List of words on the command line.
1322 :    
1323 :     =item RETURN
1324 :    
1325 :     Returns a reference to the option table and a list of the positional arguments.
1326 :    
1327 :     =back
1328 :    
1329 :     =cut
1330 :    
1331 :     sub ParseCommand {
1332 : parrello 1.12 # Get the parameters.
1333 :     my ($optionTable, @inputList) = @_;
1334 :     # Process any options in the input list.
1335 :     my %overrides = ();
1336 : parrello 1.84 while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1337 : parrello 1.12 # Get the current option.
1338 :     my $arg = shift @inputList;
1339 :     # Pull out the option name.
1340 : parrello 1.84 $arg =~ /^--?([^=]*)/g;
1341 : parrello 1.12 my $name = $1;
1342 :     # Check for an option value.
1343 :     if ($arg =~ /\G=(.*)$/g) {
1344 :     # Here we have a value for the option.
1345 :     $overrides{$name} = UnEscape($1);
1346 :     } else {
1347 :     # Here there is no value, so we use 1.
1348 :     $overrides{$name} = 1;
1349 :     }
1350 :     }
1351 :     # Merge the options into the defaults.
1352 :     GetOptions($optionTable, \%overrides);
1353 :     # Translate the remaining parameters.
1354 :     my @retVal = ();
1355 :     for my $inputParm (@inputList) {
1356 :     push @retVal, UnEscape($inputParm);
1357 :     }
1358 :     # Return the results.
1359 :     return ($optionTable, @retVal);
1360 : olson 1.1 }
1361 :    
1362 : parrello 1.9 =head3 Escape
1363 :    
1364 :     C<< my $codedString = Tracer::Escape($realString); >>
1365 :    
1366 : parrello 1.25 Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines
1367 : parrello 1.28 replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
1368 :     result is to reverse the effect of L</UnEscape>.
1369 : parrello 1.9
1370 :     =over 4
1371 :    
1372 :     =item realString
1373 :    
1374 :     String to escape.
1375 :    
1376 :     =item RETURN
1377 :    
1378 :     Escaped equivalent of the real string.
1379 :    
1380 :     =back
1381 :    
1382 :     =cut
1383 :    
1384 :     sub Escape {
1385 : parrello 1.12 # Get the parameter.
1386 :     my ($realString) = @_;
1387 :     # Initialize the return variable.
1388 :     my $retVal = "";
1389 :     # Loop through the parameter string, looking for sequences to escape.
1390 :     while (length $realString > 0) {
1391 :     # Look for the first sequence to escape.
1392 : parrello 1.27 if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1393 : parrello 1.12 # Here we found it. The text preceding the sequence is in $1. The sequence
1394 :     # itself is in $2. First, move the clear text to the return variable.
1395 :     $retVal .= $1;
1396 : parrello 1.14 # Strip the processed section off the real string.
1397 :     $realString = substr $realString, (length $2) + (length $1);
1398 : parrello 1.28 # Get the matched character.
1399 : parrello 1.12 my $char = $2;
1400 : parrello 1.28 # If we have a CR, we are done.
1401 :     if ($char ne "\r") {
1402 :     # It's not a CR, so encode the escape sequence.
1403 :     $char =~ tr/\t\n/tn/;
1404 :     $retVal .= "\\" . $char;
1405 :     }
1406 : parrello 1.12 } else {
1407 :     # Here there are no more escape sequences. The rest of the string is
1408 :     # transferred unmodified.
1409 :     $retVal .= $realString;
1410 :     $realString = "";
1411 :     }
1412 :     }
1413 :     # Return the result.
1414 :     return $retVal;
1415 : parrello 1.9 }
1416 :    
1417 : olson 1.1 =head3 UnEscape
1418 :    
1419 :     C<< my $realString = Tracer::UnEscape($codedString); >>
1420 :    
1421 : parrello 1.25 Replace escape sequences with their actual equivalents. C<\t> will be replaced by
1422 : parrello 1.28 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
1423 :     be deleted.
1424 : olson 1.1
1425 :     =over 4
1426 :    
1427 :     =item codedString
1428 :    
1429 :     String to un-escape.
1430 :    
1431 :     =item RETURN
1432 :    
1433 :     Returns a copy of the original string with the escape sequences converted to their actual
1434 :     values.
1435 :    
1436 :     =back
1437 :    
1438 :     =cut
1439 :    
1440 :     sub UnEscape {
1441 : parrello 1.12 # Get the parameter.
1442 :     my ($codedString) = @_;
1443 :     # Initialize the return variable.
1444 :     my $retVal = "";
1445 :     # Only proceed if the incoming string is nonempty.
1446 :     if (defined $codedString) {
1447 :     # Loop through the parameter string, looking for escape sequences. We can't do
1448 : parrello 1.25 # translating because it causes problems with the escaped slash. ("\\t" becomes
1449 :     # "\<tab>" no matter what we do.)
1450 : parrello 1.12 while (length $codedString > 0) {
1451 :     # Look for the first escape sequence.
1452 : parrello 1.27 if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
1453 : parrello 1.12 # Here we found it. The text preceding the sequence is in $1. The sequence
1454 :     # itself is in $2. First, move the clear text to the return variable.
1455 :     $retVal .= $1;
1456 :     $codedString = substr $codedString, (2 + length $1);
1457 : parrello 1.28 # Get the escape value.
1458 : parrello 1.12 my $char = $2;
1459 : parrello 1.28 # If we have a "\r", we are done.
1460 :     if ($char ne 'r') {
1461 :     # Here it's not an 'r', so we convert it.
1462 :     $char =~ tr/\\tn/\\\t\n/;
1463 :     $retVal .= $char;
1464 :     }
1465 : parrello 1.12 } else {
1466 :     # Here there are no more escape sequences. The rest of the string is
1467 :     # transferred unmodified.
1468 :     $retVal .= $codedString;
1469 :     $codedString = "";
1470 :     }
1471 :     }
1472 :     }
1473 :     # Return the result.
1474 :     return $retVal;
1475 : olson 1.1 }
1476 :    
1477 :     =head3 ParseRecord
1478 :    
1479 :     C<< my @fields = Tracer::ParseRecord($line); >>
1480 :    
1481 :     Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1482 :     and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1483 :     These will automatically be converted.
1484 :    
1485 :     =over 4
1486 :    
1487 :     =item line
1488 :    
1489 :     Line of data containing the tab-delimited fields.
1490 :    
1491 :     =item RETURN
1492 :    
1493 :     Returns a list of the fields found in the data line.
1494 :    
1495 :     =back
1496 :    
1497 :     =cut
1498 :    
1499 :     sub ParseRecord {
1500 : parrello 1.12 # Get the parameter.
1501 :     my ($line) = @_;
1502 :     # Remove the trailing new-line, if any.
1503 :     chomp $line;
1504 :     # Split the line read into pieces using the tab character.
1505 :     my @retVal = split /\t/, $line;
1506 :     # Trim and fix the escapes in each piece.
1507 :     for my $value (@retVal) {
1508 :     # Trim leading whitespace.
1509 :     $value =~ s/^\s+//;
1510 :     # Trim trailing whitespace.
1511 :     $value =~ s/\s+$//;
1512 :     # Delete the carriage returns.
1513 :     $value =~ s/\r//g;
1514 :     # Convert the escapes into their real values.
1515 :     $value =~ s/\\t/"\t"/ge;
1516 :     $value =~ s/\\n/"\n"/ge;
1517 :     }
1518 :     # Return the result.
1519 :     return @retVal;
1520 : olson 1.1 }
1521 :    
1522 :     =head3 Merge
1523 :    
1524 :     C<< my @mergedList = Tracer::Merge(@inputList); >>
1525 :    
1526 :     Sort a list of strings and remove duplicates.
1527 :    
1528 :     =over 4
1529 :    
1530 :     =item inputList
1531 :    
1532 :     List of scalars to sort and merge.
1533 :    
1534 :     =item RETURN
1535 :    
1536 :     Returns a list containing the same elements sorted in ascending order with duplicates
1537 :     removed.
1538 :    
1539 :     =back
1540 :    
1541 :     =cut
1542 :    
1543 :     sub Merge {
1544 : parrello 1.12 # Get the input list in sort order.
1545 :     my @inputList = sort @_;
1546 :     # Only proceed if the list has at least two elements.
1547 :     if (@inputList > 1) {
1548 :     # Now we want to move through the list splicing out duplicates.
1549 :     my $i = 0;
1550 :     while ($i < @inputList) {
1551 :     # Get the current entry.
1552 :     my $thisEntry = $inputList[$i];
1553 :     # Find out how many elements duplicate the current entry.
1554 :     my $j = $i + 1;
1555 :     my $dup1 = $i + 1;
1556 :     while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
1557 :     # If the number is nonzero, splice out the duplicates found.
1558 :     if ($j > $dup1) {
1559 :     splice @inputList, $dup1, $j - $dup1;
1560 :     }
1561 :     # Now the element at position $dup1 is different from the element before it
1562 :     # at position $i. We push $i forward one position and start again.
1563 :     $i++;
1564 :     }
1565 :     }
1566 :     # Return the merged list.
1567 :     return @inputList;
1568 : olson 1.1 }
1569 :    
1570 : parrello 1.54 =head3 Percent
1571 :    
1572 :     C<< my $percent = Tracer::Percent($number, $base); >>
1573 :    
1574 :     Returns the percent of the base represented by the given number. If the base
1575 :     is zero, returns zero.
1576 :    
1577 :     =over 4
1578 :    
1579 :     =item number
1580 :    
1581 :     Percent numerator.
1582 :    
1583 :     =item base
1584 :    
1585 :     Percent base.
1586 :    
1587 :     =item RETURN
1588 :    
1589 :     Returns the percentage of the base represented by the numerator.
1590 :    
1591 :     =back
1592 :    
1593 :     =cut
1594 :    
1595 :     sub Percent {
1596 :     # Get the parameters.
1597 :     my ($number, $base) = @_;
1598 :     # Declare the return variable.
1599 :     my $retVal = 0;
1600 :     # Compute the percent.
1601 :     if ($base != 0) {
1602 :     $retVal = $number * 100 / $base;
1603 :     }
1604 :     # Return the result.
1605 :     return $retVal;
1606 :     }
1607 :    
1608 : olson 1.1 =head3 GetFile
1609 :    
1610 : parrello 1.6 C<< my @fileContents = Tracer::GetFile($fileName); >>
1611 : olson 1.1
1612 : parrello 1.35 or
1613 :    
1614 :     C<< my $fileContents = Tracer::GetFile($fileName); >>
1615 :    
1616 :     Return the entire contents of a file. In list context, line-ends are removed and
1617 :     each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1618 : olson 1.1
1619 :     =over 4
1620 :    
1621 :     =item fileName
1622 :    
1623 :     Name of the file to read.
1624 :    
1625 :     =item RETURN
1626 :    
1627 : parrello 1.6 In a list context, returns the entire file as a list with the line terminators removed.
1628 : parrello 1.39 In a scalar context, returns the entire file as a string. If an error occurs opening
1629 :     the file, an empty list will be returned.
1630 : olson 1.1
1631 :     =back
1632 :    
1633 :     =cut
1634 :    
1635 :     sub GetFile {
1636 : parrello 1.12 # Get the parameters.
1637 :     my ($fileName) = @_;
1638 :     # Declare the return variable.
1639 :     my @retVal = ();
1640 :     # Open the file for input.
1641 : parrello 1.60 my $handle = Open(undef, "<$fileName");
1642 :     # Read the whole file into the return variable, stripping off any terminator
1643 :     # characters.
1644 :     my $lineCount = 0;
1645 :     while (my $line = <$handle>) {
1646 :     $lineCount++;
1647 :     $line = Strip($line);
1648 :     push @retVal, $line;
1649 :     }
1650 :     # Close it.
1651 :     close $handle;
1652 :     my $actualLines = @retVal;
1653 : parrello 1.77 Trace("$actualLines lines read from file $fileName.") if T(File => 2);
1654 : parrello 1.12 # Return the file's contents in the desired format.
1655 : parrello 1.9 if (wantarray) {
1656 : parrello 1.12 return @retVal;
1657 : parrello 1.6 } else {
1658 :     return join "\n", @retVal;
1659 :     }
1660 : olson 1.1 }
1661 :    
1662 : parrello 1.60 =head3 PutFile
1663 :    
1664 :     C<< Tracer::PutFile($fileName, \@lines); >>
1665 :    
1666 :     Write out a file from a list of lines of text.
1667 :    
1668 :     =over 4
1669 :    
1670 :     =item fileName
1671 :    
1672 :     Name of the output file.
1673 :    
1674 :     =item lines
1675 :    
1676 :     Reference to a list of text lines. The lines will be written to the file in order, with trailing
1677 : parrello 1.66 new-line characters. Alternatively, may be a string, in which case the string will be written without
1678 :     modification.
1679 : parrello 1.60
1680 :     =back
1681 :    
1682 :     =cut
1683 :    
1684 :     sub PutFile {
1685 :     # Get the parameters.
1686 :     my ($fileName, $lines) = @_;
1687 :     # Open the output file.
1688 :     my $handle = Open(undef, ">$fileName");
1689 : parrello 1.77 # Count the lines written.
1690 : parrello 1.66 if (ref $lines ne 'ARRAY') {
1691 :     # Here we have a scalar, so we write it raw.
1692 :     print $handle $lines;
1693 : parrello 1.77 Trace("Scalar put to file $fileName.") if T(File => 3);
1694 : parrello 1.66 } else {
1695 :     # Write the lines one at a time.
1696 : parrello 1.77 my $count = 0;
1697 : parrello 1.66 for my $line (@{$lines}) {
1698 :     print $handle "$line\n";
1699 : parrello 1.77 $count++;
1700 : parrello 1.66 }
1701 : parrello 1.77 Trace("$count lines put to file $fileName.") if T(File => 3);
1702 : parrello 1.60 }
1703 :     # Close the output file.
1704 :     close $handle;
1705 :     }
1706 :    
1707 : olson 1.1 =head3 QTrace
1708 :    
1709 :     C<< my $data = QTrace($format); >>
1710 :    
1711 :     Return the queued trace data in the specified format.
1712 :    
1713 :     =over 4
1714 :    
1715 :     =item format
1716 :    
1717 :     C<html> to format the data as an HTML list, C<text> to format it as straight text.
1718 :    
1719 :     =back
1720 :    
1721 :     =cut
1722 :    
1723 :     sub QTrace {
1724 : parrello 1.12 # Get the parameter.
1725 :     my ($format) = @_;
1726 :     # Create the return variable.
1727 :     my $retVal = "";
1728 : parrello 1.14 # Only proceed if there is an actual queue.
1729 :     if (@Queue) {
1730 :     # Process according to the format.
1731 :     if ($format =~ m/^HTML$/i) {
1732 :     # Convert the queue into an HTML list.
1733 :     $retVal = "<ul>\n";
1734 :     for my $line (@Queue) {
1735 :     my $escapedLine = CGI::escapeHTML($line);
1736 :     $retVal .= "<li>$escapedLine</li>\n";
1737 :     }
1738 :     $retVal .= "</ul>\n";
1739 :     } elsif ($format =~ m/^TEXT$/i) {
1740 :     # Convert the queue into a list of text lines.
1741 :     $retVal = join("\n", @Queue) . "\n";
1742 :     }
1743 :     # Clear the queue.
1744 :     @Queue = ();
1745 : parrello 1.12 }
1746 :     # Return the formatted list.
1747 :     return $retVal;
1748 : olson 1.1 }
1749 :    
1750 :     =head3 Confess
1751 :    
1752 :     C<< Confess($message); >>
1753 :    
1754 : parrello 1.22 Trace the call stack and abort the program with the specified message. When used with
1755 : parrello 1.9 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
1756 : parrello 1.6 So, for example
1757 : olson 1.1
1758 : parrello 1.6 C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
1759 : olson 1.1
1760 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
1761 :    
1762 :     =over 4
1763 :    
1764 :     =item message
1765 :    
1766 :     Message to include in the trace.
1767 :    
1768 :     =back
1769 :    
1770 :     =cut
1771 :    
1772 :     sub Confess {
1773 : parrello 1.12 # Get the parameters.
1774 :     my ($message) = @_;
1775 :     # Trace the call stack.
1776 : parrello 1.22 Cluck($message);
1777 : parrello 1.12 # Abort the program.
1778 :     croak(">>> $message");
1779 : olson 1.1 }
1780 :    
1781 : parrello 1.6 =head3 Assert
1782 :    
1783 :     C<< Assert($condition1, $condition2, ... $conditionN); >>
1784 :    
1785 :     Return TRUE if all the conditions are true. This method can be used in conjunction with
1786 : parrello 1.29 the OR operator and the L</Confess> method as a debugging assert.
1787 : parrello 1.6 So, for example
1788 :    
1789 :     C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
1790 :    
1791 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
1792 :    
1793 :     =cut
1794 :     sub Assert {
1795 :     my $retVal = 1;
1796 :     LOOP: for my $condition (@_) {
1797 :     if (! $condition) {
1798 :     $retVal = 0;
1799 :     last LOOP;
1800 :     }
1801 :     }
1802 :     return $retVal;
1803 :     }
1804 :    
1805 : olson 1.1 =head3 Cluck
1806 :    
1807 :     C<< Cluck($message); >>
1808 :    
1809 :     Trace the call stack. Note that for best results, you should qualify the call with a
1810 :     trace condition. For example,
1811 :    
1812 :     C<< Cluck("Starting record parse.") if T(3); >>
1813 :    
1814 :     will only trace the stack if the trace level for the package is 3 or more.
1815 :    
1816 :     =over 4
1817 :    
1818 :     =item message
1819 :    
1820 :     Message to include in the trace.
1821 :    
1822 :     =back
1823 :    
1824 :     =cut
1825 :    
1826 :     sub Cluck {
1827 : parrello 1.12 # Get the parameters.
1828 :     my ($message) = @_;
1829 : parrello 1.5 # Trace what's happening.
1830 :     Trace("Stack trace for event: $message");
1831 : parrello 1.12 my $confession = longmess($message);
1832 :     # Convert the confession to a series of trace messages. Note we skip any
1833 : parrello 1.5 # messages relating to calls into Tracer.
1834 : parrello 1.12 for my $line (split /\s*\n/, $confession) {
1835 :     Trace($line) if ($line !~ /Tracer\.pm/);
1836 :     }
1837 : olson 1.1 }
1838 :    
1839 : parrello 1.5 =head3 Min
1840 :    
1841 :     C<< my $min = Min($value1, $value2, ... $valueN); >>
1842 :    
1843 :     Return the minimum argument. The arguments are treated as numbers.
1844 :    
1845 :     =over 4
1846 :    
1847 :     =item $value1, $value2, ... $valueN
1848 :    
1849 :     List of numbers to compare.
1850 :    
1851 :     =item RETURN
1852 :    
1853 :     Returns the lowest number in the list.
1854 :    
1855 :     =back
1856 :    
1857 :     =cut
1858 :    
1859 :     sub Min {
1860 : parrello 1.12 # Get the parameters. Note that we prime the return value with the first parameter.
1861 :     my ($retVal, @values) = @_;
1862 :     # Loop through the remaining parameters, looking for the lowest.
1863 :     for my $value (@values) {
1864 :     if ($value < $retVal) {
1865 :     $retVal = $value;
1866 :     }
1867 :     }
1868 :     # Return the minimum found.
1869 :     return $retVal;
1870 : parrello 1.5 }
1871 :    
1872 :     =head3 Max
1873 :    
1874 :     C<< my $max = Max($value1, $value2, ... $valueN); >>
1875 :    
1876 :     Return the maximum argument. The arguments are treated as numbers.
1877 :    
1878 :     =over 4
1879 :    
1880 :     =item $value1, $value2, ... $valueN
1881 :    
1882 :     List of numbers to compare.
1883 :    
1884 :     =item RETURN
1885 :    
1886 :     Returns the highest number in the list.
1887 :    
1888 :     =back
1889 :    
1890 :     =cut
1891 :    
1892 :     sub Max {
1893 : parrello 1.12 # Get the parameters. Note that we prime the return value with the first parameter.
1894 :     my ($retVal, @values) = @_;
1895 :     # Loop through the remaining parameters, looking for the highest.
1896 :     for my $value (@values) {
1897 :     if ($value > $retVal) {
1898 :     $retVal = $value;
1899 :     }
1900 :     }
1901 :     # Return the maximum found.
1902 :     return $retVal;
1903 : parrello 1.5 }
1904 :    
1905 :     =head3 AddToListMap
1906 :    
1907 : parrello 1.53 C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>
1908 : parrello 1.5
1909 :     Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list
1910 :     is created for the key. Otherwise, the new value is pushed onto the list.
1911 :    
1912 :     =over 4
1913 :    
1914 :     =item hash
1915 :    
1916 :     Reference to the target hash.
1917 :    
1918 :     =item key
1919 :    
1920 :     Key for which the value is to be added.
1921 :    
1922 : parrello 1.53 =item value1, value2, ... valueN
1923 : parrello 1.5
1924 : parrello 1.53 List of values to add to the key's value list.
1925 : parrello 1.5
1926 :     =back
1927 :    
1928 :     =cut
1929 :    
1930 :     sub AddToListMap {
1931 :     # Get the parameters.
1932 : parrello 1.53 my ($hash, $key, @values) = @_;
1933 : parrello 1.5 # Process according to whether or not the key already has a value.
1934 :     if (! exists $hash->{$key}) {
1935 : parrello 1.53 $hash->{$key} = [@values];
1936 : parrello 1.5 } else {
1937 : parrello 1.53 push @{$hash->{$key}}, @values;
1938 : parrello 1.5 }
1939 :     }
1940 : olson 1.1
1941 : parrello 1.7 =head3 DebugMode
1942 :    
1943 :     C<< if (Tracer::DebugMode) { ...code... } >>
1944 :    
1945 : parrello 1.69 Return TRUE if debug mode has been turned on, else abort.
1946 : parrello 1.7
1947 :     Certain CGI scripts are too dangerous to exist in the production
1948 :     environment. This method provides a simple way to prevent them
1949 : parrello 1.21 from working unless they are explicitly turned on by creating a password
1950 :     cookie via the B<SetPassword> script. If debugging mode
1951 : parrello 1.69 is not turned on, an error will occur.
1952 : parrello 1.7
1953 :     =cut
1954 :    
1955 :     sub DebugMode {
1956 : parrello 1.12 # Declare the return variable.
1957 : parrello 1.21 my $retVal = 0;
1958 : parrello 1.12 # Check the debug configuration.
1959 : parrello 1.21 my $password = CGI::cookie("DebugMode");
1960 :     my $encrypted = Digest::MD5::md5_hex($password);
1961 :     if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1962 : parrello 1.12 $retVal = 1;
1963 :     } else {
1964 : parrello 1.69 # Here debug mode is off, so we generate an error.
1965 :     Confess("Cannot use this facility without logging in.");
1966 : parrello 1.12 }
1967 :     # Return the determination indicator.
1968 : parrello 1.18 return $retVal;
1969 : parrello 1.9 }
1970 :    
1971 :     =head3 Strip
1972 :    
1973 :     C<< my $string = Tracer::Strip($line); >>
1974 :    
1975 :     Strip all line terminators off a string. This is necessary when dealing with files
1976 :     that may have been transferred back and forth several times among different
1977 :     operating environments.
1978 :    
1979 :     =over 4
1980 :    
1981 :     =item line
1982 :    
1983 :     Line of text to be stripped.
1984 :    
1985 :     =item RETURN
1986 :    
1987 :     The same line of text with all the line-ending characters chopped from the end.
1988 :    
1989 :     =back
1990 :    
1991 :     =cut
1992 :    
1993 :     sub Strip {
1994 : parrello 1.12 # Get a copy of the parameter string.
1995 :     my ($string) = @_;
1996 : parrello 1.29 my $retVal = (defined $string ? $string : "");
1997 : parrello 1.9 # Strip the line terminator characters.
1998 :     $retVal =~ s/(\r|\n)+$//g;
1999 : parrello 1.12 # Return the result.
2000 :     return $retVal;
2001 : parrello 1.9 }
2002 :    
2003 :     =head3 Pad
2004 :    
2005 :     C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>
2006 :    
2007 :     Pad a string to a specified length. The pad character will be a
2008 :     space, and the padding will be on the right side unless specified
2009 :     in the third parameter.
2010 :    
2011 :     =over 4
2012 :    
2013 :     =item string
2014 :    
2015 :     String to be padded.
2016 :    
2017 :     =item len
2018 :    
2019 :     Desired length of the padded string.
2020 :    
2021 :     =item left (optional)
2022 :    
2023 :     TRUE if the string is to be left-padded; otherwise it will be padded on the right.
2024 :    
2025 :     =item padChar (optional)
2026 :    
2027 : parrello 1.22 Character to use for padding. The default is a space.
2028 :    
2029 : parrello 1.9 =item RETURN
2030 :    
2031 : parrello 1.22 Returns a copy of the original string with the pad character added to the
2032 :     specified end so that it achieves the desired length.
2033 : parrello 1.9
2034 :     =back
2035 :    
2036 :     =cut
2037 :    
2038 :     sub Pad {
2039 : parrello 1.12 # Get the parameters.
2040 :     my ($string, $len, $left, $padChar) = @_;
2041 :     # Compute the padding character.
2042 :     if (! defined $padChar) {
2043 :     $padChar = " ";
2044 :     }
2045 :     # Compute the number of spaces needed.
2046 :     my $needed = $len - length $string;
2047 :     # Copy the string into the return variable.
2048 :     my $retVal = $string;
2049 :     # Only proceed if padding is needed.
2050 :     if ($needed > 0) {
2051 :     # Create the pad string.
2052 :     my $pad = $padChar x $needed;
2053 :     # Affix it to the return value.
2054 :     if ($left) {
2055 :     $retVal = $pad . $retVal;
2056 :     } else {
2057 :     $retVal .= $pad;
2058 :     }
2059 :     }
2060 :     # Return the result.
2061 :     return $retVal;
2062 : parrello 1.7 }
2063 :    
2064 : parrello 1.29 =head3 EOF
2065 :    
2066 :     This is a constant that is lexically greater than any useful string.
2067 :    
2068 :     =cut
2069 :    
2070 :     sub EOF {
2071 :     return "\xFF\xFF\xFF\xFF\xFF";
2072 :     }
2073 :    
2074 : parrello 1.15 =head3 TICK
2075 :    
2076 :     C<< my @results = TICK($commandString); >>
2077 :    
2078 :     Perform a back-tick operation on a command. If this is a Windows environment, any leading
2079 :     dot-slash (C<./> will be removed. So, for example, if you were doing
2080 :    
2081 :     `./protein.cgi`
2082 :    
2083 :     from inside a CGI script, it would work fine in Unix, but would issue an error message
2084 :     in Windows complaining that C<'.'> is not a valid command. If instead you code
2085 :    
2086 :     TICK("./protein.cgi")
2087 :    
2088 :     it will work correctly in both environments.
2089 :    
2090 :     =over 4
2091 :    
2092 :     =item commandString
2093 :    
2094 :     The command string to pass to the system.
2095 :    
2096 :     =item RETURN
2097 :    
2098 :     Returns the standard output from the specified command, as a list.
2099 :    
2100 :     =back
2101 :    
2102 :     =cut
2103 :     #: Return Type @;
2104 :     sub TICK {
2105 :     # Get the parameters.
2106 :     my ($commandString) = @_;
2107 :     # Chop off the dot-slash if this is Windows.
2108 :     if ($FIG_Config::win_mode) {
2109 :     $commandString =~ s!^\./!!;
2110 :     }
2111 :     # Activate the command and return the result.
2112 :     return `$commandString`;
2113 :     }
2114 :    
2115 : parrello 1.35 =head3 ScriptSetup
2116 :    
2117 : parrello 1.69 C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>
2118 : parrello 1.35
2119 :     Perform standard tracing and debugging setup for scripts. The value returned is
2120 : parrello 1.81 the CGI object followed by a pre-built variable hash. At the end of the script,
2121 :     the client should call L</ScriptFinish> to output the web page.
2122 : parrello 1.35
2123 : parrello 1.81 This method calls L</ETracing> to configure tracing, which allows the tracing
2124 :     to be configured via the emergency tracing form on the debugging control panel.
2125 : parrello 1.72 Tracing will then be turned on automatically for all programs that use the L</ETracing>
2126 :     method, which includes every program that uses this method or L</StandardSetup>.
2127 : parrello 1.69
2128 :     =over 4
2129 :    
2130 :     =item noTrace (optional)
2131 :    
2132 :     If specified, tracing will be suppressed. This is useful if the script wants to set up
2133 :     tracing manually.
2134 :    
2135 :     =item RETURN
2136 :    
2137 :     Returns a two-element list consisting of a CGI query object and a variable hash for
2138 :     the output page.
2139 :    
2140 :     =back
2141 : parrello 1.35
2142 :     =cut
2143 :    
2144 :     sub ScriptSetup {
2145 : parrello 1.69 # Get the parameters.
2146 :     my ($noTrace) = @_;
2147 : parrello 1.35 # Get the CGI query object.
2148 : parrello 1.69 my $cgi = CGI->new();
2149 :     # Set up tracing if it's not suppressed.
2150 : parrello 1.72 ETracing($cgi) unless $noTrace;
2151 : parrello 1.69 # Create the variable hash.
2152 :     my $varHash = { results => '' };
2153 :     # Return the query object and variable hash.
2154 :     return ($cgi, $varHash);
2155 :     }
2156 :    
2157 : parrello 1.72 =head3 ETracing
2158 : parrello 1.69
2159 : parrello 1.72 C<< ETracing($parameter); >>
2160 : parrello 1.69
2161 : parrello 1.72 Set up emergency tracing. Emergency tracing is tracing that is turned
2162 :     on automatically for any program that calls this method. The emergency
2163 :     tracing parameters are stored in a a file identified by a tracing key.
2164 :     If this method is called with a CGI object, then the tracing key is
2165 :     taken from a cookie. If it is called with no parameters, then the tracing
2166 :     key is taken from an environment variable. If it is called with a string,
2167 :     the tracing key is that string.
2168 : parrello 1.69
2169 :     =over 4
2170 :    
2171 : parrello 1.72 =item parameter
2172 : parrello 1.69
2173 : parrello 1.72 A parameter from which the tracing key is computed. If it is a scalar,
2174 :     that scalar is used as the tracing key. If it is a CGI object, the
2175 :     tracing key is taken from the C<IP> cookie. If it is omitted, the
2176 :     tracing key is taken from the C<TRACING> environment variable. If it
2177 :     is a CGI object and emergency tracing is not on, the C<Trace> and
2178 :     C<TF> parameters will be used to determine the type of tracing.
2179 : parrello 1.69
2180 :     =back
2181 :    
2182 :     =cut
2183 :    
2184 : parrello 1.72 sub ETracing {
2185 :     # Get the parameter.
2186 :     my ($parameter) = @_;
2187 :     # Check for CGI mode.
2188 :     my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
2189 : parrello 1.69 # Default to no tracing except errors.
2190 :     my ($tracing, $dest) = ("0", "WARN");
2191 :     # Check for emergency tracing.
2192 : parrello 1.72 my $tkey = EmergencyKey($parameter);
2193 :     my $emergencyFile = EmergencyFileName($tkey);
2194 : parrello 1.69 if (-e $emergencyFile) {
2195 :     # We have the file. Read in the data.
2196 :     my @tracing = GetFile($emergencyFile);
2197 :     # Pull off the time limit.
2198 :     my $expire = shift @tracing;
2199 :     # Convert it to seconds.
2200 :     $expire *= 3600;
2201 :     # Check the file data.
2202 :     my $stat = stat($emergencyFile);
2203 :     my ($now) = gettimeofday;
2204 :     if ($now - $stat->mtime > $expire) {
2205 :     # Delete the expired file.
2206 :     unlink $emergencyFile;
2207 :     } else {
2208 :     # Emergency tracing is on. Pull off the destination and
2209 :     # the trace level;
2210 :     $dest = shift @tracing;
2211 :     my $level = shift @tracing;
2212 :     # Convert the destination to a real tracing destination.
2213 :     # temp directory.
2214 : parrello 1.72 $dest = EmergencyTracingDest($tkey, $dest);
2215 : parrello 1.69 # Insure Tracer is specified.
2216 :     my %moduleHash = map { $_ => 1 } @tracing;
2217 :     $moduleHash{Tracer} = 1;
2218 :     # Set the trace parameter.
2219 :     $tracing = join(" ", $level, sort keys %moduleHash);
2220 : parrello 1.72 }
2221 :     } elsif (defined $cgi) {
2222 :     # There's no emergency tracing, but we have a CGI object, so check
2223 :     # for tracing from the form parameters.
2224 :     if ($cgi->param('Trace')) {
2225 :     # Here the user has requested tracing via a form.
2226 :     $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
2227 :     $tracing = $cgi->param('Trace') . " Tracer";
2228 :     }
2229 :     }
2230 : parrello 1.69 # Setup the tracing we've determined from all the stuff above.
2231 :     TSetup($tracing, $dest);
2232 : parrello 1.72 # If we're a web script, trace the parameter and environment data.
2233 :     if (defined $cgi) {
2234 :     TraceParms($cgi);
2235 :     }
2236 : parrello 1.69 }
2237 :    
2238 :     =head3 EmergencyFileName
2239 :    
2240 : parrello 1.72 C<< my $fileName = Tracer::EmergencyFileName($tkey); >>
2241 : parrello 1.69
2242 :     Return the emergency tracing file name. This is the file that specifies
2243 :     the tracing information.
2244 :    
2245 :     =over 4
2246 :    
2247 : parrello 1.72 =item tkey
2248 : parrello 1.69
2249 : parrello 1.72 Tracing key for the current program.
2250 : parrello 1.69
2251 :     =item RETURN
2252 :    
2253 :     Returns the name of the file to contain the emergency tracing information.
2254 :    
2255 :     =back
2256 :    
2257 :     =cut
2258 :    
2259 :     sub EmergencyFileName {
2260 :     # Get the parameters.
2261 : parrello 1.72 my ($tkey) = @_;
2262 : parrello 1.69 # Compute the emergency tracing file name.
2263 : parrello 1.72 return "$FIG_Config::temp/Emergency$tkey.txt";
2264 : parrello 1.69 }
2265 :    
2266 :     =head3 EmergencyFileTarget
2267 :    
2268 : parrello 1.72 C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>
2269 : parrello 1.69
2270 :     Return the emergency tracing target file name. This is the file that receives
2271 :     the tracing output for file-based tracing.
2272 :    
2273 :     =over 4
2274 :    
2275 : parrello 1.72 =item tkey
2276 : parrello 1.69
2277 : parrello 1.72 Tracing key for the current program.
2278 : parrello 1.69
2279 :     =item RETURN
2280 :    
2281 : parrello 1.72 Returns the name of the file to contain the trace output.
2282 : parrello 1.69
2283 :     =back
2284 :    
2285 :     =cut
2286 :    
2287 :     sub EmergencyFileTarget {
2288 :     # Get the parameters.
2289 : parrello 1.72 my ($tkey) = @_;
2290 : parrello 1.69 # Compute the emergency tracing file name.
2291 : parrello 1.72 return "$FIG_Config::temp/trace$tkey.log";
2292 : parrello 1.69 }
2293 :    
2294 :     =head3 EmergencyTracingDest
2295 :    
2296 : parrello 1.72 C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>
2297 : parrello 1.69
2298 :     This method converts an emergency tracing destination to a real
2299 :     tracing destination. The main difference is that if the
2300 :     destination is C<FILE> or C<APPEND>, we convert it to file
2301 : parrello 1.84 output. If the destination is C<DUAL>, we convert it to file
2302 :     and standard output.
2303 : parrello 1.69
2304 :     =over 4
2305 :    
2306 : parrello 1.72 =item tkey
2307 : parrello 1.69
2308 : parrello 1.72 Tracing key for this environment.
2309 : parrello 1.69
2310 :     =item myDest
2311 :    
2312 :     Destination from the emergency tracing file.
2313 :    
2314 :     =item RETURN
2315 :    
2316 :     Returns a destination that can be passed into L</TSetup>.
2317 :    
2318 :     =back
2319 :    
2320 :     =cut
2321 :    
2322 :     sub EmergencyTracingDest {
2323 :     # Get the parameters.
2324 : parrello 1.72 my ($tkey, $myDest) = @_;
2325 : parrello 1.69 # Declare the return variable.
2326 :     my $retVal;
2327 :     # Process according to the destination value.
2328 :     if ($myDest eq 'FILE') {
2329 : parrello 1.72 $retVal = ">" . EmergencyFileTarget($tkey);
2330 : parrello 1.69 } elsif ($myDest eq 'APPEND') {
2331 : parrello 1.72 $retVal = ">>" . EmergencyFileTarget($tkey);
2332 : parrello 1.84 } elsif ($myDest eq 'DUAL') {
2333 :     $retVal = "+>" . EmergencyFileTarget($tkey);
2334 : parrello 1.35 }
2335 : parrello 1.69 # Return the result.
2336 :     return $retVal;
2337 :     }
2338 :    
2339 :     =head3 Emergency
2340 :    
2341 : parrello 1.72 C<< Emergency($key, $hours, $dest, $level, @modules); >>
2342 : parrello 1.69
2343 : parrello 1.84 Turn on emergency tracing. This method is normally invoked over the web from
2344 :     a debugging console, but it can also be called by the C<trace.pl> script.
2345 :     The caller specifies the duration of the emergency in hours, the desired tracing
2346 :     destination, the trace level, and a list of the trace modules to activate.
2347 :     For the length of the duration, when a program in an environment with the
2348 :     specified tracing key active invokes a Sprout CGI script, tracing will be
2349 :     turned on automatically. See L</TSetup> for more about tracing setup and
2350 :     L</ETracing> for more about emergency tracing.
2351 : parrello 1.69
2352 :     =over 4
2353 :    
2354 : parrello 1.72 =item tkey
2355 : parrello 1.69
2356 : parrello 1.72 The tracing key. This is used to identify the control file and the trace file.
2357 : parrello 1.69
2358 :     =item hours
2359 :    
2360 :     Number of hours to keep emergency tracing alive.
2361 :    
2362 :     =item dest
2363 :    
2364 :     Tracing destination. If no path information is specified for a file
2365 :     destination, it is put in the FIG temporary directory.
2366 :    
2367 :     =item level
2368 :    
2369 :     Tracing level. A higher level means more trace messages.
2370 :    
2371 :     =item modules
2372 :    
2373 :     A list of the tracing modules to activate.
2374 :    
2375 :     =back
2376 :    
2377 :     =cut
2378 :    
2379 :     sub Emergency {
2380 :     # Get the parameters.
2381 : parrello 1.72 my ($tkey, $hours, $dest, $level, @modules) = @_;
2382 : parrello 1.69 # Create the emergency file.
2383 : parrello 1.72 my $specFile = EmergencyFileName($tkey);
2384 : parrello 1.69 my $outHandle = Open(undef, ">$specFile");
2385 : parrello 1.71 print $outHandle join("\n", $hours, $dest, $level, @modules, "");
2386 : parrello 1.69 }
2387 :    
2388 : parrello 1.72 =head3 EmergencyKey
2389 : parrello 1.69
2390 : parrello 1.72 C<< my $tkey = EmergencyKey($parameter); >>
2391 : parrello 1.69
2392 : parrello 1.72 Return the Key to be used for emergency tracing. This could be an IP address,
2393 :     a session ID, or a user name, depending on the environment.
2394 : parrello 1.69
2395 :     =over 4
2396 :    
2397 : parrello 1.72 =item parameter
2398 : parrello 1.69
2399 : parrello 1.72 Parameter defining the method for finding the tracing key. If it is a scalar,
2400 :     then it is presumed to be the tracing key itself. If it is a CGI object, then
2401 :     the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
2402 :     taken from the C<TRACING> environment variable.
2403 : parrello 1.69
2404 :     =item RETURN
2405 :    
2406 : parrello 1.72 Returns the key to be used for labels in emergency tracing.
2407 : parrello 1.69
2408 :     =back
2409 :    
2410 :     =cut
2411 :    
2412 : parrello 1.72 sub EmergencyKey {
2413 : parrello 1.69 # Get the parameters.
2414 : parrello 1.72 my ($parameter) = @_;
2415 :     # Declare the return variable.
2416 :     my $retVal;
2417 :     # Determine the parameter type.
2418 :     if (! defined $parameter) {
2419 :     # Here we're supposed to check the environment.
2420 :     $retVal = $ENV{TRACING};
2421 :     } else {
2422 :     my $ptype = ref $parameter;
2423 :     if ($ptype eq 'CGI') {
2424 :     # Here we were invoked from a web page. Look for a cookie.
2425 :     $retVal = $parameter->cookie('IP');
2426 :     } elsif (! $ptype) {
2427 :     # Here the key was passed in.
2428 :     $retVal = $parameter;
2429 :     }
2430 :     }
2431 :     # If no luck finding a key, use the PID.
2432 :     if (! defined $retVal) {
2433 :     $retVal = $$;
2434 :     }
2435 : parrello 1.69 # Return the result.
2436 : parrello 1.70 return $retVal;
2437 : parrello 1.35 }
2438 :    
2439 : parrello 1.69
2440 : parrello 1.65 =head3 TraceParms
2441 :    
2442 : parrello 1.69 C<< Tracer::TraceParms($cgi); >>
2443 : parrello 1.65
2444 :     Trace the CGI parameters at trace level CGI => 3 and the environment variables
2445 :     at level CGI => 4.
2446 :    
2447 :     =over 4
2448 :    
2449 : parrello 1.69 =item cgi
2450 : parrello 1.65
2451 :     CGI query object containing the parameters to trace.
2452 :    
2453 :     =back
2454 :    
2455 :     =cut
2456 :    
2457 :     sub TraceParms {
2458 :     # Get the parameters.
2459 : parrello 1.69 my ($cgi) = @_;
2460 : parrello 1.65 if (T(CGI => 3)) {
2461 :     # Here we want to trace the parameter data.
2462 : parrello 1.69 my @names = $cgi->param;
2463 : parrello 1.65 for my $parmName (sort @names) {
2464 : parrello 1.68 # Note we skip the Trace parameters, which are for our use only.
2465 :     if ($parmName ne 'Trace' && $parmName ne 'TF') {
2466 : parrello 1.69 my @values = $cgi->param($parmName);
2467 : parrello 1.65 Trace("CGI: $parmName = " . join(", ", @values));
2468 :     }
2469 :     }
2470 : parrello 1.67 # Display the request method.
2471 : parrello 1.69 my $method = $cgi->request_method();
2472 : parrello 1.67 Trace("Method: $method");
2473 : parrello 1.65 }
2474 :     if (T(CGI => 4)) {
2475 :     # Here we want the environment data too.
2476 :     for my $envName (sort keys %ENV) {
2477 :     Trace("ENV: $envName = $ENV{$envName}");
2478 :     }
2479 :     }
2480 :     }
2481 :    
2482 : parrello 1.35 =head3 ScriptFinish
2483 :    
2484 :     C<< ScriptFinish($webData, $varHash); >>
2485 :    
2486 :     Output a web page at the end of a script. Either the string to be output or the
2487 :     name of a template file can be specified. If the second parameter is omitted,
2488 :     it is assumed we have a string to be output; otherwise, it is assumed we have the
2489 :     name of a template file. The template should have the variable C<DebugData>
2490 :     specified in any form that invokes a standard script. If debugging mode is turned
2491 :     on, a form field will be put in that allows the user to enter tracing data.
2492 :     Trace messages will be placed immediately before the terminal C<BODY> tag in
2493 :     the output, formatted as a list.
2494 :    
2495 :     A typical standard script would loook like the following.
2496 :    
2497 :     BEGIN {
2498 :     # Print the HTML header.
2499 :     print "CONTENT-TYPE: text/html\n\n";
2500 :     }
2501 :     use Tracer;
2502 :     use CGI;
2503 :     use FIG;
2504 :     # ... more uses ...
2505 : parrello 1.61
2506 : parrello 1.69 my ($cgi, $varHash) = ScriptSetup();
2507 : parrello 1.35 eval {
2508 : parrello 1.69 # ... get data from $cgi, put it in $varHash ...
2509 : parrello 1.35 };
2510 :     if ($@) {
2511 :     Trace("Script Error: $@") if T(0);
2512 :     }
2513 :     ScriptFinish("Html/MyTemplate.html", $varHash);
2514 :    
2515 :     The idea here is that even if the script fails, you'll see trace messages and
2516 :     useful output.
2517 :    
2518 :     =over 4
2519 :    
2520 :     =item webData
2521 :    
2522 :     A string containing either the full web page to be written to the output or the
2523 :     name of a template file from which the page is to be constructed. If the name
2524 :     of a template file is specified, then the second parameter must be present;
2525 :     otherwise, it must be absent.
2526 :    
2527 :     =item varHash (optional)
2528 :    
2529 :     If specified, then a reference to a hash mapping variable names for a template
2530 :     to their values. The template file will be read into memory, and variable markers
2531 :     will be replaced by data in this hash reference.
2532 :    
2533 : parrello 1.37 =back
2534 :    
2535 : parrello 1.35 =cut
2536 :    
2537 :     sub ScriptFinish {
2538 :     # Get the parameters.
2539 :     my ($webData, $varHash) = @_;
2540 :     # Check for a template file situation.
2541 :     my $outputString;
2542 :     if (defined $varHash) {
2543 : parrello 1.64 # Here we have a template file. We need to determine the template type.
2544 :     my $template;
2545 :     if ($FIG_Config::template_url && $webData =~ /\.php$/) {
2546 :     $template = "$FIG_Config::template_url/$webData";
2547 :     } else {
2548 :     $template = "<<$webData";
2549 :     }
2550 :     $outputString = PageBuilder::Build($template, $varHash, "Html");
2551 : parrello 1.35 } else {
2552 :     # Here the user gave us a raw string.
2553 :     $outputString = $webData;
2554 :     }
2555 :     # Check for trace messages.
2556 : parrello 1.68 if ($Destination ne "NONE" && $TraceLevel > 0) {
2557 : parrello 1.35 # We have trace messages, so we want to put them at the end of the body. This
2558 :     # is either at the end of the whole string or at the beginning of the BODY
2559 :     # end-tag.
2560 :     my $pos = length $outputString;
2561 :     if ($outputString =~ m#</body>#gi) {
2562 :     $pos = (pos $outputString) - 7;
2563 :     }
2564 : parrello 1.68 # If the trace messages were queued, we unroll them. Otherwise, we display the
2565 :     # destination.
2566 :     my $traceHtml;
2567 :     if ($Destination eq "QUEUE") {
2568 :     $traceHtml = QTrace('Html');
2569 :     } elsif ($Destination =~ /^>>(.+)$/) {
2570 :     # Here the tracing output it to a file. We code it as a hyperlink so the user
2571 :     # can copy the file name into the clipboard easily.
2572 :     my $actualDest = $1;
2573 : parrello 1.73 $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
2574 : parrello 1.68 } else {
2575 :     # Here we have one of the special destinations.
2576 :     $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
2577 :     }
2578 :     substr $outputString, $pos, 0, $traceHtml;
2579 : parrello 1.35 }
2580 :     # Write the output string.
2581 :     print $outputString;
2582 :     }
2583 :    
2584 : parrello 1.37 =head3 Insure
2585 :    
2586 :     C<< Insure($dirName); >>
2587 :    
2588 :     Insure a directory is present.
2589 :    
2590 :     =over 4
2591 :    
2592 :     =item dirName
2593 :    
2594 :     Name of the directory to check. If it does not exist, it will be created.
2595 :    
2596 :     =back
2597 :    
2598 :     =cut
2599 :    
2600 :     sub Insure {
2601 :     my ($dirName) = @_;
2602 :     if (! -d $dirName) {
2603 : parrello 1.77 Trace("Creating $dirName directory.") if T(File => 2);
2604 : parrello 1.43 eval { mkpath $dirName; };
2605 :     if ($@) {
2606 :     Confess("Error creating $dirName: $@");
2607 :     }
2608 :     }
2609 :     }
2610 :    
2611 :     =head3 ChDir
2612 :    
2613 :     C<< ChDir($dirName); >>
2614 :    
2615 :     Change to the specified directory.
2616 :    
2617 :     =over 4
2618 :    
2619 :     =item dirName
2620 :    
2621 :     Name of the directory to which we want to change.
2622 :    
2623 :     =back
2624 :    
2625 :     =cut
2626 :    
2627 :     sub ChDir {
2628 :     my ($dirName) = @_;
2629 :     if (! -d $dirName) {
2630 :     Confess("Cannot change to directory $dirName: no such directory.");
2631 :     } else {
2632 : parrello 1.77 Trace("Changing to directory $dirName.") if T(File => 4);
2633 : parrello 1.43 my $okFlag = chdir $dirName;
2634 :     if (! $okFlag) {
2635 :     Confess("Error switching to directory $dirName.");
2636 :     }
2637 : parrello 1.37 }
2638 :     }
2639 :    
2640 : parrello 1.59 =head3 SendSMS
2641 :    
2642 :     C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>
2643 :    
2644 :     Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
2645 :     user name, password, and API ID for the relevant account in the hash reference variable
2646 :     I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
2647 :     example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
2648 :     is C<2561022>, then the FIG_Config file must contain
2649 :    
2650 :     $phone = { user => 'BruceTheHumanPet',
2651 :     password => 'silly',
2652 :     api_id => '2561022' };
2653 :    
2654 :     The original purpose of this method was to insure Bruce would be notified immediately when the
2655 :     Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
2656 :     when you call this method.
2657 :    
2658 :     The message ID will be returned if successful, and C<undef> if an error occurs.
2659 :    
2660 :     =over 4
2661 :    
2662 :     =item phoneNumber
2663 :    
2664 :     Phone number to receive the message, in international format. A United States phone number
2665 :     would be prefixed by "1". A British phone number would be prefixed by "44".
2666 :    
2667 :     =item msg
2668 :    
2669 :     Message to send to the specified phone.
2670 :    
2671 :     =item RETURN
2672 :    
2673 :     Returns the message ID if successful, and C<undef> if the message could not be sent.
2674 :    
2675 :     =back
2676 :    
2677 :     =cut
2678 :    
2679 :     sub SendSMS {
2680 :     # Get the parameters.
2681 :     my ($phoneNumber, $msg) = @_;
2682 :     # Declare the return variable. If we do not change it, C<undef> will be returned.
2683 :     my $retVal;
2684 :     # Only proceed if we have phone support.
2685 :     if (! defined $FIG_Config::phone) {
2686 :     Trace("Phone support not present in FIG_Config.") if T(1);
2687 :     } else {
2688 :     # Get the phone data.
2689 :     my $parms = $FIG_Config::phone;
2690 :     # Get the Clickatell URL.
2691 :     my $url = "http://api.clickatell.com/http/";
2692 :     # Create the user agent.
2693 :     my $ua = LWP::UserAgent->new;
2694 :     # Request a Clickatell session.
2695 :     my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
2696 :     password => $parms->{password},
2697 :     api_id => $parms->{api_id},
2698 :     to => $phoneNumber,
2699 :     text => $msg});
2700 :     # Check for an error.
2701 :     if (! $resp->is_success) {
2702 :     Trace("Alert failed.") if T(1);
2703 :     } else {
2704 :     # Get the message ID.
2705 :     my $rstring = $resp->content;
2706 :     if ($rstring =~ /^ID:\s+(.*)$/) {
2707 :     $retVal = $1;
2708 :     } else {
2709 :     Trace("Phone attempt failed with $rstring") if T(1);
2710 :     }
2711 :     }
2712 :     }
2713 :     # Return the result.
2714 :     return $retVal;
2715 :     }
2716 :    
2717 : parrello 1.55 =head3 CommaFormat
2718 :    
2719 :     C<< my $formatted = Tracer::CommaFormat($number); >>
2720 :    
2721 :     Insert commas into a number.
2722 :    
2723 :     =over 4
2724 :    
2725 :     =item number
2726 :    
2727 :     A sequence of digits.
2728 :    
2729 :     =item RETURN
2730 :    
2731 :     Returns the same digits with commas strategically inserted.
2732 :    
2733 :     =back
2734 :    
2735 :     =cut
2736 :    
2737 :     sub CommaFormat {
2738 :     # Get the parameters.
2739 :     my ($number) = @_;
2740 :     # Pad the length up to a multiple of three.
2741 :     my $padded = "$number";
2742 :     $padded = " " . $padded while length($padded) % 3 != 0;
2743 :     # This is a fancy PERL trick. The parentheses in the SPLIT pattern
2744 :     # cause the delimiters to be included in the output stream. The
2745 :     # GREP removes the empty strings in between the delimiters.
2746 :     my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
2747 :     # Clean out the spaces.
2748 :     $retVal =~ s/ //g;
2749 :     # Return the result.
2750 :     return $retVal;
2751 :     }
2752 : parrello 1.46 =head3 SetPermissions
2753 :    
2754 : parrello 1.49 C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>
2755 : parrello 1.46
2756 :     Set the permissions for a directory and all the files and folders inside it.
2757 :     In addition, the group ownership will be changed to the specified value.
2758 :    
2759 :     This method is more vulnerable than most to permission and compatability
2760 :     problems, so it does internal error recovery.
2761 :    
2762 :     =over 4
2763 :    
2764 :     =item dirName
2765 :    
2766 :     Name of the directory to process.
2767 :    
2768 :     =item group
2769 :    
2770 :     Name of the group to be assigned.
2771 :    
2772 :     =item mask
2773 :    
2774 :     Permission mask. Bits that are C<1> in this mask will be ORed into the
2775 :     permission bits of any file or directory that does not already have them
2776 :     set to 1.
2777 :    
2778 : parrello 1.49 =item otherMasks
2779 :    
2780 :     Map of search patterns to permission masks. If a directory name matches
2781 :     one of the patterns, that directory and all its members and subdirectories
2782 :     will be assigned the new pattern. For example, the following would
2783 :     assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2784 :    
2785 :     Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2786 :    
2787 :     The list is ordered, so the following would use 0777 for C<tmp1> and
2788 :     0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2789 :    
2790 :     Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2791 :     '^tmp' => 0666);
2792 :    
2793 :     Note that the pattern matches are all case-insensitive, and only directory
2794 :     names are matched, not file names.
2795 :    
2796 : parrello 1.46 =back
2797 :    
2798 :     =cut
2799 :    
2800 :     sub SetPermissions {
2801 :     # Get the parameters.
2802 : parrello 1.49 my ($dirName, $group, $mask, @otherMasks) = @_;
2803 : parrello 1.46 # Set up for error recovery.
2804 :     eval {
2805 : parrello 1.49 # Switch to the specified directory.
2806 : parrello 1.46 ChDir($dirName);
2807 :     # Get the group ID.
2808 :     my $gid = getgrnam($group);
2809 : parrello 1.50 # Get the mask for tracing.
2810 : parrello 1.51 my $traceMask = sprintf("%04o", $mask) . "($mask)";
2811 : parrello 1.77 Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2812 : parrello 1.46 my $fixCount = 0;
2813 :     my $lookCount = 0;
2814 :     # @dirs will be a stack of directories to be processed.
2815 :     my @dirs = (getcwd());
2816 :     while (scalar(@dirs) > 0) {
2817 :     # Get the current directory.
2818 :     my $dir = pop @dirs;
2819 : parrello 1.49 # Check for a match to one of the specified directory names. To do
2820 :     # that, we need to pull the individual part of the name off of the
2821 :     # whole path.
2822 :     my $simpleName = $dir;
2823 : parrello 1.57 if ($dir =~ m!/([^/]+)$!) {
2824 : parrello 1.49 $simpleName = $1;
2825 :     }
2826 : parrello 1.77 Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2827 : parrello 1.49 # Search for a match.
2828 :     my $match = 0;
2829 :     my $i;
2830 :     for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2831 :     my $pattern = $otherMasks[$i];
2832 :     if ($simpleName =~ /$pattern/i) {
2833 :     $match = 1;
2834 : parrello 1.46 }
2835 : parrello 1.49 }
2836 : parrello 1.52 # Check for a match. Note we use $i-1 because the loop added 2
2837 :     # before terminating due to the match.
2838 :     if ($match && $otherMasks[$i-1] != $mask) {
2839 : parrello 1.49 # This directory matches one of the incoming patterns, and it's
2840 :     # a different mask, so we process it recursively with that mask.
2841 : parrello 1.52 SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2842 : parrello 1.49 } else {
2843 :     # Here we can process normally. Get all of the non-hidden members.
2844 :     my @submems = OpenDir($dir, 1);
2845 :     for my $submem (@submems) {
2846 :     # Get the full name.
2847 :     my $thisMem = "$dir/$submem";
2848 :     Trace("Checking member $thisMem.") if T(4);
2849 :     $lookCount++;
2850 :     if ($lookCount % 1000 == 0) {
2851 : parrello 1.77 Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2852 : parrello 1.49 }
2853 :     # Fix the group.
2854 :     chown -1, $gid, $thisMem;
2855 :     # Insure this member is not a symlink.
2856 :     if (! -l $thisMem) {
2857 :     # Get its info.
2858 :     my $fileInfo = stat $thisMem;
2859 :     # Only proceed if we got the info. Otherwise, it's a hard link
2860 :     # and we want to skip it anyway.
2861 :     if ($fileInfo) {
2862 :     my $fileMode = $fileInfo->mode;
2863 : parrello 1.58 if (($fileMode & $mask) != $mask) {
2864 : parrello 1.49 # Fix this member.
2865 :     $fileMode |= $mask;
2866 :     chmod $fileMode, $thisMem;
2867 :     $fixCount++;
2868 :     }
2869 :     # If it's a subdirectory, stack it.
2870 :     if (-d $thisMem) {
2871 :     push @dirs, $thisMem;
2872 :     }
2873 : parrello 1.46 }
2874 :     }
2875 :     }
2876 :     }
2877 :     }
2878 : parrello 1.77 Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2879 : parrello 1.46 };
2880 :     # Check for an error.
2881 :     if ($@) {
2882 :     Confess("SetPermissions error: $@");
2883 :     }
2884 :     }
2885 :    
2886 : parrello 1.62 =head3 CompareLists
2887 :    
2888 :     C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>
2889 :    
2890 :     Compare two lists of tuples, and return a hash analyzing the differences. The lists
2891 :     are presumed to be sorted alphabetically by the value in the $keyIndex column.
2892 :     The return value contains a list of items that are only in the new list
2893 :     (inserted) and only in the old list (deleted).
2894 :    
2895 :     =over 4
2896 :    
2897 :     =item newList
2898 :    
2899 :     Reference to a list of new tuples.
2900 :    
2901 :     =item oldList
2902 :    
2903 :     Reference to a list of old tuples.
2904 :    
2905 :     =item keyIndex (optional)
2906 :    
2907 :     Index into each tuple of its key field. The default is 0.
2908 :    
2909 :     =item RETURN
2910 :    
2911 :     Returns a 2-tuple consisting of a reference to the list of items that are only in the new
2912 :     list (inserted) followed by a reference to the list of items that are only in the old
2913 :     list (deleted).
2914 :    
2915 :     =back
2916 :    
2917 :     =cut
2918 :    
2919 :     sub CompareLists {
2920 :     # Get the parameters.
2921 :     my ($newList, $oldList, $keyIndex) = @_;
2922 :     if (! defined $keyIndex) {
2923 :     $keyIndex = 0;
2924 :     }
2925 :     # Declare the return variables.
2926 :     my ($inserted, $deleted) = ([], []);
2927 :     # Loop through the two lists simultaneously.
2928 :     my ($newI, $oldI) = (0, 0);
2929 :     my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
2930 :     while ($newI < $newN || $oldI < $oldN) {
2931 :     # Get the current object in each list. Note that if one
2932 :     # of the lists is past the end, we'll get undef.
2933 :     my $newItem = $newList->[$newI];
2934 :     my $oldItem = $oldList->[$oldI];
2935 : parrello 1.63 if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
2936 : parrello 1.62 # The old item is not in the new list, so mark it deleted.
2937 :     push @{$deleted}, $oldItem;
2938 :     $oldI++;
2939 :     } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
2940 :     # The new item is not in the old list, so mark it inserted.
2941 :     push @{$inserted}, $newItem;
2942 :     $newI++;
2943 :     } else {
2944 :     # The item is in both lists, so push forward.
2945 :     $oldI++;
2946 :     $newI++;
2947 :     }
2948 :     }
2949 :     # Return the result.
2950 :     return ($inserted, $deleted);
2951 :     }
2952 :    
2953 : parrello 1.65 =head3 GetLine
2954 :    
2955 :     C<< my @data = Tracer::GetLine($handle); >>
2956 :    
2957 :     Read a line of data from a tab-delimited file.
2958 :    
2959 :     =over 4
2960 :    
2961 :     =item handle
2962 :    
2963 :     Open file handle from which to read.
2964 :    
2965 :     =item RETURN
2966 :    
2967 :     Returns a list of the fields in the record read. The fields are presumed to be
2968 :     tab-delimited. If we are at the end of the file, then an empty list will be
2969 :     returned. If an empty line is read, a single list item consisting of a null
2970 :     string will be returned.
2971 :    
2972 :     =back
2973 :    
2974 :     =cut
2975 :    
2976 :     sub GetLine {
2977 :     # Get the parameters.
2978 :     my ($handle) = @_;
2979 :     # Declare the return variable.
2980 :     my @retVal = ();
2981 : parrello 1.77 Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2982 : parrello 1.65 # Read from the file.
2983 :     my $line = <$handle>;
2984 :     # Only proceed if we found something.
2985 :     if (defined $line) {
2986 : parrello 1.80 # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2987 :     # upload control and have a nonstandard EOL combination.
2988 :     $line =~ s/(\r|\n)+$//;
2989 :     # Here we do some fancy tracing to help in debugging complicated EOL marks.
2990 :     if (T(File => 4)) {
2991 :     my $escapedLine = $line;
2992 :     $escapedLine =~ s/\n/\\n/g;
2993 :     $escapedLine =~ s/\r/\\r/g;
2994 :     $escapedLine =~ s/\t/\\t/g;
2995 :     Trace("Line read: -->$escapedLine<--");
2996 :     }
2997 : parrello 1.65 # If the line is empty, return a single empty string; otherwise, parse
2998 :     # it into fields.
2999 :     if ($line eq "") {
3000 :     push @retVal, "";
3001 :     } else {
3002 :     push @retVal, split /\t/,$line;
3003 :     }
3004 : parrello 1.77 } else {
3005 :     # Trace the reason the read failed.
3006 :     Trace("End of file: $!") if T(File => 3);
3007 : parrello 1.65 }
3008 :     # Return the result.
3009 :     return @retVal;
3010 :     }
3011 :    
3012 :     =head3 PutLine
3013 :    
3014 : parrello 1.82 C<< Tracer::PutLine($handle, \@fields, $eol); >>
3015 : parrello 1.65
3016 :     Write a line of data to a tab-delimited file. The specified field values will be
3017 :     output in tab-separated form, with a trailing new-line.
3018 :    
3019 :     =over 4
3020 :    
3021 :     =item handle
3022 :    
3023 :     Output file handle.
3024 :    
3025 :     =item fields
3026 :    
3027 :     List of field values.
3028 :    
3029 : parrello 1.82 =item eol (optional)
3030 :    
3031 :     End-of-line character (default is "\n").
3032 :    
3033 : parrello 1.65 =back
3034 :    
3035 :     =cut
3036 :    
3037 :     sub PutLine {
3038 :     # Get the parameters.
3039 : parrello 1.82 my ($handle, $fields, $eol) = @_;
3040 : parrello 1.65 # Write the data.
3041 : parrello 1.82 print $handle join("\t", @{$fields}) . ($eol || "\n");
3042 : parrello 1.65 }
3043 :    
3044 :     =head3 GenerateURL
3045 :    
3046 :     C<< my $queryUrl = Tracer::GenerateURL($page, %parameters); >>
3047 :    
3048 :     Generate a GET-style URL for the specified page with the specified parameter
3049 :     names and values. The values will be URL-escaped automatically. So, for
3050 :     example
3051 :    
3052 :     Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3053 :    
3054 :     would return
3055 :    
3056 : parrello 1.79 form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3057 : parrello 1.65
3058 :     =over 4
3059 :    
3060 :     =item page
3061 :    
3062 :     Page URL.
3063 :    
3064 :     =item parameters
3065 :    
3066 :     Hash mapping parameter names to parameter values.
3067 :    
3068 :     =item RETURN
3069 :    
3070 :     Returns a GET-style URL that goes to the specified page and passes in the
3071 :     specified parameters and values.
3072 :    
3073 :     =back
3074 :    
3075 :     =cut
3076 :    
3077 :     sub GenerateURL {
3078 :     # Get the parameters.
3079 :     my ($page, %parameters) = @_;
3080 :     # Prime the return variable with the page URL.
3081 :     my $retVal = $page;
3082 :     # Loop through the parameters, creating parameter elements in a list.
3083 :     my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3084 :     # If the list is nonempty, tack it on.
3085 :     if (@parmList) {
3086 : parrello 1.79 $retVal .= "?" . join(";", @parmList);
3087 : parrello 1.65 }
3088 :     # Return the result.
3089 :     return $retVal;
3090 :     }
3091 :    
3092 : parrello 1.78 =head3 ApplyURL
3093 :    
3094 :     C<< Tracer::ApplyURL($table, $target, $url); >>
3095 :    
3096 :     Run through a two-dimensional table (or more accurately, a list of lists), converting the
3097 :     I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3098 :     URL column will be deleted by this process and the target column will be HTML-escaped.
3099 :    
3100 :     This provides a simple way to process the results of a database query into something
3101 :     displayable by combining a URL with text.
3102 :    
3103 :     =over 4
3104 :    
3105 :     =item table
3106 :    
3107 :     Reference to a list of lists. The elements in the containing list will be updated by
3108 :     this method.
3109 :    
3110 :     =item target
3111 :    
3112 :     The index of the column to be converted into HTML.
3113 :    
3114 :     =item url
3115 :    
3116 :     The index of the column containing the URL. Note that the URL must have a recognizable
3117 :     C<http:> at the beginning.
3118 :    
3119 :     =back
3120 :    
3121 :     =cut
3122 :    
3123 :     sub ApplyURL {
3124 :     # Get the parameters.
3125 :     my ($table, $target, $url) = @_;
3126 :     # Loop through the table.
3127 :     for my $row (@{$table}) {
3128 :     # Apply the URL to the target cell.
3129 :     $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3130 :     # Delete the URL from the row.
3131 :     delete $row->[$url];
3132 :     }
3133 :     }
3134 :    
3135 :     =head3 CombineURL
3136 :    
3137 :     C<< my $combinedHtml = Tracer::CombineURL($text, $url); >>
3138 :    
3139 :     This method will convert the specified text into HTML hyperlinked to the specified
3140 :     URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3141 :     is defined and begins with an C<http:> header.
3142 :    
3143 :     =over 4
3144 :    
3145 :     =item text
3146 :    
3147 :     Text to return. This will be HTML-escaped automatically.
3148 :    
3149 :     =item url
3150 :    
3151 :     A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3152 :     will be returned without any hyperlinking.
3153 :    
3154 :     =item RETURN
3155 :    
3156 :     Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3157 :     doesn't look right, the HTML-escaped text will be returned without any further
3158 :     modification.
3159 :    
3160 :     =back
3161 :    
3162 :     =cut
3163 :    
3164 :     sub CombineURL {
3165 :     # Get the parameters.
3166 :     my ($text, $url) = @_;
3167 :     # Declare the return variable.
3168 :     my $retVal = CGI::escapeHTML($text);
3169 :     # Verify the URL.
3170 :     if (defined($url) && $url =~ m!http://!i) {
3171 :     # It's good, so we apply it to the text.
3172 :     $retVal = "<a href=\"$url\">$retVal</a>";
3173 :     }
3174 :     # Return the result.
3175 :     return $retVal;
3176 :     }
3177 :    
3178 : parrello 1.65 1;

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