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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 : parrello 1.93 =head2 Tracing Methods
300 :    
301 :     =head3 Setups
302 :    
303 :     my $count = Tracer::Setups();
304 :    
305 :     Return the number of times L</TSetup> has been called.
306 :    
307 :     This method allows for the creation of conditional tracing setups where, for example, we
308 :     may want to set up tracing if nobody else has done it before us.
309 :    
310 :     =cut
311 :    
312 :     sub Setups {
313 :     return $SetupCount;
314 :     }
315 : olson 1.1
316 :     =head3 TSetup
317 :    
318 : parrello 1.92 TSetup($categoryList, $target);
319 : olson 1.1
320 :     This method is used to specify the trace options. The options are stored as package data
321 :     and interrogated by the L</Trace> and L</T> methods.
322 :    
323 :     =over 4
324 :    
325 :     =item categoryList
326 :    
327 :     A string specifying the trace level and the categories to be traced, separated by spaces.
328 :     The trace level must come first.
329 :    
330 :     =item target
331 :    
332 :     The destination for the trace output. To send the trace output to a file, specify the file
333 :     name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
334 : parrello 1.10 to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
335 :     symbol with a C<+> to echo output to a file AND to the standard output. In addition to
336 :     sending the trace messages to a file, you can specify a special destination. C<HTML> will
337 :     cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
338 : parrello 1.5 will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
339 : parrello 1.9 messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
340 : parrello 1.6 messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
341 : parrello 1.9 cause trace messages to be emitted as warnings using the B<warn> directive. C<NONE> will
342 : parrello 1.6 cause tracing to be suppressed.
343 : olson 1.1
344 :     =back
345 :    
346 :     =cut
347 :    
348 :     sub TSetup {
349 : parrello 1.12 # Get the parameters.
350 :     my ($categoryList, $target) = @_;
351 :     # Parse the category list.
352 :     my @categoryData = split /\s+/, $categoryList;
353 :     # Extract the trace level.
354 :     $TraceLevel = shift @categoryData;
355 :     # Presume category-based tracing until we learn otherwise.
356 :     $AllTrace = 0;
357 :     # Build the category hash. Note that if we find a "*", we turn on non-category
358 : parrello 1.33 # tracing. We must also clear away any pre-existing data.
359 : parrello 1.34 %Categories = ( main => 1 );
360 : parrello 1.12 for my $category (@categoryData) {
361 :     if ($category eq '*') {
362 :     $AllTrace = 1;
363 :     } else {
364 : parrello 1.13 $Categories{lc $category} = 1;
365 : parrello 1.12 }
366 :     }
367 :     # Now we need to process the destination information. The most important special
368 :     # cases are the single ">", which requires we clear the file first, and the
369 :     # "+" prefix which indicates a double echo.
370 :     if ($target =~ m/^\+?>>?/) {
371 :     if ($target =~ m/^\+/) {
372 :     $TeeFlag = 1;
373 :     $target = substr($target, 1);
374 :     }
375 :     if ($target =~ m/^>[^>]/) {
376 :     open TRACEFILE, $target;
377 : parrello 1.69 print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";
378 : parrello 1.12 close TRACEFILE;
379 :     $Destination = ">$target";
380 :     } else {
381 :     $Destination = $target;
382 :     }
383 :     } else {
384 :     $Destination = uc($target);
385 :     }
386 :     # Increment the setup counter.
387 :     $SetupCount++;
388 : parrello 1.11 }
389 :    
390 : parrello 1.93 =head3 SetLevel
391 : parrello 1.31
392 : parrello 1.93 Tracer::SetLevel($newLevel);
393 : parrello 1.31
394 : parrello 1.93 Modify the trace level. A higher trace level will cause more messages to appear.
395 : parrello 1.31
396 : parrello 1.93 =over 4
397 : parrello 1.31
398 : parrello 1.93 =item newLevel
399 : parrello 1.31
400 : parrello 1.93 Proposed new trace level.
401 : parrello 1.31
402 : parrello 1.93 =back
403 : parrello 1.31
404 : parrello 1.93 =cut
405 : parrello 1.31
406 : parrello 1.93 sub SetLevel {
407 :     $TraceLevel = $_[0];
408 :     }
409 : parrello 1.31
410 : parrello 1.93 =head3 ParseTraceDate
411 : parrello 1.31
412 : parrello 1.93 my $time = Tracer::ParseTraceDate($dateString);
413 : parrello 1.31
414 : parrello 1.93 Convert a date from the trace file into a PERL timestamp.
415 : parrello 1.31
416 : parrello 1.93 =over 4
417 : parrello 1.31
418 : parrello 1.93 =item dateString
419 : parrello 1.31
420 : parrello 1.93 The date string from the trace file. The format of the string is determined by the
421 :     L</Now> method.
422 : parrello 1.31
423 : parrello 1.93 =item RETURN
424 : parrello 1.31
425 : parrello 1.93 Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
426 :     the time string is invalid.
427 : parrello 1.31
428 : parrello 1.93 =back
429 : parrello 1.38
430 : parrello 1.93 =cut
431 : parrello 1.38
432 : parrello 1.93 sub ParseTraceDate {
433 :     # Get the parameters.
434 :     my ($dateString) = @_;
435 :     # Declare the return variable.
436 :     my $retVal;
437 :     # Parse the date.
438 :     if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {
439 :     # Create a time object. Note we need to convert the day, month,
440 :     # and year to a different base. Years count from 1900, and
441 :     # the internal month value is relocated to January = 0.
442 :     $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);
443 :     }
444 :     # Return the result.
445 :     return $retVal;
446 :     }
447 : parrello 1.31
448 : parrello 1.93 =head3 LogErrors
449 : parrello 1.42
450 : parrello 1.93 Tracer::LogErrors($fileName);
451 : parrello 1.31
452 : parrello 1.93 Route the standard error output to a log file.
453 : parrello 1.31
454 : parrello 1.93 =over 4
455 : parrello 1.31
456 : parrello 1.93 =item fileName
457 : parrello 1.31
458 : parrello 1.93 Name of the file to receive the error output.
459 : parrello 1.31
460 : parrello 1.93 =back
461 : parrello 1.31
462 : parrello 1.93 =cut
463 : parrello 1.84
464 : parrello 1.93 sub LogErrors {
465 :     # Get the file name.
466 :     my ($fileName) = @_;
467 :     # Open the file as the standard error output.
468 :     open STDERR, '>', $fileName;
469 :     }
470 : parrello 1.84
471 : parrello 1.93 =head3 Trace
472 : parrello 1.31
473 : parrello 1.93 Trace($message);
474 : parrello 1.31
475 : parrello 1.93 Write a trace message to the target location specified in L</TSetup>. If there has not been
476 :     any prior call to B<TSetup>.
477 : parrello 1.31
478 : parrello 1.93 =over 4
479 : parrello 1.42
480 : parrello 1.93 =item message
481 : parrello 1.42
482 : parrello 1.93 Message to write.
483 : parrello 1.42
484 : parrello 1.93 =back
485 : parrello 1.72
486 : parrello 1.93 =cut
487 : parrello 1.36
488 : parrello 1.93 sub Trace {
489 :     # Get the parameters.
490 :     my ($message) = @_;
491 :     # Get the timestamp.
492 :     my $timeStamp = Now();
493 :     # Format the message. Note we strip off any line terminators at the end.
494 :     my $prefix = "[$timeStamp] <$LastCategory>: ";
495 :     my $formatted = $prefix . Strip($message);
496 :     # Process according to the destination.
497 :     if ($Destination eq "TEXT") {
498 :     # Write the message to the standard output.
499 :     print "$formatted\n";
500 :     } elsif ($Destination eq "ERROR") {
501 :     # Write the message to the error output.
502 :     print STDERR "$formatted\n";
503 :     } elsif ($Destination eq "QUEUE") {
504 :     # Push the message into the queue.
505 :     push @Queue, "$formatted";
506 :     } elsif ($Destination eq "HTML") {
507 :     # Convert the message to HTML and write it to the standard output.
508 :     my $escapedMessage = CGI::escapeHTML($message);
509 :     print "<p>$timeStamp $LastCategory: $escapedMessage</p>\n";
510 :     } elsif ($Destination eq "WARN") {
511 :     # Emit the message as a warning.
512 :     warn $message;
513 :     } elsif ($Destination =~ m/^>>/) {
514 :     # Write the trace message to an output file.
515 :     (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
516 :     print TRACING "$formatted\n";
517 :     close TRACING;
518 :     # If the Tee flag is on, echo it to the standard output.
519 :     if ($TeeFlag) {
520 :     print "$formatted\n";
521 :     }
522 :     }
523 :     }
524 : parrello 1.36
525 : parrello 1.93 =head3 T
526 : parrello 1.36
527 : parrello 1.93 my $switch = T($category, $traceLevel);
528 : parrello 1.36
529 : parrello 1.93 or
530 : parrello 1.44
531 : parrello 1.93 my $switch = T($traceLevel);
532 : parrello 1.44
533 : parrello 1.93 Return TRUE if the trace level is at or above a specified value and the specified category
534 :     is active, else FALSE. If no category is specified, the caller's package name is used.
535 : parrello 1.44
536 : parrello 1.93 =over 4
537 : parrello 1.44
538 : parrello 1.93 =item category
539 : parrello 1.44
540 : parrello 1.93 Category to which the message belongs. If not specified, the caller's package name is
541 :     used.
542 : parrello 1.31
543 : parrello 1.93 =item traceLevel
544 : parrello 1.31
545 : parrello 1.93 Relevant tracing level.
546 : parrello 1.31
547 : parrello 1.93 =item RETURN
548 : parrello 1.31
549 : parrello 1.93 TRUE if a message at the specified trace level would appear in the trace, else FALSE.
550 : parrello 1.31
551 : parrello 1.93 =back
552 : parrello 1.36
553 : parrello 1.93 =cut
554 :    
555 :     sub T {
556 :     # Declare the return variable.
557 :     my $retVal = 0;
558 :     # Only proceed if tracing is turned on.
559 :     if ($Destination ne "NONE") {
560 :     # Get the parameters.
561 :     my ($category, $traceLevel) = @_;
562 :     if (!defined $traceLevel) {
563 :     # Here we have no category, so we need to get the calling package.
564 :     # The calling package is normally the first parameter. If it is
565 :     # omitted, the first parameter will be the tracelevel. So, the
566 :     # first thing we do is shift the so-called category into the
567 :     # $traceLevel variable where it belongs.
568 :     $traceLevel = $category;
569 :     my ($package, $fileName, $line) = caller;
570 :     # If there is no calling package, we default to "main".
571 :     if (!$package) {
572 :     $category = "main";
573 :     } else {
574 :     my @cats = split /::/, $package;
575 :     $category = $cats[$#cats];
576 :     }
577 :     }
578 :     # Save the category name.
579 :     $LastCategory = $category;
580 :     # Convert it to lower case before we hash it.
581 :     $category = lc $category;
582 :     # Use the category and tracelevel to compute the result.
583 :     if (ref $traceLevel) {
584 :     Confess("Bad trace level.");
585 :     } elsif (ref $TraceLevel) {
586 :     Confess("Bad trace config.");
587 :     }
588 :     $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
589 :     }
590 :     # Return the computed result.
591 :     return $retVal;
592 :     }
593 :    
594 :     =head3 QTrace
595 :    
596 :     my $data = QTrace($format);
597 :    
598 :     Return the queued trace data in the specified format.
599 :    
600 :     =over 4
601 :    
602 :     =item format
603 :    
604 :     C<html> to format the data as an HTML list, C<text> to format it as straight text.
605 :    
606 :     =back
607 :    
608 :     =cut
609 :    
610 :     sub QTrace {
611 :     # Get the parameter.
612 :     my ($format) = @_;
613 :     # Create the return variable.
614 :     my $retVal = "";
615 :     # Only proceed if there is an actual queue.
616 :     if (@Queue) {
617 :     # Process according to the format.
618 :     if ($format =~ m/^HTML$/i) {
619 :     # Convert the queue into an HTML list.
620 :     $retVal = "<ul>\n";
621 :     for my $line (@Queue) {
622 :     my $escapedLine = CGI::escapeHTML($line);
623 :     $retVal .= "<li>$escapedLine</li>\n";
624 :     }
625 :     $retVal .= "</ul>\n";
626 :     } elsif ($format =~ m/^TEXT$/i) {
627 :     # Convert the queue into a list of text lines.
628 :     $retVal = join("\n", @Queue) . "\n";
629 :     }
630 :     # Clear the queue.
631 :     @Queue = ();
632 :     }
633 :     # Return the formatted list.
634 :     return $retVal;
635 :     }
636 :    
637 :     =head3 Confess
638 :    
639 :     Confess($message);
640 :    
641 :     Trace the call stack and abort the program with the specified message. When used with
642 :     the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
643 :     So, for example
644 :    
645 :     Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
646 :    
647 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
648 :    
649 :     =over 4
650 :    
651 :     =item message
652 :    
653 :     Message to include in the trace.
654 :    
655 :     =back
656 :    
657 :     =cut
658 :    
659 :     sub Confess {
660 :     # Get the parameters.
661 :     my ($message) = @_;
662 :     if (! defined($FIG_Config::no_tool_hdr)) {
663 :     # Here we have a tool header. Display its length so that the user can adjust the line numbers.
664 :     my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
665 :     # Only proceed if the tool header file is actually present.
666 :     if (-f $toolHeaderFile) {
667 :     my @lines = GetFile($toolHeaderFile);
668 :     Trace("Tool header has " . scalar(@lines) . " lines.");
669 :     }
670 :     }
671 :     # Trace the call stack.
672 :     Cluck($message);
673 :     # Abort the program.
674 :     croak(">>> $message");
675 :     }
676 :    
677 :     =head3 Assert
678 :    
679 :     Assert($condition1, $condition2, ... $conditionN);
680 :    
681 :     Return TRUE if all the conditions are true. This method can be used in conjunction with
682 :     the OR operator and the L</Confess> method as a debugging assert.
683 :     So, for example
684 :    
685 :     Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
686 :    
687 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
688 :    
689 :     =cut
690 :     sub Assert {
691 :     my $retVal = 1;
692 :     LOOP: for my $condition (@_) {
693 :     if (! $condition) {
694 :     $retVal = 0;
695 :     last LOOP;
696 :     }
697 :     }
698 :     return $retVal;
699 :     }
700 :    
701 :     =head3 Cluck
702 :    
703 :     Cluck($message);
704 :    
705 :     Trace the call stack. Note that for best results, you should qualify the call with a
706 :     trace condition. For example,
707 :    
708 :     Cluck("Starting record parse.") if T(3);
709 :    
710 :     will only trace the stack if the trace level for the package is 3 or more.
711 :    
712 :     =over 4
713 :    
714 :     =item message
715 :    
716 :     Message to include in the trace.
717 :    
718 :     =back
719 :    
720 :     =cut
721 :    
722 :     sub Cluck {
723 :     # Get the parameters.
724 :     my ($message) = @_;
725 :     # Trace what's happening.
726 :     Trace("Stack trace for event: $message");
727 :     my $confession = longmess($message);
728 :     # Convert the confession to a series of trace messages. Note we skip any
729 :     # messages relating to calls into Tracer.
730 :     for my $line (split /\s*\n/, $confession) {
731 :     Trace($line) if ($line !~ /Tracer\.pm/);
732 :     }
733 :     }
734 :    
735 :     =head3 ScriptSetup
736 :    
737 :     my ($cgi, $varHash) = ScriptSetup($noTrace);
738 :    
739 :     Perform standard tracing and debugging setup for scripts. The value returned is
740 :     the CGI object followed by a pre-built variable hash. At the end of the script,
741 :     the client should call L</ScriptFinish> to output the web page.
742 :    
743 :     This method calls L</ETracing> to configure tracing, which allows the tracing
744 :     to be configured via the emergency tracing form on the debugging control panel.
745 :     Tracing will then be turned on automatically for all programs that use the L</ETracing>
746 :     method, which includes every program that uses this method or L</StandardSetup>.
747 : parrello 1.36
748 : parrello 1.93 =over 4
749 : parrello 1.31
750 : parrello 1.93 =item noTrace (optional)
751 : parrello 1.31
752 : parrello 1.93 If specified, tracing will be suppressed. This is useful if the script wants to set up
753 :     tracing manually.
754 : parrello 1.31
755 :     =item RETURN
756 :    
757 : parrello 1.93 Returns a two-element list consisting of a CGI query object and a variable hash for
758 :     the output page.
759 : parrello 1.31
760 :     =back
761 :    
762 :     =cut
763 :    
764 : parrello 1.93 sub ScriptSetup {
765 : parrello 1.31 # Get the parameters.
766 : parrello 1.93 my ($noTrace) = @_;
767 :     # Get the CGI query object.
768 :     my $cgi = CGI->new();
769 :     # Set up tracing if it's not suppressed.
770 :     ETracing($cgi) unless $noTrace;
771 :     # Create the variable hash.
772 :     my $varHash = { results => '' };
773 :     # Return the query object and variable hash.
774 :     return ($cgi, $varHash);
775 :     }
776 :    
777 :     =head3 ETracing
778 :    
779 :     ETracing($parameter);
780 :    
781 :     Set up emergency tracing. Emergency tracing is tracing that is turned
782 :     on automatically for any program that calls this method. The emergency
783 :     tracing parameters are stored in a a file identified by a tracing key.
784 :     If this method is called with a CGI object, then the tracing key is
785 :     taken from a cookie. If it is called with no parameters, then the tracing
786 :     key is taken from an environment variable. If it is called with a string,
787 :     the tracing key is that string.
788 :    
789 :     =over 4
790 :    
791 :     =item parameter
792 :    
793 :     A parameter from which the tracing key is computed. If it is a scalar,
794 :     that scalar is used as the tracing key. If it is a CGI object, the
795 :     tracing key is taken from the C<IP> cookie. If it is omitted, the
796 :     tracing key is taken from the C<TRACING> environment variable. If it
797 :     is a CGI object and emergency tracing is not on, the C<Trace> and
798 :     C<TF> parameters will be used to determine the type of tracing.
799 :    
800 :     =back
801 :    
802 :     =cut
803 :    
804 :     sub ETracing {
805 :     # Get the parameter.
806 :     my ($parameter) = @_;
807 :     # Check for CGI mode.
808 :     my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
809 :     # Default to no tracing except errors.
810 :     my ($tracing, $dest) = ("0", "WARN");
811 :     # Check for emergency tracing.
812 :     my $tkey = EmergencyKey($parameter);
813 :     my $emergencyFile = EmergencyFileName($tkey);
814 :     if (-e $emergencyFile) {
815 :     # We have the file. Read in the data.
816 :     my @tracing = GetFile($emergencyFile);
817 :     # Pull off the time limit.
818 :     my $expire = shift @tracing;
819 :     # Convert it to seconds.
820 :     $expire *= 3600;
821 :     # Check the file data.
822 :     my $stat = stat($emergencyFile);
823 :     my ($now) = gettimeofday;
824 :     if ($now - $stat->mtime > $expire) {
825 :     # Delete the expired file.
826 :     unlink $emergencyFile;
827 : parrello 1.44 } else {
828 : parrello 1.93 # Emergency tracing is on. Pull off the destination and
829 :     # the trace level;
830 :     $dest = shift @tracing;
831 :     my $level = shift @tracing;
832 :     # Convert the destination to a real tracing destination.
833 :     # temp directory.
834 :     $dest = EmergencyTracingDest($tkey, $dest);
835 :     # Insure Tracer is specified.
836 :     my %moduleHash = map { $_ => 1 } @tracing;
837 :     $moduleHash{Tracer} = 1;
838 :     # Set the trace parameter.
839 :     $tracing = join(" ", $level, sort keys %moduleHash);
840 : parrello 1.44 }
841 : parrello 1.93 } elsif (defined $cgi) {
842 :     # There's no emergency tracing, but we have a CGI object, so check
843 :     # for tracing from the form parameters.
844 :     if ($cgi->param('Trace')) {
845 :     # Here the user has requested tracing via a form.
846 :     $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
847 :     $tracing = $cgi->param('Trace') . " Tracer";
848 : parrello 1.36 }
849 :     }
850 : parrello 1.93 # Setup the tracing we've determined from all the stuff above.
851 :     TSetup($tracing, $dest);
852 :     # If we're a web script, trace the parameter and environment data.
853 :     if (defined $cgi) {
854 :     TraceParms($cgi);
855 : parrello 1.83 }
856 : parrello 1.31 }
857 :    
858 : parrello 1.93 =head3 EmergencyFileName
859 :    
860 :     my $fileName = Tracer::EmergencyFileName($tkey);
861 :    
862 :     Return the emergency tracing file name. This is the file that specifies
863 :     the tracing information.
864 :    
865 :     =over 4
866 :    
867 :     =item tkey
868 :    
869 :     Tracing key for the current program.
870 : parrello 1.11
871 : parrello 1.93 =item RETURN
872 : parrello 1.11
873 : parrello 1.93 Returns the name of the file to contain the emergency tracing information.
874 : parrello 1.11
875 : parrello 1.93 =back
876 : parrello 1.11
877 :     =cut
878 :    
879 : parrello 1.93 sub EmergencyFileName {
880 :     # Get the parameters.
881 :     my ($tkey) = @_;
882 :     # Compute the emergency tracing file name.
883 :     return "$FIG_Config::temp/Emergency$tkey.txt";
884 : olson 1.1 }
885 :    
886 : parrello 1.93 =head3 EmergencyFileTarget
887 : parrello 1.10
888 : parrello 1.93 my $fileName = Tracer::EmergencyFileTarget($tkey);
889 : parrello 1.10
890 : parrello 1.93 Return the emergency tracing target file name. This is the file that receives
891 :     the tracing output for file-based tracing.
892 : parrello 1.10
893 : parrello 1.93 =over 4
894 : parrello 1.10
895 : parrello 1.93 =item tkey
896 : parrello 1.10
897 : parrello 1.93 Tracing key for the current program.
898 : parrello 1.10
899 : parrello 1.93 =item RETURN
900 : parrello 1.10
901 : parrello 1.93 Returns the name of the file to contain the trace output.
902 : parrello 1.10
903 : parrello 1.93 =back
904 : parrello 1.10
905 : parrello 1.93 =cut
906 : parrello 1.10
907 : parrello 1.93 sub EmergencyFileTarget {
908 :     # Get the parameters.
909 :     my ($tkey) = @_;
910 :     # Compute the emergency tracing file name.
911 :     return "$FIG_Config::temp/trace$tkey.log";
912 :     }
913 : parrello 1.10
914 : parrello 1.93 =head3 EmergencyTracingDest
915 : parrello 1.10
916 : parrello 1.93 my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
917 : parrello 1.10
918 : parrello 1.93 This method converts an emergency tracing destination to a real
919 :     tracing destination. The main difference is that if the
920 :     destination is C<FILE> or C<APPEND>, we convert it to file
921 :     output. If the destination is C<DUAL>, we convert it to file
922 :     and standard output.
923 : parrello 1.10
924 :     =over 4
925 :    
926 : parrello 1.93 =item tkey
927 : parrello 1.10
928 : parrello 1.93 Tracing key for this environment.
929 : parrello 1.10
930 : parrello 1.93 =item myDest
931 : parrello 1.10
932 : parrello 1.93 Destination from the emergency tracing file.
933 : parrello 1.10
934 :     =item RETURN
935 :    
936 : parrello 1.93 Returns a destination that can be passed into L</TSetup>.
937 : parrello 1.10
938 :     =back
939 :    
940 :     =cut
941 :    
942 : parrello 1.93 sub EmergencyTracingDest {
943 : parrello 1.12 # Get the parameters.
944 : parrello 1.93 my ($tkey, $myDest) = @_;
945 :     # Declare the return variable.
946 :     my $retVal = $myDest;
947 :     # Process according to the destination value.
948 :     if ($myDest eq 'FILE') {
949 :     $retVal = ">" . EmergencyFileTarget($tkey);
950 :     } elsif ($myDest eq 'APPEND') {
951 :     $retVal = ">>" . EmergencyFileTarget($tkey);
952 :     } elsif ($myDest eq 'DUAL') {
953 :     $retVal = "+>" . EmergencyFileTarget($tkey);
954 : parrello 1.12 }
955 : parrello 1.93 # Return the result.
956 :     return $retVal;
957 : parrello 1.10 }
958 :    
959 : parrello 1.93 =head3 Emergency
960 :    
961 :     Emergency($key, $hours, $dest, $level, @modules);
962 :    
963 :     Turn on emergency tracing. This method is normally invoked over the web from
964 :     a debugging console, but it can also be called by the C<trace.pl> script.
965 :     The caller specifies the duration of the emergency in hours, the desired tracing
966 :     destination, the trace level, and a list of the trace modules to activate.
967 :     For the length of the duration, when a program in an environment with the
968 :     specified tracing key active invokes a Sprout CGI script, tracing will be
969 :     turned on automatically. See L</TSetup> for more about tracing setup and
970 :     L</ETracing> for more about emergency tracing.
971 :    
972 :     =over 4
973 : parrello 1.11
974 : parrello 1.93 =item tkey
975 : parrello 1.11
976 : parrello 1.93 The tracing key. This is used to identify the control file and the trace file.
977 : parrello 1.11
978 : parrello 1.93 =item hours
979 : parrello 1.11
980 : parrello 1.93 Number of hours to keep emergency tracing alive.
981 : parrello 1.11
982 : parrello 1.93 =item dest
983 : parrello 1.11
984 : parrello 1.93 Tracing destination. If no path information is specified for a file
985 :     destination, it is put in the FIG temporary directory.
986 : parrello 1.11
987 : parrello 1.93 =item level
988 : parrello 1.11
989 : parrello 1.93 Tracing level. A higher level means more trace messages.
990 : parrello 1.11
991 : parrello 1.93 =item modules
992 : parrello 1.11
993 : parrello 1.93 A list of the tracing modules to activate.
994 : parrello 1.11
995 :     =back
996 :    
997 :     =cut
998 : parrello 1.93
999 :     sub Emergency {
1000 : parrello 1.11 # Get the parameters.
1001 : parrello 1.93 my ($tkey, $hours, $dest, $level, @modules) = @_;
1002 :     # Create the emergency file.
1003 :     my $specFile = EmergencyFileName($tkey);
1004 :     my $outHandle = Open(undef, ">$specFile");
1005 :     print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1006 : parrello 1.11 }
1007 :    
1008 : parrello 1.93 =head3 EmergencyKey
1009 :    
1010 :     my $tkey = EmergencyKey($parameter);
1011 :    
1012 :     Return the Key to be used for emergency tracing. This could be an IP address,
1013 :     a session ID, or a user name, depending on the environment.
1014 : parrello 1.11
1015 : parrello 1.93 =over 4
1016 : parrello 1.11
1017 : parrello 1.93 =item parameter
1018 : parrello 1.11
1019 : parrello 1.93 Parameter defining the method for finding the tracing key. If it is a scalar,
1020 :     then it is presumed to be the tracing key itself. If it is a CGI object, then
1021 :     the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1022 :     taken from the C<TRACING> environment variable.
1023 : parrello 1.29
1024 : parrello 1.93 =item RETURN
1025 : parrello 1.11
1026 : parrello 1.93 Returns the key to be used for labels in emergency tracing.
1027 : parrello 1.11
1028 : parrello 1.93 =back
1029 : parrello 1.11
1030 : parrello 1.93 =cut
1031 : parrello 1.29
1032 : parrello 1.93 sub EmergencyKey {
1033 :     # Get the parameters.
1034 :     my ($parameter) = @_;
1035 :     # Declare the return variable.
1036 :     my $retVal;
1037 :     # Determine the parameter type.
1038 :     if (! defined $parameter) {
1039 :     # Here we're supposed to check the environment.
1040 :     $retVal = $ENV{TRACING};
1041 :     } else {
1042 :     my $ptype = ref $parameter;
1043 :     if ($ptype eq 'CGI') {
1044 :     # Here we were invoked from a web page. Look for a cookie.
1045 :     $retVal = $parameter->cookie('IP');
1046 :     } elsif (! $ptype) {
1047 :     # Here the key was passed in.
1048 :     $retVal = $parameter;
1049 :     }
1050 :     }
1051 :     # If no luck finding a key, use the PID.
1052 :     if (! defined $retVal) {
1053 :     $retVal = $$;
1054 :     }
1055 :     # Return the result.
1056 :     return $retVal;
1057 :     }
1058 : parrello 1.11
1059 :    
1060 : parrello 1.93 =head3 TraceParms
1061 : parrello 1.11
1062 : parrello 1.93 Tracer::TraceParms($cgi);
1063 : parrello 1.11
1064 : parrello 1.93 Trace the CGI parameters at trace level CGI => 3 and the environment variables
1065 :     at level CGI => 4.
1066 : parrello 1.11
1067 : parrello 1.93 =over 4
1068 : parrello 1.11
1069 : parrello 1.93 =item cgi
1070 : parrello 1.31
1071 : parrello 1.93 CGI query object containing the parameters to trace.
1072 : parrello 1.31
1073 : parrello 1.11 =back
1074 :    
1075 :     =cut
1076 : parrello 1.93
1077 :     sub TraceParms {
1078 : parrello 1.11 # Get the parameters.
1079 : parrello 1.93 my ($cgi) = @_;
1080 :     if (T(CGI => 3)) {
1081 :     # Here we want to trace the parameter data.
1082 :     my @names = $cgi->param;
1083 :     for my $parmName (sort @names) {
1084 :     # Note we skip the Trace parameters, which are for our use only.
1085 :     if ($parmName ne 'Trace' && $parmName ne 'TF') {
1086 :     my @values = $cgi->param($parmName);
1087 :     Trace("CGI: $parmName = " . join(", ", @values));
1088 :     }
1089 :     }
1090 :     # Display the request method.
1091 :     my $method = $cgi->request_method();
1092 :     Trace("Method: $method");
1093 :     }
1094 :     if (T(CGI => 4)) {
1095 :     # Here we want the environment data too.
1096 :     for my $envName (sort keys %ENV) {
1097 :     Trace("ENV: $envName = $ENV{$envName}");
1098 : parrello 1.12 }
1099 :     }
1100 : parrello 1.11 }
1101 :    
1102 : parrello 1.93 =head3 ScriptFinish
1103 :    
1104 :     ScriptFinish($webData, $varHash);
1105 :    
1106 :     Output a web page at the end of a script. Either the string to be output or the
1107 :     name of a template file can be specified. If the second parameter is omitted,
1108 :     it is assumed we have a string to be output; otherwise, it is assumed we have the
1109 :     name of a template file. The template should have the variable C<DebugData>
1110 :     specified in any form that invokes a standard script. If debugging mode is turned
1111 :     on, a form field will be put in that allows the user to enter tracing data.
1112 :     Trace messages will be placed immediately before the terminal C<BODY> tag in
1113 :     the output, formatted as a list.
1114 :    
1115 :     A typical standard script would loook like the following.
1116 :    
1117 :     BEGIN {
1118 :     # Print the HTML header.
1119 :     print "CONTENT-TYPE: text/html\n\n";
1120 :     }
1121 :     use Tracer;
1122 :     use CGI;
1123 :     use FIG;
1124 :     # ... more uses ...
1125 : parrello 1.6
1126 : parrello 1.93 my ($cgi, $varHash) = ScriptSetup();
1127 :     eval {
1128 :     # ... get data from $cgi, put it in $varHash ...
1129 :     };
1130 :     if ($@) {
1131 :     Trace("Script Error: $@") if T(0);
1132 :     }
1133 :     ScriptFinish("Html/MyTemplate.html", $varHash);
1134 : parrello 1.6
1135 : parrello 1.93 The idea here is that even if the script fails, you'll see trace messages and
1136 :     useful output.
1137 : parrello 1.6
1138 :     =over 4
1139 :    
1140 : parrello 1.93 =item webData
1141 :    
1142 :     A string containing either the full web page to be written to the output or the
1143 :     name of a template file from which the page is to be constructed. If the name
1144 :     of a template file is specified, then the second parameter must be present;
1145 :     otherwise, it must be absent.
1146 :    
1147 :     =item varHash (optional)
1148 : parrello 1.6
1149 : parrello 1.93 If specified, then a reference to a hash mapping variable names for a template
1150 :     to their values. The template file will be read into memory, and variable markers
1151 :     will be replaced by data in this hash reference.
1152 : parrello 1.6
1153 :     =back
1154 :    
1155 :     =cut
1156 :    
1157 : parrello 1.93 sub ScriptFinish {
1158 :     # Get the parameters.
1159 :     my ($webData, $varHash) = @_;
1160 :     # Check for a template file situation.
1161 :     my $outputString;
1162 :     if (defined $varHash) {
1163 :     # Here we have a template file. We need to determine the template type.
1164 :     my $template;
1165 :     if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1166 :     $template = "$FIG_Config::template_url/$webData";
1167 :     } else {
1168 :     $template = "<<$webData";
1169 :     }
1170 :     $outputString = PageBuilder::Build($template, $varHash, "Html");
1171 :     } else {
1172 :     # Here the user gave us a raw string.
1173 :     $outputString = $webData;
1174 :     }
1175 :     # Check for trace messages.
1176 :     if ($Destination ne "NONE" && $TraceLevel > 0) {
1177 :     # We have trace messages, so we want to put them at the end of the body. This
1178 :     # is either at the end of the whole string or at the beginning of the BODY
1179 :     # end-tag.
1180 :     my $pos = length $outputString;
1181 :     if ($outputString =~ m#</body>#gi) {
1182 :     $pos = (pos $outputString) - 7;
1183 :     }
1184 :     # If the trace messages were queued, we unroll them. Otherwise, we display the
1185 :     # destination.
1186 :     my $traceHtml;
1187 :     if ($Destination eq "QUEUE") {
1188 :     $traceHtml = QTrace('Html');
1189 :     } elsif ($Destination =~ /^>>(.+)$/) {
1190 :     # Here the tracing output it to a file. We code it as a hyperlink so the user
1191 :     # can copy the file name into the clipboard easily.
1192 :     my $actualDest = $1;
1193 :     $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1194 :     } else {
1195 :     # Here we have one of the special destinations.
1196 :     $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1197 :     }
1198 :     substr $outputString, $pos, 0, $traceHtml;
1199 :     }
1200 :     # Write the output string.
1201 :     print $outputString;
1202 : parrello 1.6 }
1203 :    
1204 : parrello 1.93 =head2 Command-Line Utility Methods
1205 : olson 1.1
1206 : parrello 1.93 =head3 SendSMS
1207 : olson 1.1
1208 : parrello 1.93 my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1209 : olson 1.1
1210 : parrello 1.93 Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1211 :     user name, password, and API ID for the relevant account in the hash reference variable
1212 :     I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1213 :     example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1214 :     is C<2561022>, then the FIG_Config file must contain
1215 : olson 1.1
1216 : parrello 1.93 $phone = { user => 'BruceTheHumanPet',
1217 :     password => 'silly',
1218 :     api_id => '2561022' };
1219 : olson 1.1
1220 : parrello 1.93 The original purpose of this method was to insure Bruce would be notified immediately when the
1221 :     Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1222 :     when you call this method.
1223 : olson 1.1
1224 : parrello 1.93 The message ID will be returned if successful, and C<undef> if an error occurs.
1225 : parrello 1.74
1226 : parrello 1.93 =over 4
1227 : parrello 1.74
1228 : parrello 1.93 =item phoneNumber
1229 : parrello 1.74
1230 : parrello 1.93 Phone number to receive the message, in international format. A United States phone number
1231 :     would be prefixed by "1". A British phone number would be prefixed by "44".
1232 : parrello 1.74
1233 : parrello 1.93 =item msg
1234 : parrello 1.74
1235 : parrello 1.93 Message to send to the specified phone.
1236 : parrello 1.74
1237 :     =item RETURN
1238 :    
1239 : parrello 1.93 Returns the message ID if successful, and C<undef> if the message could not be sent.
1240 : parrello 1.74
1241 : parrello 1.78 =back
1242 :    
1243 : parrello 1.74 =cut
1244 :    
1245 : parrello 1.93 sub SendSMS {
1246 : parrello 1.74 # Get the parameters.
1247 : parrello 1.93 my ($phoneNumber, $msg) = @_;
1248 :     # Declare the return variable. If we do not change it, C<undef> will be returned.
1249 : parrello 1.74 my $retVal;
1250 : parrello 1.93 # Only proceed if we have phone support.
1251 :     if (! defined $FIG_Config::phone) {
1252 :     Trace("Phone support not present in FIG_Config.") if T(1);
1253 :     } else {
1254 :     # Get the phone data.
1255 :     my $parms = $FIG_Config::phone;
1256 :     # Get the Clickatell URL.
1257 :     my $url = "http://api.clickatell.com/http/";
1258 :     # Create the user agent.
1259 :     my $ua = LWP::UserAgent->new;
1260 :     # Request a Clickatell session.
1261 :     my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1262 :     password => $parms->{password},
1263 :     api_id => $parms->{api_id},
1264 :     to => $phoneNumber,
1265 :     text => $msg});
1266 :     # Check for an error.
1267 :     if (! $resp->is_success) {
1268 :     Trace("Alert failed.") if T(1);
1269 :     } else {
1270 :     # Get the message ID.
1271 :     my $rstring = $resp->content;
1272 :     if ($rstring =~ /^ID:\s+(.*)$/) {
1273 :     $retVal = $1;
1274 :     } else {
1275 :     Trace("Phone attempt failed with $rstring") if T(1);
1276 :     }
1277 :     }
1278 : parrello 1.74 }
1279 :     # Return the result.
1280 :     return $retVal;
1281 :     }
1282 :    
1283 : parrello 1.93 =head3 StandardSetup
1284 : olson 1.1
1285 : parrello 1.93 my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1286 : olson 1.1
1287 : parrello 1.93 This method performs standard command-line parsing and tracing setup. The return
1288 :     values are a hash of the command-line options and a list of the positional
1289 :     parameters. Tracing is automatically set up and the command-line options are
1290 :     validated.
1291 : olson 1.1
1292 : parrello 1.93 This is a complex method that does a lot of grunt work. The parameters can
1293 :     be more easily understood, however, once they are examined individually.
1294 : olson 1.1
1295 : parrello 1.93 The I<categories> parameter is the most obtuse. It is a reference to a list of
1296 :     special-purpose tracing categories. Most tracing categories are PERL package
1297 :     names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1298 :     B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1299 : olson 1.1
1300 : parrello 1.93 ["Sprout", "SproutLoad", "ERDB"]
1301 : olson 1.1
1302 : parrello 1.93 This would cause trace messages in the specified three packages to appear in
1303 :     the output. There are two special tracing categories that are automatically
1304 :     handled by this method. In other words, if you used L</TSetup> you would need
1305 :     to include these categories manually, but if you use this method they are turned
1306 :     on automatically.
1307 : parrello 1.5
1308 :     =over 4
1309 :    
1310 : parrello 1.93 =item SQL
1311 : parrello 1.5
1312 : parrello 1.93 Traces SQL commands and activity.
1313 : parrello 1.5
1314 : parrello 1.93 =item Tracer
1315 : parrello 1.5
1316 : parrello 1.93 Traces error messages and call stacks.
1317 : parrello 1.5
1318 :     =back
1319 :    
1320 : parrello 1.93 C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1321 :     The trace level is specified using the C<-trace> command-line option. For example,
1322 :     the following command line for C<TransactFeatures> turns on SQL tracing and runs
1323 :     all tracing at level 3.
1324 : parrello 1.5
1325 : parrello 1.93 TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1326 : parrello 1.5
1327 : parrello 1.93 Standard tracing is output to the standard output and echoed to the file
1328 :     C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1329 :     process ID. You can also specify the C<user> parameter to put a user ID
1330 :     instead of a process ID in the trace file name. So, for example
1331 : olson 1.1
1332 : parrello 1.93 The default trace level is 2. To get all messages, specify a trace level of 4.
1333 :     For a genome-by-genome update, use 3.
1334 : olson 1.1
1335 : parrello 1.93 TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1336 : olson 1.1
1337 : parrello 1.93 would send the trace output to C<traceBruce.log> in the temporary directory.
1338 : olson 1.1
1339 : parrello 1.93 The I<options> parameter is a reference to a hash containing the command-line
1340 :     options, their default values, and an explanation of what they mean. Command-line
1341 :     options may be in the form of switches or keywords. In the case of a switch, the
1342 :     option value is 1 if it is specified and 0 if it is not specified. In the case
1343 :     of a keyword, the value is separated from the option name by an equal sign. You
1344 :     can see this last in the command-line example above.
1345 : olson 1.1
1346 : parrello 1.93 You can specify a different default trace level by setting C<$options->{trace}>
1347 :     prior to calling this method.
1348 : olson 1.1
1349 : parrello 1.93 An example at this point would help. Consider, for example, the command-line utility
1350 :     C<TransactFeatures>. It accepts a list of positional parameters plus the options
1351 :     C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1352 :     the following code.
1353 : olson 1.1
1354 : parrello 1.93 my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1355 :     { safe => [0, "use database transactions"],
1356 :     noAlias => [0, "do not expect aliases in CHANGE transactions"],
1357 :     start => [' ', "start with this genome"],
1358 :     tblFiles => [0, "output TBL files containing the corrected IDs"] },
1359 :     "<command> <transactionDirectory> <IDfile>",
1360 :     @ARGV);
1361 : olson 1.1
1362 :    
1363 : parrello 1.93 The call to C<ParseCommand> specifies the default values for the options and
1364 :     stores the actual options in a hash that is returned as C<$options>. The
1365 :     positional parameters are returned in C<@parameters>.
1366 : olson 1.1
1367 : parrello 1.93 The following is a sample command line for C<TransactFeatures>.
1368 : olson 1.1
1369 : parrello 1.93 TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1370 : olson 1.1
1371 : parrello 1.93 Single and double hyphens are equivalent. So, you could also code the
1372 :     above command as
1373 : olson 1.1
1374 : parrello 1.93 TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1375 : olson 1.1
1376 : parrello 1.93 In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1377 :     parameters, and would find themselves in I<@parameters> after executing the
1378 :     above code fragment. The tracing would be set to level 2, and the categories
1379 :     would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1380 :     and C<DocUtils> was included because it came in within the first parameter
1381 :     to this method. The I<$options> hash would be
1382 : olson 1.1
1383 : parrello 1.93 { trace => 2, sql => 0, safe => 0,
1384 :     noAlias => 1, start => ' ', tblFiles => 0 }
1385 : olson 1.1
1386 : parrello 1.93 Use of C<StandardSetup> in this way provides a simple way of performing
1387 :     standard tracing setup and command-line parsing. Note that the caller is
1388 :     not even aware of the command-line switches C<-trace> and C<-sql>, which
1389 :     are used by this method to control the tracing. If additional tracing features
1390 :     need to be added in the future, they can be processed by this method without
1391 :     upsetting the command-line utilities.
1392 : olson 1.1
1393 : parrello 1.93 If the C<background> option is specified on the command line, then the
1394 :     standard and error outputs will be directed to files in the temporary
1395 :     directory, using the same suffix as the trace file. So, if the command
1396 :     line specified
1397 : olson 1.1
1398 : parrello 1.93 -user=Bruce -background
1399 : olson 1.1
1400 : parrello 1.93 then the trace output would go to C<traceBruce.log>, the standard output to
1401 :     C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1402 :     simplify starting a command in the background.
1403 : olson 1.1
1404 : parrello 1.93 The user name is also used as the tracing key for L</Emergency Tracing>.
1405 :     Specifying a value of C<E> for the trace level causes emergency tracing to
1406 :     be used instead of custom tracing. If the user name is not specified,
1407 :     the tracing key is taken from the C<Tracing> environment variable. If there
1408 :     is no value for that variable, the tracing key will be computed from the PID.
1409 : olson 1.1
1410 : parrello 1.93 Finally, if the special option C<-help> is specified, the option
1411 :     names will be traced at level 0 and the program will exit without processing.
1412 :     This provides a limited help capability. For example, if the user enters
1413 : olson 1.1
1414 : parrello 1.93 TransactFeatures -help
1415 : olson 1.1
1416 : parrello 1.93 he would see the following output.
1417 : olson 1.1
1418 : parrello 1.93 TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1419 :     -trace tracing level (default E)
1420 :     -sql trace SQL commands
1421 :     -safe use database transactions
1422 :     -noAlias do not expect aliases in CHANGE transactions
1423 :     -start start with this genome
1424 :     -tblFiles output TBL files containing the corrected IDs
1425 : olson 1.1
1426 : parrello 1.93 The caller has the option of modifying the tracing scheme by placing a value
1427 :     for C<trace> in the incoming options hash. The default value can be overridden,
1428 :     or the tracing to the standard output can be turned off by suffixing a minus
1429 :     sign to the trace level. So, for example,
1430 : olson 1.1
1431 : parrello 1.93 { trace => [0, "tracing level (default 0)"],
1432 :     ...
1433 : olson 1.1
1434 : parrello 1.93 would set the default trace level to 0 instead of E, while
1435 : olson 1.1
1436 : parrello 1.93 { trace => ["2-", "tracing level (default 2)"],
1437 :     ...
1438 : olson 1.1
1439 : parrello 1.93 would set the default to 2, but trace only to the log file, not to the
1440 :     standard output.
1441 : olson 1.1
1442 : parrello 1.93 The parameters to this method are as follows.
1443 : olson 1.1
1444 : parrello 1.93 =over 4
1445 : olson 1.1
1446 : parrello 1.93 =item categories
1447 : parrello 1.2
1448 : parrello 1.93 Reference to a list of tracing category names. These should be names of
1449 :     packages whose internal workings will need to be debugged to get the
1450 :     command working.
1451 : olson 1.1
1452 : parrello 1.93 =item options
1453 : olson 1.1
1454 : parrello 1.93 Reference to a hash containing the legal options for the current command mapped
1455 :     to their default values and descriptions. The user can override the defaults
1456 :     by specifying the options as command-line switches prefixed by a hyphen.
1457 :     Tracing-related options may be added to this hash. If the C<-h> option is
1458 :     specified on the command line, the option descriptions will be used to
1459 :     explain the options. To turn off tracing to the standard output, add a
1460 :     minus sign to the value for C<trace> (see above).
1461 : olson 1.1
1462 : parrello 1.93 =item parmHelp
1463 : olson 1.1
1464 : parrello 1.93 A string that vaguely describes the positional parameters. This is used
1465 :     if the user specifies the C<-h> option.
1466 : olson 1.1
1467 : parrello 1.93 =item argv
1468 : olson 1.1
1469 : parrello 1.93 List of command line parameters, including the option switches, which must
1470 :     precede the positional parameters and be prefixed by a hyphen.
1471 : olson 1.1
1472 :     =item RETURN
1473 :    
1474 : parrello 1.93 Returns a list. The first element of the list is the reference to a hash that
1475 :     maps the command-line option switches to their values. These will either be the
1476 :     default values or overrides specified on the command line. The remaining
1477 :     elements of the list are the position parameters, in order.
1478 : olson 1.1
1479 :     =back
1480 :    
1481 :     =cut
1482 :    
1483 : parrello 1.93 sub StandardSetup {
1484 :     # Get the parameters.
1485 :     my ($categories, $options, $parmHelp, @argv) = @_;
1486 :     # Get the default tracing key.
1487 :     my $tkey = EmergencyKey();
1488 :     # Add the tracing options.
1489 :     if (! exists $options->{trace}) {
1490 :     $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1491 :     }
1492 :     $options->{sql} = [0, "turn on SQL tracing"];
1493 :     $options->{help} = [0, "display command-line options"];
1494 :     $options->{user} = [$tkey, "tracing key"];
1495 :     $options->{background} = [0, "spool standard and error output"];
1496 :     # Create a parsing hash from the options hash. The parsing hash
1497 :     # contains the default values rather than the default value
1498 :     # and the description. While we're at it, we'll memorize the
1499 :     # length of the longest option name.
1500 :     my $longestName = 0;
1501 :     my %parseOptions = ();
1502 :     for my $key (keys %{$options}) {
1503 :     if (length $key > $longestName) {
1504 :     $longestName = length $key;
1505 :     }
1506 :     $parseOptions{$key} = $options->{$key}->[0];
1507 :     }
1508 :     # Parse the command line.
1509 :     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1510 :     # Get the logfile suffix.
1511 :     my $suffix = $retOptions->{user};
1512 :     # Check for background mode.
1513 :     if ($retOptions->{background}) {
1514 :     my $outFileName = "$FIG_Config::temp/out$suffix.log";
1515 :     my $errFileName = "$FIG_Config::temp/err$suffix.log";
1516 :     open STDOUT, ">$outFileName";
1517 :     open STDERR, ">$errFileName";
1518 :     # Check for phone support. If we have phone support and a phone number,
1519 :     # we want to turn it on.
1520 :     if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1521 :     $retOptions->{phone} = $ENV{PHONE};
1522 :     }
1523 :     }
1524 :     # Now we want to set up tracing. First, we need to know if the user
1525 :     # wants emergency tracing.
1526 :     if ($retOptions->{trace} eq 'E') {
1527 :     ETracing($retOptions->{user});
1528 :     } else {
1529 :     # Here the tracing is controlled from the command line.
1530 :     my @cats = @{$categories};
1531 :     if ($retOptions->{sql}) {
1532 :     push @cats, "SQL";
1533 :     }
1534 :     # Add the default categories.
1535 :     push @cats, "Tracer";
1536 :     # Next, we create the category string by joining the categories.
1537 :     my $cats = join(" ", @cats);
1538 :     # Check to determine whether or not the caller wants to turn off tracing
1539 :     # to the standard output.
1540 :     my $traceLevel = $retOptions->{trace};
1541 :     my $textOKFlag = 1;
1542 :     if ($traceLevel =~ /^(.)-/) {
1543 :     $traceLevel = $1;
1544 :     $textOKFlag = 0;
1545 :     }
1546 :     # Now we set up the trace mode.
1547 :     my $traceMode;
1548 :     # Verify that we can open a file in the FIG temporary directory.
1549 :     my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1550 :     if (open TESTTRACE, ">$traceFileName") {
1551 :     # Here we can trace to a file.
1552 :     $traceMode = ">$traceFileName";
1553 :     if ($textOKFlag) {
1554 :     # Echo to standard output if the text-OK flag is set.
1555 :     $traceMode = "+$traceMode";
1556 :     }
1557 :     # Close the test file.
1558 :     close TESTTRACE;
1559 :     } else {
1560 :     # Here we can't trace to a file. We trace to the standard output if it's
1561 :     # okay, and the error log otherwise.
1562 :     if ($textOKFlag) {
1563 :     $traceMode = "TEXT";
1564 : parrello 1.12 } else {
1565 : parrello 1.93 $traceMode = "WARN";
1566 : parrello 1.12 }
1567 :     }
1568 : parrello 1.93 # Now set up the tracing.
1569 :     TSetup("$traceLevel $cats", $traceMode);
1570 :     }
1571 :     # Check for the "help" option. If it is specified, dump the command-line
1572 :     # options and exit the program.
1573 :     if ($retOptions->{help}) {
1574 :     $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1575 :     print "$1 [options] $parmHelp\n";
1576 :     for my $key (sort keys %{$options}) {
1577 :     my $name = Pad($key, $longestName, 0, ' ');
1578 :     my $desc = $options->{$key}->[1];
1579 :     if ($options->{$key}->[0]) {
1580 :     $desc .= " (default " . $options->{$key}->[0] . ")";
1581 :     }
1582 :     print " $name $desc\n";
1583 : parrello 1.36 }
1584 : parrello 1.93 exit(0);
1585 :     }
1586 :     # Trace the options, if applicable.
1587 :     if (T(3)) {
1588 :     my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1589 :     Trace("Selected options: " . join(", ", sort @parms) . ".");
1590 : parrello 1.3 }
1591 : parrello 1.93 # Return the parsed parameters.
1592 :     return ($retOptions, @retParameters);
1593 : olson 1.1 }
1594 :    
1595 : parrello 1.93 =head3 ReadOptions
1596 : olson 1.1
1597 : parrello 1.93 my %options = Tracer::ReadOptions($fileName);
1598 : olson 1.1
1599 : parrello 1.93 Read a set of options from a file. Each option is encoded in a line of text that has the
1600 :     format
1601 : olson 1.1
1602 : parrello 1.93 I<optionName>C<=>I<optionValue>C<; >I<comment>
1603 : olson 1.1
1604 : parrello 1.93 The option name must consist entirely of letters, digits, and the punctuation characters
1605 :     C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1606 :     character is a semi-colon will be ignored. The return hash will map each option name to
1607 :     the corresponding option value.
1608 : olson 1.1
1609 :     =over 4
1610 :    
1611 : parrello 1.93 =item fileName
1612 : olson 1.1
1613 : parrello 1.93 Name of the file containing the option data.
1614 : olson 1.1
1615 :     =item RETURN
1616 :    
1617 : parrello 1.93 Returns a hash mapping the option names specified in the file to their corresponding option
1618 :     value.
1619 : olson 1.1
1620 :     =back
1621 :    
1622 :     =cut
1623 :    
1624 : parrello 1.93 sub ReadOptions {
1625 : parrello 1.12 # Get the parameters.
1626 : parrello 1.93 my ($fileName) = @_;
1627 :     # Open the file.
1628 :     (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1629 :     # Count the number of records read.
1630 :     my ($records, $comments) = 0;
1631 :     # Create the return hash.
1632 :     my %retVal = ();
1633 :     # Loop through the file, accumulating key-value pairs.
1634 :     while (my $line = <CONFIGFILE>) {
1635 :     # Denote we've read a line.
1636 :     $records++;
1637 :     # Determine the line type.
1638 :     if ($line =~ /^\s*[\n\r]/) {
1639 :     # A blank line is a comment.
1640 :     $comments++;
1641 :     } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1642 :     # Here we have an option assignment.
1643 :     retVal{$1} = $2;
1644 :     } elsif ($line =~ /^\s*;/) {
1645 :     # Here we have a text comment.
1646 :     $comments++;
1647 : parrello 1.12 } else {
1648 : parrello 1.93 # Here we have an invalid line.
1649 :     Trace("Invalid option statement in record $records.") if T(0);
1650 : parrello 1.12 }
1651 :     }
1652 : parrello 1.93 # Return the hash created.
1653 :     return %retVal;
1654 : olson 1.1 }
1655 :    
1656 : parrello 1.93 =head3 GetOptions
1657 : parrello 1.9
1658 : parrello 1.93 Tracer::GetOptions(\%defaults, \%options);
1659 : parrello 1.9
1660 : parrello 1.93 Merge a specified set of options into a table of defaults. This method takes two hash references
1661 :     as input and uses the data from the second to update the first. If the second does not exist,
1662 :     there will be no effect. An error will be thrown if one of the entries in the second hash does not
1663 :     exist in the first.
1664 : parrello 1.9
1665 : parrello 1.93 Consider the following example.
1666 : parrello 1.9
1667 : parrello 1.93 my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1668 : parrello 1.9
1669 : parrello 1.93 In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1670 :     B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1671 :     B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1672 :     the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1673 :     will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1674 : parrello 1.9
1675 : parrello 1.93 {databaseType => 'Oracle'}
1676 : parrello 1.9
1677 : parrello 1.93 an error will occur because the B<databaseType> option does not exist.
1678 : parrello 1.9
1679 : parrello 1.93 =over 4
1680 : parrello 1.9
1681 : parrello 1.93 =item defaults
1682 : parrello 1.9
1683 : parrello 1.93 Table of default option values.
1684 : parrello 1.9
1685 : parrello 1.93 =item options
1686 : olson 1.1
1687 : parrello 1.93 Table of overrides, if any.
1688 : olson 1.1
1689 :     =item RETURN
1690 :    
1691 : parrello 1.93 Returns a reference to the default table passed in as the first parameter.
1692 : olson 1.1
1693 :     =back
1694 :    
1695 :     =cut
1696 :    
1697 : parrello 1.93 sub GetOptions {
1698 :     # Get the parameters.
1699 :     my ($defaults, $options) = @_;
1700 :     # Check for overrides.
1701 :     if ($options) {
1702 :     # Loop through the overrides.
1703 :     while (my ($option, $setting) = each %{$options}) {
1704 :     # Insure this override exists.
1705 :     if (!exists $defaults->{$option}) {
1706 :     croak "Unrecognized option $option encountered.";
1707 : parrello 1.12 } else {
1708 : parrello 1.93 # Apply the override.
1709 :     $defaults->{$option} = $setting;
1710 : parrello 1.12 }
1711 :     }
1712 :     }
1713 : parrello 1.93 # Return the merged table.
1714 :     return $defaults;
1715 : olson 1.1 }
1716 :    
1717 : parrello 1.93 =head3 MergeOptions
1718 : olson 1.1
1719 : parrello 1.93 Tracer::MergeOptions(\%table, \%defaults);
1720 : olson 1.1
1721 : parrello 1.93 Merge default values into a hash table. This method looks at the key-value pairs in the
1722 :     second (default) hash, and if a matching key is not found in the first hash, the default
1723 :     pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1724 :     checking and no return value.
1725 : olson 1.1
1726 :     =over 4
1727 :    
1728 : parrello 1.93 =item table
1729 : olson 1.1
1730 : parrello 1.93 Hash table to be updated with the default values.
1731 : olson 1.1
1732 : parrello 1.93 =item defaults
1733 : olson 1.1
1734 : parrello 1.93 Default values to be merged into the first hash table if they are not already present.
1735 : olson 1.1
1736 :     =back
1737 :    
1738 :     =cut
1739 :    
1740 : parrello 1.93 sub MergeOptions {
1741 :     # Get the parameters.
1742 :     my ($table, $defaults) = @_;
1743 :     # Loop through the defaults.
1744 :     while (my ($key, $value) = each %{$defaults}) {
1745 :     if (!exists $table->{$key}) {
1746 :     $table->{$key} = $value;
1747 :     }
1748 : parrello 1.12 }
1749 : olson 1.1 }
1750 :    
1751 : parrello 1.93 =head3 ParseCommand
1752 : olson 1.1
1753 : parrello 1.93 my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1754 : olson 1.1
1755 : parrello 1.93 Parse a command line consisting of a list of parameters. The initial parameters may be option
1756 :     specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1757 :     off and merged into a table of default options. The remainder of the command line is
1758 :     returned as a list of positional arguments. For example, consider the following invocation.
1759 : olson 1.1
1760 : parrello 1.93 my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1761 : olson 1.1
1762 : parrello 1.93 In this case, the list @words will be treated as a command line and there are two options available,
1763 :     B<errors> and B<logFile>. If @words has the following format
1764 : olson 1.1
1765 : parrello 1.93 -logFile=error.log apple orange rutabaga
1766 : olson 1.1
1767 : parrello 1.93 then at the end of the invocation, C<$options> will be
1768 : olson 1.1
1769 : parrello 1.93 { errors => 0, logFile => 'error.log' }
1770 : olson 1.1
1771 : parrello 1.93 and C<@arguments> will contain
1772 : olson 1.1
1773 : parrello 1.93 apple orange rutabaga
1774 : olson 1.1
1775 : parrello 1.93 The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1776 :     support for quote characters. Options can be specified with single or double hyphens.
1777 : parrello 1.54
1778 :     =over 4
1779 :    
1780 : parrello 1.93 =item optionTable
1781 : parrello 1.54
1782 : parrello 1.93 Table of default options.
1783 : parrello 1.54
1784 : parrello 1.93 =item inputList
1785 : parrello 1.54
1786 : parrello 1.93 List of words on the command line.
1787 : parrello 1.54
1788 :     =item RETURN
1789 :    
1790 : parrello 1.93 Returns a reference to the option table and a list of the positional arguments.
1791 : parrello 1.54
1792 :     =back
1793 :    
1794 :     =cut
1795 :    
1796 : parrello 1.93 sub ParseCommand {
1797 : parrello 1.54 # Get the parameters.
1798 : parrello 1.93 my ($optionTable, @inputList) = @_;
1799 :     # Process any options in the input list.
1800 :     my %overrides = ();
1801 :     while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1802 :     # Get the current option.
1803 :     my $arg = shift @inputList;
1804 :     # Pull out the option name.
1805 :     $arg =~ /^--?([^=]*)/g;
1806 :     my $name = $1;
1807 :     # Check for an option value.
1808 :     if ($arg =~ /\G=(.*)$/g) {
1809 :     # Here we have a value for the option.
1810 :     $overrides{$name} = UnEscape($1);
1811 :     } else {
1812 :     # Here there is no value, so we use 1.
1813 :     $overrides{$name} = 1;
1814 :     }
1815 :     }
1816 :     # Merge the options into the defaults.
1817 :     GetOptions($optionTable, \%overrides);
1818 :     # Translate the remaining parameters.
1819 :     my @retVal = ();
1820 :     for my $inputParm (@inputList) {
1821 :     push @retVal, UnEscape($inputParm);
1822 : parrello 1.54 }
1823 : parrello 1.93 # Return the results.
1824 :     return ($optionTable, @retVal);
1825 : parrello 1.54 }
1826 :    
1827 : parrello 1.93
1828 :     =head2 File Utility Methods
1829 :    
1830 : olson 1.1 =head3 GetFile
1831 :    
1832 : parrello 1.92 my @fileContents = Tracer::GetFile($fileName);
1833 : olson 1.1
1834 : parrello 1.35 or
1835 :    
1836 : parrello 1.92 my $fileContents = Tracer::GetFile($fileName);
1837 : parrello 1.35
1838 :     Return the entire contents of a file. In list context, line-ends are removed and
1839 :     each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1840 : olson 1.1
1841 :     =over 4
1842 :    
1843 :     =item fileName
1844 :    
1845 :     Name of the file to read.
1846 :    
1847 :     =item RETURN
1848 :    
1849 : parrello 1.6 In a list context, returns the entire file as a list with the line terminators removed.
1850 : parrello 1.39 In a scalar context, returns the entire file as a string. If an error occurs opening
1851 :     the file, an empty list will be returned.
1852 : olson 1.1
1853 :     =back
1854 :    
1855 :     =cut
1856 :    
1857 :     sub GetFile {
1858 : parrello 1.12 # Get the parameters.
1859 :     my ($fileName) = @_;
1860 :     # Declare the return variable.
1861 :     my @retVal = ();
1862 :     # Open the file for input.
1863 : parrello 1.60 my $handle = Open(undef, "<$fileName");
1864 :     # Read the whole file into the return variable, stripping off any terminator
1865 :     # characters.
1866 :     my $lineCount = 0;
1867 :     while (my $line = <$handle>) {
1868 :     $lineCount++;
1869 :     $line = Strip($line);
1870 :     push @retVal, $line;
1871 :     }
1872 :     # Close it.
1873 :     close $handle;
1874 :     my $actualLines = @retVal;
1875 : parrello 1.77 Trace("$actualLines lines read from file $fileName.") if T(File => 2);
1876 : parrello 1.12 # Return the file's contents in the desired format.
1877 : parrello 1.9 if (wantarray) {
1878 : parrello 1.12 return @retVal;
1879 : parrello 1.6 } else {
1880 :     return join "\n", @retVal;
1881 :     }
1882 : olson 1.1 }
1883 :    
1884 : parrello 1.60 =head3 PutFile
1885 :    
1886 : parrello 1.92 Tracer::PutFile($fileName, \@lines);
1887 : parrello 1.60
1888 :     Write out a file from a list of lines of text.
1889 :    
1890 :     =over 4
1891 :    
1892 :     =item fileName
1893 :    
1894 :     Name of the output file.
1895 :    
1896 :     =item lines
1897 :    
1898 :     Reference to a list of text lines. The lines will be written to the file in order, with trailing
1899 : parrello 1.66 new-line characters. Alternatively, may be a string, in which case the string will be written without
1900 :     modification.
1901 : parrello 1.60
1902 :     =back
1903 :    
1904 :     =cut
1905 :    
1906 :     sub PutFile {
1907 :     # Get the parameters.
1908 :     my ($fileName, $lines) = @_;
1909 :     # Open the output file.
1910 :     my $handle = Open(undef, ">$fileName");
1911 : parrello 1.77 # Count the lines written.
1912 : parrello 1.66 if (ref $lines ne 'ARRAY') {
1913 :     # Here we have a scalar, so we write it raw.
1914 :     print $handle $lines;
1915 : parrello 1.77 Trace("Scalar put to file $fileName.") if T(File => 3);
1916 : parrello 1.66 } else {
1917 :     # Write the lines one at a time.
1918 : parrello 1.77 my $count = 0;
1919 : parrello 1.66 for my $line (@{$lines}) {
1920 :     print $handle "$line\n";
1921 : parrello 1.77 $count++;
1922 : parrello 1.66 }
1923 : parrello 1.77 Trace("$count lines put to file $fileName.") if T(File => 3);
1924 : parrello 1.60 }
1925 :     # Close the output file.
1926 :     close $handle;
1927 :     }
1928 :    
1929 : parrello 1.93 =head3 ParseRecord
1930 : olson 1.1
1931 : parrello 1.93 my @fields = Tracer::ParseRecord($line);
1932 : olson 1.1
1933 : parrello 1.93 Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1934 :     and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1935 :     These will automatically be converted.
1936 : olson 1.1
1937 :     =over 4
1938 :    
1939 : parrello 1.93 =item line
1940 :    
1941 :     Line of data containing the tab-delimited fields.
1942 :    
1943 :     =item RETURN
1944 : olson 1.1
1945 : parrello 1.93 Returns a list of the fields found in the data line.
1946 : olson 1.1
1947 :     =back
1948 :    
1949 :     =cut
1950 :    
1951 : parrello 1.93 sub ParseRecord {
1952 : parrello 1.12 # Get the parameter.
1953 : parrello 1.93 my ($line) = @_;
1954 :     # Remove the trailing new-line, if any.
1955 :     chomp $line;
1956 :     # Split the line read into pieces using the tab character.
1957 :     my @retVal = split /\t/, $line;
1958 :     # Trim and fix the escapes in each piece.
1959 :     for my $value (@retVal) {
1960 :     # Trim leading whitespace.
1961 :     $value =~ s/^\s+//;
1962 :     # Trim trailing whitespace.
1963 :     $value =~ s/\s+$//;
1964 :     # Delete the carriage returns.
1965 :     $value =~ s/\r//g;
1966 :     # Convert the escapes into their real values.
1967 :     $value =~ s/\\t/"\t"/ge;
1968 :     $value =~ s/\\n/"\n"/ge;
1969 :     }
1970 :     # Return the result.
1971 :     return @retVal;
1972 :     }
1973 :    
1974 :     =head3 Merge
1975 :    
1976 :     my @mergedList = Tracer::Merge(@inputList);
1977 :    
1978 :     Sort a list of strings and remove duplicates.
1979 :    
1980 :     =over 4
1981 :    
1982 :     =item inputList
1983 :    
1984 :     List of scalars to sort and merge.
1985 :    
1986 :     =item RETURN
1987 :    
1988 :     Returns a list containing the same elements sorted in ascending order with duplicates
1989 :     removed.
1990 :    
1991 :     =back
1992 :    
1993 :     =cut
1994 :    
1995 :     sub Merge {
1996 :     # Get the input list in sort order.
1997 :     my @inputList = sort @_;
1998 :     # Only proceed if the list has at least two elements.
1999 :     if (@inputList > 1) {
2000 :     # Now we want to move through the list splicing out duplicates.
2001 :     my $i = 0;
2002 :     while ($i < @inputList) {
2003 :     # Get the current entry.
2004 :     my $thisEntry = $inputList[$i];
2005 :     # Find out how many elements duplicate the current entry.
2006 :     my $j = $i + 1;
2007 :     my $dup1 = $i + 1;
2008 :     while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2009 :     # If the number is nonzero, splice out the duplicates found.
2010 :     if ($j > $dup1) {
2011 :     splice @inputList, $dup1, $j - $dup1;
2012 : parrello 1.14 }
2013 : parrello 1.93 # Now the element at position $dup1 is different from the element before it
2014 :     # at position $i. We push $i forward one position and start again.
2015 :     $i++;
2016 : parrello 1.14 }
2017 : parrello 1.12 }
2018 : parrello 1.93 # Return the merged list.
2019 :     return @inputList;
2020 : olson 1.1 }
2021 :    
2022 : parrello 1.93 =head3 Open
2023 : olson 1.1
2024 : parrello 1.93 my $handle = Open($fileHandle, $fileSpec, $message);
2025 : olson 1.1
2026 : parrello 1.93 Open a file.
2027 : olson 1.1
2028 : parrello 1.93 The I<$fileSpec> is essentially the second argument of the PERL C<open>
2029 :     function. The mode is specified using Unix-like shell information. So, for
2030 :     example,
2031 : olson 1.1
2032 : parrello 1.93 Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2033 : olson 1.1
2034 : parrello 1.93 would open for output appended to the specified file, and
2035 : olson 1.1
2036 : parrello 1.93 Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2037 : olson 1.1
2038 : parrello 1.93 would open a pipe that sorts the records written and removes duplicates. Note
2039 :     the use of file handle syntax in the Open call. To use anonymous file handles,
2040 :     code as follows.
2041 : olson 1.1
2042 : parrello 1.93 my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2043 : olson 1.1
2044 : parrello 1.93 The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2045 :     the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2046 :     failed open will throw an exception and the third parameter will be used to construct
2047 :     an error message. If the parameter is omitted, a standard message is constructed
2048 :     using the file spec.
2049 : olson 1.1
2050 : parrello 1.93 Could not open "/usr/spool/news/twitlog"
2051 : olson 1.1
2052 : parrello 1.93 Note that the mode characters are automatically cleaned from the file name.
2053 :     The actual error message from the file system will be captured and appended to the
2054 :     message in any case.
2055 : parrello 1.6
2056 : parrello 1.93 Could not open "/usr/spool/news/twitlog": file not found.
2057 : parrello 1.6
2058 : parrello 1.93 In some versions of PERL the only error message we get is a number, which
2059 :     corresponds to the C++ C<errno> value.
2060 : parrello 1.6
2061 : parrello 1.93 Could not open "/usr/spool/news/twitlog": 6.
2062 : parrello 1.6
2063 : parrello 1.93 =over 4
2064 : parrello 1.6
2065 : parrello 1.93 =item fileHandle
2066 : parrello 1.6
2067 : parrello 1.93 File handle. If this parameter is C<undef>, a file handle will be generated
2068 :     and returned as the value of this method.
2069 : olson 1.1
2070 : parrello 1.93 =item fileSpec
2071 : olson 1.1
2072 : parrello 1.93 File name and mode, as per the PERL C<open> function.
2073 : olson 1.1
2074 : parrello 1.93 =item message (optional)
2075 : olson 1.1
2076 : parrello 1.93 Error message to use if the open fails. If omitted, a standard error message
2077 :     will be generated. In either case, the error information from the file system
2078 :     is appended to the message. To specify a conditional open that does not throw
2079 :     an error if it fails, use C<0>.
2080 : olson 1.1
2081 : parrello 1.93 =item RETURN
2082 : olson 1.1
2083 : parrello 1.93 Returns the name of the file handle assigned to the file, or C<undef> if the
2084 :     open failed.
2085 : olson 1.1
2086 :     =back
2087 :    
2088 :     =cut
2089 :    
2090 : parrello 1.93 sub Open {
2091 : parrello 1.12 # Get the parameters.
2092 : parrello 1.93 my ($fileHandle, $fileSpec, $message) = @_;
2093 :     # Attempt to open the file.
2094 :     my $rv = open $fileHandle, $fileSpec;
2095 :     # If the open failed, generate an error message.
2096 :     if (! $rv) {
2097 :     # Save the system error message.
2098 :     my $sysMessage = $!;
2099 :     # See if we need a default message.
2100 :     if (!$message) {
2101 :     # Clean any obvious mode characters and leading spaces from the
2102 :     # filename.
2103 :     my ($fileName) = FindNamePart($fileSpec);
2104 :     $message = "Could not open \"$fileName\"";
2105 :     }
2106 :     # Terminate with an error using the supplied message and the
2107 :     # error message from the file system.
2108 :     Confess("$message: $!");
2109 : parrello 1.12 }
2110 : parrello 1.93 # Return the file handle.
2111 :     return $fileHandle;
2112 : olson 1.1 }
2113 :    
2114 : parrello 1.93 =head3 FindNamePart
2115 :    
2116 :     my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2117 :    
2118 :     Extract the portion of a file specification that contains the file name.
2119 :    
2120 :     A file specification is the string passed to an C<open> call. It specifies the file
2121 :     mode and name. In a truly complex situation, it can specify a pipe sequence. This
2122 :     method assumes that the file name is whatever follows the first angle bracket
2123 :     sequence. So, for example, in the following strings the file name is
2124 :     C</usr/fig/myfile.txt>.
2125 : parrello 1.5
2126 : parrello 1.93 >>/usr/fig/myfile.txt
2127 :     </usr/fig/myfile.txt
2128 :     | sort -u > /usr/fig/myfile.txt
2129 : parrello 1.5
2130 : parrello 1.93 If the method cannot find a file name using its normal methods, it will return the
2131 :     whole incoming string.
2132 : parrello 1.5
2133 :     =over 4
2134 :    
2135 : parrello 1.93 =item fileSpec
2136 : parrello 1.5
2137 : parrello 1.93 File specification string from which the file name is to be extracted.
2138 : parrello 1.5
2139 :     =item RETURN
2140 :    
2141 : parrello 1.93 Returns a three-element list. The first element contains the file name portion of
2142 :     the specified string, or the whole string if a file name cannot be found via normal
2143 :     methods. The second element contains the start position of the file name portion and
2144 :     the third element contains the length.
2145 : parrello 1.5
2146 :     =back
2147 :    
2148 :     =cut
2149 : parrello 1.93 #: Return Type $;
2150 :     sub FindNamePart {
2151 :     # Get the parameters.
2152 :     my ($fileSpec) = @_;
2153 :     # Default to the whole input string.
2154 :     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2155 :     # Parse out the file name if we can.
2156 :     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2157 :     $retVal = $2;
2158 :     $len = length $retVal;
2159 :     $pos = (length $fileSpec) - (length $3) - $len;
2160 : parrello 1.12 }
2161 : parrello 1.93 # Return the result.
2162 :     return ($retVal, $pos, $len);
2163 : parrello 1.5 }
2164 :    
2165 : parrello 1.93 =head3 OpenDir
2166 : parrello 1.5
2167 : parrello 1.93 my @files = OpenDir($dirName, $filtered, $flag);
2168 : parrello 1.5
2169 : parrello 1.93 Open a directory and return all the file names. This function essentially performs
2170 :     the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2171 :     set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2172 :     or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2173 :     filtered out of the return list. If the directory does not open and I<$flag> is not
2174 :     set, an exception is thrown. So, for example,
2175 : parrello 1.5
2176 : parrello 1.93 my @files = OpenDir("/Volumes/fig/contigs", 1);
2177 : parrello 1.5
2178 : parrello 1.93 is effectively the same as
2179 : parrello 1.5
2180 : parrello 1.93 opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2181 :     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2182 : parrello 1.5
2183 : parrello 1.93 Similarly, the following code
2184 : parrello 1.5
2185 : parrello 1.93 my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2186 : parrello 1.5
2187 : parrello 1.93 Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2188 :     automatically returns an empty list if the directory fails to open.
2189 : parrello 1.5
2190 : parrello 1.93 =over 4
2191 : parrello 1.5
2192 : parrello 1.93 =item dirName
2193 : parrello 1.5
2194 : parrello 1.93 Name of the directory to open.
2195 : parrello 1.5
2196 : parrello 1.93 =item filtered
2197 : parrello 1.5
2198 : parrello 1.93 TRUE if files whose names begin with a period (C<.>) should be automatically removed
2199 :     from the list, else FALSE.
2200 : parrello 1.5
2201 : parrello 1.93 =item flag
2202 : parrello 1.5
2203 : parrello 1.93 TRUE if a failure to open is okay, else FALSE
2204 : parrello 1.5
2205 : parrello 1.93 =back
2206 : parrello 1.5
2207 : parrello 1.93 =cut
2208 :     #: Return Type @;
2209 :     sub OpenDir {
2210 :     # Get the parameters.
2211 :     my ($dirName, $filtered, $flag) = @_;
2212 :     # Declare the return variable.
2213 :     my @retVal = ();
2214 :     # Open the directory.
2215 :     if (opendir(my $dirHandle, $dirName)) {
2216 :     # The directory opened successfully. Get the appropriate list according to the
2217 :     # strictures of the filter parameter.
2218 :     if ($filtered) {
2219 :     @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2220 :     } else {
2221 :     @retVal = readdir $dirHandle;
2222 :     }
2223 :     } elsif (! $flag) {
2224 :     # Here the directory would not open and it's considered an error.
2225 :     Confess("Could not open directory $dirName.");
2226 :     }
2227 :     # Return the result.
2228 :     return @retVal;
2229 :     }
2230 : parrello 1.5
2231 :    
2232 : parrello 1.93 =head3 Insure
2233 : parrello 1.5
2234 : parrello 1.93 Insure($dirName, $chmod);
2235 : parrello 1.5
2236 : parrello 1.93 Insure a directory is present.
2237 : parrello 1.5
2238 : parrello 1.93 =over 4
2239 : parrello 1.5
2240 : parrello 1.93 =item dirName
2241 : olson 1.1
2242 : parrello 1.93 Name of the directory to check. If it does not exist, it will be created.
2243 : parrello 1.7
2244 : parrello 1.93 =item chmod (optional)
2245 : parrello 1.7
2246 : parrello 1.93 Security privileges to be given to the directory if it is created.
2247 : parrello 1.7
2248 : parrello 1.93 =back
2249 : parrello 1.7
2250 :     =cut
2251 :    
2252 : parrello 1.93 sub Insure {
2253 :     my ($dirName, $chmod) = @_;
2254 :     if (! -d $dirName) {
2255 :     Trace("Creating $dirName directory.") if T(2);
2256 :     eval {
2257 :     mkpath $dirName;
2258 :     # If we have permissions specified, set them here.
2259 :     if (defined($chmod)) {
2260 :     chmod $chmod, $dirName;
2261 :     }
2262 :     };
2263 :     if ($@) {
2264 :     Confess("Error creating $dirName: $@");
2265 :     }
2266 : parrello 1.12 }
2267 : parrello 1.9 }
2268 :    
2269 : parrello 1.93 =head3 ChDir
2270 : parrello 1.9
2271 : parrello 1.93 ChDir($dirName);
2272 : parrello 1.9
2273 : parrello 1.93 Change to the specified directory.
2274 : parrello 1.9
2275 :     =over 4
2276 :    
2277 : parrello 1.93 =item dirName
2278 : parrello 1.9
2279 : parrello 1.93 Name of the directory to which we want to change.
2280 : parrello 1.9
2281 :     =back
2282 :    
2283 :     =cut
2284 :    
2285 : parrello 1.93 sub ChDir {
2286 :     my ($dirName) = @_;
2287 :     if (! -d $dirName) {
2288 :     Confess("Cannot change to directory $dirName: no such directory.");
2289 :     } else {
2290 :     Trace("Changing to directory $dirName.") if T(File => 4);
2291 :     my $okFlag = chdir $dirName;
2292 :     if (! $okFlag) {
2293 :     Confess("Error switching to directory $dirName.");
2294 :     }
2295 :     }
2296 : parrello 1.9 }
2297 :    
2298 : parrello 1.93 =head3 SetPermissions
2299 :    
2300 :     Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2301 : parrello 1.9
2302 : parrello 1.93 Set the permissions for a directory and all the files and folders inside it.
2303 :     In addition, the group ownership will be changed to the specified value.
2304 : parrello 1.9
2305 : parrello 1.93 This method is more vulnerable than most to permission and compatability
2306 :     problems, so it does internal error recovery.
2307 : parrello 1.9
2308 :     =over 4
2309 :    
2310 : parrello 1.93 =item dirName
2311 :    
2312 :     Name of the directory to process.
2313 :    
2314 :     =item group
2315 : parrello 1.9
2316 : parrello 1.93 Name of the group to be assigned.
2317 : parrello 1.9
2318 : parrello 1.93 =item mask
2319 : parrello 1.9
2320 : parrello 1.93 Permission mask. Bits that are C<1> in this mask will be ORed into the
2321 :     permission bits of any file or directory that does not already have them
2322 :     set to 1.
2323 : parrello 1.9
2324 : parrello 1.93 =item otherMasks
2325 : parrello 1.9
2326 : parrello 1.93 Map of search patterns to permission masks. If a directory name matches
2327 :     one of the patterns, that directory and all its members and subdirectories
2328 :     will be assigned the new pattern. For example, the following would
2329 :     assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2330 : parrello 1.9
2331 : parrello 1.93 Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2332 : parrello 1.9
2333 : parrello 1.93 The list is ordered, so the following would use 0777 for C<tmp1> and
2334 :     0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2335 : parrello 1.22
2336 : parrello 1.93 Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2337 :     '^tmp' => 0666);
2338 : parrello 1.9
2339 : parrello 1.93 Note that the pattern matches are all case-insensitive, and only directory
2340 :     names are matched, not file names.
2341 : parrello 1.9
2342 :     =back
2343 :    
2344 :     =cut
2345 :    
2346 : parrello 1.93 sub SetPermissions {
2347 : parrello 1.12 # Get the parameters.
2348 : parrello 1.93 my ($dirName, $group, $mask, @otherMasks) = @_;
2349 :     # Set up for error recovery.
2350 :     eval {
2351 :     # Switch to the specified directory.
2352 :     ChDir($dirName);
2353 :     # Get the group ID.
2354 :     my $gid = getgrnam($group);
2355 :     # Get the mask for tracing.
2356 :     my $traceMask = sprintf("%04o", $mask) . "($mask)";
2357 :     Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2358 :     my $fixCount = 0;
2359 :     my $lookCount = 0;
2360 :     # @dirs will be a stack of directories to be processed.
2361 :     my @dirs = (getcwd());
2362 :     while (scalar(@dirs) > 0) {
2363 :     # Get the current directory.
2364 :     my $dir = pop @dirs;
2365 :     # Check for a match to one of the specified directory names. To do
2366 :     # that, we need to pull the individual part of the name off of the
2367 :     # whole path.
2368 :     my $simpleName = $dir;
2369 :     if ($dir =~ m!/([^/]+)$!) {
2370 :     $simpleName = $1;
2371 :     }
2372 :     Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2373 :     # Search for a match.
2374 :     my $match = 0;
2375 :     my $i;
2376 :     for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2377 :     my $pattern = $otherMasks[$i];
2378 :     if ($simpleName =~ /$pattern/i) {
2379 :     $match = 1;
2380 :     }
2381 :     }
2382 :     # Check for a match. Note we use $i-1 because the loop added 2
2383 :     # before terminating due to the match.
2384 :     if ($match && $otherMasks[$i-1] != $mask) {
2385 :     # This directory matches one of the incoming patterns, and it's
2386 :     # a different mask, so we process it recursively with that mask.
2387 :     SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2388 :     } else {
2389 :     # Here we can process normally. Get all of the non-hidden members.
2390 :     my @submems = OpenDir($dir, 1);
2391 :     for my $submem (@submems) {
2392 :     # Get the full name.
2393 :     my $thisMem = "$dir/$submem";
2394 :     Trace("Checking member $thisMem.") if T(4);
2395 :     $lookCount++;
2396 :     if ($lookCount % 1000 == 0) {
2397 :     Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2398 :     }
2399 :     # Fix the group.
2400 :     chown -1, $gid, $thisMem;
2401 :     # Insure this member is not a symlink.
2402 :     if (! -l $thisMem) {
2403 :     # Get its info.
2404 :     my $fileInfo = stat $thisMem;
2405 :     # Only proceed if we got the info. Otherwise, it's a hard link
2406 :     # and we want to skip it anyway.
2407 :     if ($fileInfo) {
2408 :     my $fileMode = $fileInfo->mode;
2409 :     if (($fileMode & $mask) != $mask) {
2410 :     # Fix this member.
2411 :     $fileMode |= $mask;
2412 :     chmod $fileMode, $thisMem;
2413 :     $fixCount++;
2414 :     }
2415 :     # If it's a subdirectory, stack it.
2416 :     if (-d $thisMem) {
2417 :     push @dirs, $thisMem;
2418 :     }
2419 :     }
2420 :     }
2421 :     }
2422 :     }
2423 : parrello 1.12 }
2424 : parrello 1.93 Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2425 :     };
2426 :     # Check for an error.
2427 :     if ($@) {
2428 :     Confess("SetPermissions error: $@");
2429 : parrello 1.12 }
2430 : parrello 1.7 }
2431 :    
2432 : parrello 1.93 =head3 GetLine
2433 : parrello 1.29
2434 : parrello 1.93 my @data = Tracer::GetLine($handle);
2435 : parrello 1.15
2436 : parrello 1.93 Read a line of data from a tab-delimited file.
2437 : parrello 1.15
2438 :     =over 4
2439 :    
2440 : parrello 1.93 =item handle
2441 : parrello 1.15
2442 : parrello 1.93 Open file handle from which to read.
2443 : parrello 1.15
2444 :     =item RETURN
2445 :    
2446 : parrello 1.93 Returns a list of the fields in the record read. The fields are presumed to be
2447 :     tab-delimited. If we are at the end of the file, then an empty list will be
2448 :     returned. If an empty line is read, a single list item consisting of a null
2449 :     string will be returned.
2450 : parrello 1.15
2451 :     =back
2452 :    
2453 :     =cut
2454 : parrello 1.93
2455 :     sub GetLine {
2456 : parrello 1.15 # Get the parameters.
2457 : parrello 1.93 my ($handle) = @_;
2458 :     # Declare the return variable.
2459 :     my @retVal = ();
2460 :     Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2461 :     # Read from the file.
2462 :     my $line = <$handle>;
2463 :     # Only proceed if we found something.
2464 :     if (defined $line) {
2465 :     # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2466 :     # upload control and have a nonstandard EOL combination.
2467 :     $line =~ s/(\r|\n)+$//;
2468 :     # Here we do some fancy tracing to help in debugging complicated EOL marks.
2469 :     if (T(File => 4)) {
2470 :     my $escapedLine = $line;
2471 :     $escapedLine =~ s/\n/\\n/g;
2472 :     $escapedLine =~ s/\r/\\r/g;
2473 :     $escapedLine =~ s/\t/\\t/g;
2474 :     Trace("Line read: -->$escapedLine<--");
2475 :     }
2476 :     # If the line is empty, return a single empty string; otherwise, parse
2477 :     # it into fields.
2478 :     if ($line eq "") {
2479 :     push @retVal, "";
2480 :     } else {
2481 :     push @retVal, split /\t/,$line;
2482 :     }
2483 :     } else {
2484 :     # Trace the reason the read failed.
2485 :     Trace("End of file: $!") if T(File => 3);
2486 : parrello 1.15 }
2487 : parrello 1.93 # Return the result.
2488 :     return @retVal;
2489 : parrello 1.15 }
2490 :    
2491 : parrello 1.93 =head3 PutLine
2492 :    
2493 :     Tracer::PutLine($handle, \@fields, $eol);
2494 : parrello 1.35
2495 : parrello 1.93 Write a line of data to a tab-delimited file. The specified field values will be
2496 :     output in tab-separated form, with a trailing new-line.
2497 : parrello 1.35
2498 : parrello 1.93 =over 4
2499 : parrello 1.35
2500 : parrello 1.93 =item handle
2501 : parrello 1.69
2502 : parrello 1.93 Output file handle.
2503 : parrello 1.69
2504 : parrello 1.93 =item fields
2505 : parrello 1.69
2506 : parrello 1.93 List of field values.
2507 : parrello 1.69
2508 : parrello 1.93 =item eol (optional)
2509 : parrello 1.69
2510 : parrello 1.93 End-of-line character (default is "\n").
2511 : parrello 1.69
2512 :     =back
2513 : parrello 1.35
2514 :     =cut
2515 :    
2516 : parrello 1.93 sub PutLine {
2517 : parrello 1.69 # Get the parameters.
2518 : parrello 1.93 my ($handle, $fields, $eol) = @_;
2519 :     # Write the data.
2520 :     print $handle join("\t", @{$fields}) . ($eol || "\n");
2521 : parrello 1.69 }
2522 :    
2523 :    
2524 :    
2525 : parrello 1.93 =head2 Other Useful Methods
2526 :    
2527 :     =head3 ParseParm
2528 :    
2529 :     my $listValue = Tracer::ParseParm($string);
2530 :    
2531 :     Convert a parameter into a list reference. If the parameter is undefined,
2532 :     an undefined value will be returned. Otherwise, it will be parsed as a
2533 :     comma-separated list of values.
2534 : parrello 1.69
2535 :     =over 4
2536 :    
2537 : parrello 1.93 =item string
2538 :    
2539 :     Incoming string.
2540 :    
2541 :     =item RETURN
2542 : parrello 1.69
2543 : parrello 1.93 Returns a reference to a list of values, or C<undef> if the incoming value
2544 :     was undefined.
2545 : parrello 1.69
2546 :     =back
2547 :    
2548 :     =cut
2549 :    
2550 : parrello 1.93 sub ParseParm {
2551 :     # Get the parameters.
2552 :     my ($string) = @_;
2553 :     # Declare the return variable.
2554 :     my $retVal;
2555 :     # Check for data.
2556 :     if (defined $string) {
2557 :     # We have some, so split it into a list.
2558 :     $retVal = [ split /\s*,\s*/, $string];
2559 : parrello 1.72 }
2560 : parrello 1.93 # Return the result.
2561 :     return $retVal;
2562 : parrello 1.69 }
2563 :    
2564 :    
2565 :    
2566 :    
2567 : parrello 1.93 =head3 Now
2568 : parrello 1.69
2569 : parrello 1.93 my $string = Tracer::Now();
2570 : parrello 1.69
2571 : parrello 1.93 Return a displayable time stamp containing the local time.
2572 : parrello 1.69
2573 : parrello 1.93 =cut
2574 : parrello 1.69
2575 : parrello 1.93 sub Now {
2576 :     my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
2577 :     my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2578 :     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2579 :     return $retVal;
2580 :     }
2581 : parrello 1.69
2582 : parrello 1.93 # Pad a number to 2 digits.
2583 :     sub _p2 {
2584 :     my ($value) = @_;
2585 :     $value = "0$value" if ($value < 10);
2586 :     return $value;
2587 : parrello 1.69 }
2588 :    
2589 : parrello 1.93 =head3 Escape
2590 : parrello 1.69
2591 : parrello 1.93 my $codedString = Tracer::Escape($realString);
2592 : parrello 1.69
2593 : parrello 1.93 Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2594 :     replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2595 :     result is to reverse the effect of L</UnEscape>.
2596 : parrello 1.69
2597 :     =over 4
2598 :    
2599 : parrello 1.93 =item realString
2600 : parrello 1.69
2601 : parrello 1.93 String to escape.
2602 : parrello 1.69
2603 :     =item RETURN
2604 :    
2605 : parrello 1.93 Escaped equivalent of the real string.
2606 :    
2607 :     =back
2608 :    
2609 :     =cut
2610 :    
2611 :     sub Escape {
2612 :     # Get the parameter.
2613 :     my ($realString) = @_;
2614 :     # Initialize the return variable.
2615 :     my $retVal = "";
2616 :     # Loop through the parameter string, looking for sequences to escape.
2617 :     while (length $realString > 0) {
2618 :     # Look for the first sequence to escape.
2619 :     if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2620 :     # Here we found it. The text preceding the sequence is in $1. The sequence
2621 :     # itself is in $2. First, move the clear text to the return variable.
2622 :     $retVal .= $1;
2623 :     # Strip the processed section off the real string.
2624 :     $realString = substr $realString, (length $2) + (length $1);
2625 :     # Get the matched character.
2626 :     my $char = $2;
2627 :     # If we have a CR, we are done.
2628 :     if ($char ne "\r") {
2629 :     # It's not a CR, so encode the escape sequence.
2630 :     $char =~ tr/\t\n/tn/;
2631 :     $retVal .= "\\" . $char;
2632 :     }
2633 :     } else {
2634 :     # Here there are no more escape sequences. The rest of the string is
2635 :     # transferred unmodified.
2636 :     $retVal .= $realString;
2637 :     $realString = "";
2638 :     }
2639 :     }
2640 :     # Return the result.
2641 :     return $retVal;
2642 : parrello 1.69 }
2643 :    
2644 : parrello 1.93 =head3 UnEscape
2645 : parrello 1.69
2646 : parrello 1.93 my $realString = Tracer::UnEscape($codedString);
2647 : parrello 1.69
2648 : parrello 1.93 Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2649 :     a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2650 :     be deleted.
2651 : parrello 1.69
2652 :     =over 4
2653 :    
2654 : parrello 1.93 =item codedString
2655 : parrello 1.69
2656 : parrello 1.93 String to un-escape.
2657 : parrello 1.69
2658 :     =item RETURN
2659 :    
2660 : parrello 1.93 Returns a copy of the original string with the escape sequences converted to their actual
2661 :     values.
2662 : parrello 1.69
2663 :     =back
2664 :    
2665 :     =cut
2666 :    
2667 : parrello 1.93 sub UnEscape {
2668 :     # Get the parameter.
2669 :     my ($codedString) = @_;
2670 :     # Initialize the return variable.
2671 :     my $retVal = "";
2672 :     # Only proceed if the incoming string is nonempty.
2673 :     if (defined $codedString) {
2674 :     # Loop through the parameter string, looking for escape sequences. We can't do
2675 :     # translating because it causes problems with the escaped slash. ("\\t" becomes
2676 :     # "\<tab>" no matter what we do.)
2677 :     while (length $codedString > 0) {
2678 :     # Look for the first escape sequence.
2679 :     if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2680 :     # Here we found it. The text preceding the sequence is in $1. The sequence
2681 :     # itself is in $2. First, move the clear text to the return variable.
2682 :     $retVal .= $1;
2683 :     $codedString = substr $codedString, (2 + length $1);
2684 :     # Get the escape value.
2685 :     my $char = $2;
2686 :     # If we have a "\r", we are done.
2687 :     if ($char ne 'r') {
2688 :     # Here it's not an 'r', so we convert it.
2689 :     $char =~ tr/\\tn/\\\t\n/;
2690 :     $retVal .= $char;
2691 :     }
2692 :     } else {
2693 :     # Here there are no more escape sequences. The rest of the string is
2694 :     # transferred unmodified.
2695 :     $retVal .= $codedString;
2696 :     $codedString = "";
2697 :     }
2698 :     }
2699 : parrello 1.35 }
2700 : parrello 1.69 # Return the result.
2701 :     return $retVal;
2702 :     }
2703 :    
2704 : parrello 1.93 =head3 Percent
2705 : parrello 1.69
2706 : parrello 1.93 my $percent = Tracer::Percent($number, $base);
2707 : parrello 1.69
2708 : parrello 1.93 Returns the percent of the base represented by the given number. If the base
2709 :     is zero, returns zero.
2710 : parrello 1.69
2711 :     =over 4
2712 :    
2713 : parrello 1.93 =item number
2714 : parrello 1.69
2715 : parrello 1.93 Percent numerator.
2716 : parrello 1.69
2717 : parrello 1.93 =item base
2718 : parrello 1.69
2719 : parrello 1.93 Percent base.
2720 : parrello 1.69
2721 : parrello 1.93 =item RETURN
2722 : parrello 1.69
2723 : parrello 1.93 Returns the percentage of the base represented by the numerator.
2724 : parrello 1.69
2725 :     =back
2726 :    
2727 :     =cut
2728 :    
2729 : parrello 1.93 sub Percent {
2730 : parrello 1.69 # Get the parameters.
2731 : parrello 1.93 my ($number, $base) = @_;
2732 :     # Declare the return variable.
2733 :     my $retVal = 0;
2734 :     # Compute the percent.
2735 :     if ($base != 0) {
2736 :     $retVal = $number * 100 / $base;
2737 :     }
2738 :     # Return the result.
2739 :     return $retVal;
2740 : parrello 1.69 }
2741 :    
2742 : parrello 1.93 =head3 Min
2743 : parrello 1.69
2744 : parrello 1.93 my $min = Min($value1, $value2, ... $valueN);
2745 : parrello 1.69
2746 : parrello 1.93 Return the minimum argument. The arguments are treated as numbers.
2747 : parrello 1.69
2748 :     =over 4
2749 :    
2750 : parrello 1.93 =item $value1, $value2, ... $valueN
2751 : parrello 1.69
2752 : parrello 1.93 List of numbers to compare.
2753 : parrello 1.69
2754 :     =item RETURN
2755 :    
2756 : parrello 1.93 Returns the lowest number in the list.
2757 : parrello 1.69
2758 :     =back
2759 :    
2760 :     =cut
2761 :    
2762 : parrello 1.93 sub Min {
2763 :     # Get the parameters. Note that we prime the return value with the first parameter.
2764 :     my ($retVal, @values) = @_;
2765 :     # Loop through the remaining parameters, looking for the lowest.
2766 :     for my $value (@values) {
2767 :     if ($value < $retVal) {
2768 :     $retVal = $value;
2769 : parrello 1.72 }
2770 :     }
2771 : parrello 1.93 # Return the minimum found.
2772 : parrello 1.70 return $retVal;
2773 : parrello 1.35 }
2774 :    
2775 : parrello 1.93 =head3 Max
2776 :    
2777 :     my $max = Max($value1, $value2, ... $valueN);
2778 : parrello 1.69
2779 : parrello 1.93 Return the maximum argument. The arguments are treated as numbers.
2780 : parrello 1.65
2781 : parrello 1.93 =over 4
2782 : parrello 1.65
2783 : parrello 1.93 =item $value1, $value2, ... $valueN
2784 : parrello 1.65
2785 : parrello 1.93 List of numbers to compare.
2786 : parrello 1.65
2787 : parrello 1.93 =item RETURN
2788 : parrello 1.65
2789 : parrello 1.93 Returns the highest number in the list.
2790 : parrello 1.65
2791 :     =back
2792 :    
2793 :     =cut
2794 :    
2795 : parrello 1.93 sub Max {
2796 :     # Get the parameters. Note that we prime the return value with the first parameter.
2797 :     my ($retVal, @values) = @_;
2798 :     # Loop through the remaining parameters, looking for the highest.
2799 :     for my $value (@values) {
2800 :     if ($value > $retVal) {
2801 :     $retVal = $value;
2802 : parrello 1.65 }
2803 :     }
2804 : parrello 1.93 # Return the maximum found.
2805 :     return $retVal;
2806 : parrello 1.65 }
2807 :    
2808 : parrello 1.93 =head3 DebugMode
2809 : parrello 1.35
2810 : parrello 1.93 if (Tracer::DebugMode) { ...code... }
2811 : parrello 1.35
2812 : parrello 1.93 Return TRUE if debug mode has been turned on, else abort.
2813 : parrello 1.35
2814 : parrello 1.93 Certain CGI scripts are too dangerous to exist in the production
2815 :     environment. This method provides a simple way to prevent them
2816 :     from working unless they are explicitly turned on by creating a password
2817 :     cookie via the B<SetPassword> script. If debugging mode
2818 :     is not turned on, an error will occur.
2819 : parrello 1.37
2820 : parrello 1.35 =cut
2821 :    
2822 : parrello 1.93 sub DebugMode {
2823 :     # Declare the return variable.
2824 :     my $retVal = 0;
2825 :     # Check the debug configuration.
2826 :     my $password = CGI::cookie("DebugMode");
2827 :     my $encrypted = Digest::MD5::md5_hex($password);
2828 :     if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
2829 :     $retVal = 1;
2830 : parrello 1.35 } else {
2831 : parrello 1.93 # Here debug mode is off, so we generate an error.
2832 :     Confess("Cannot use this facility without logging in.");
2833 : parrello 1.35 }
2834 : parrello 1.93 # Return the determination indicator.
2835 :     return $retVal;
2836 : parrello 1.35 }
2837 :    
2838 : parrello 1.93 =head3 Strip
2839 : parrello 1.37
2840 : parrello 1.93 my $string = Tracer::Strip($line);
2841 : parrello 1.37
2842 : parrello 1.93 Strip all line terminators off a string. This is necessary when dealing with files
2843 :     that may have been transferred back and forth several times among different
2844 :     operating environments.
2845 : parrello 1.37
2846 :     =over 4
2847 :    
2848 : parrello 1.93 =item line
2849 : parrello 1.37
2850 : parrello 1.93 Line of text to be stripped.
2851 : parrello 1.37
2852 : parrello 1.93 =item RETURN
2853 : parrello 1.91
2854 : parrello 1.93 The same line of text with all the line-ending characters chopped from the end.
2855 : parrello 1.91
2856 : parrello 1.37 =back
2857 :    
2858 :     =cut
2859 :    
2860 : parrello 1.93 sub Strip {
2861 :     # Get a copy of the parameter string.
2862 :     my ($string) = @_;
2863 :     my $retVal = (defined $string ? $string : "");
2864 :     # Strip the line terminator characters.
2865 :     $retVal =~ s/(\r|\n)+$//g;
2866 :     # Return the result.
2867 :     return $retVal;
2868 : parrello 1.43 }
2869 :    
2870 : parrello 1.93 =head3 Pad
2871 : parrello 1.43
2872 : parrello 1.93 my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
2873 : parrello 1.43
2874 : parrello 1.93 Pad a string to a specified length. The pad character will be a
2875 :     space, and the padding will be on the right side unless specified
2876 :     in the third parameter.
2877 : parrello 1.43
2878 :     =over 4
2879 :    
2880 : parrello 1.93 =item string
2881 :    
2882 :     String to be padded.
2883 :    
2884 :     =item len
2885 :    
2886 :     Desired length of the padded string.
2887 :    
2888 :     =item left (optional)
2889 :    
2890 :     TRUE if the string is to be left-padded; otherwise it will be padded on the right.
2891 :    
2892 :     =item padChar (optional)
2893 :    
2894 :     Character to use for padding. The default is a space.
2895 :    
2896 :     =item RETURN
2897 : parrello 1.43
2898 : parrello 1.93 Returns a copy of the original string with the pad character added to the
2899 :     specified end so that it achieves the desired length.
2900 : parrello 1.43
2901 :     =back
2902 :    
2903 :     =cut
2904 :    
2905 : parrello 1.93 sub Pad {
2906 :     # Get the parameters.
2907 :     my ($string, $len, $left, $padChar) = @_;
2908 :     # Compute the padding character.
2909 :     if (! defined $padChar) {
2910 :     $padChar = " ";
2911 :     }
2912 :     # Compute the number of spaces needed.
2913 :     my $needed = $len - length $string;
2914 :     # Copy the string into the return variable.
2915 :     my $retVal = $string;
2916 :     # Only proceed if padding is needed.
2917 :     if ($needed > 0) {
2918 :     # Create the pad string.
2919 :     my $pad = $padChar x $needed;
2920 :     # Affix it to the return value.
2921 :     if ($left) {
2922 :     $retVal = $pad . $retVal;
2923 :     } else {
2924 :     $retVal .= $pad;
2925 : parrello 1.43 }
2926 : parrello 1.37 }
2927 : parrello 1.93 # Return the result.
2928 :     return $retVal;
2929 : parrello 1.37 }
2930 :    
2931 : parrello 1.93 =head3 EOF
2932 :    
2933 :     This is a constant that is lexically greater than any useful string.
2934 :    
2935 :     =cut
2936 :    
2937 :     sub EOF {
2938 :     return "\xFF\xFF\xFF\xFF\xFF";
2939 :     }
2940 : parrello 1.59
2941 : parrello 1.93 =head3 TICK
2942 : parrello 1.59
2943 : parrello 1.93 my @results = TICK($commandString);
2944 : parrello 1.59
2945 : parrello 1.93 Perform a back-tick operation on a command. If this is a Windows environment, any leading
2946 :     dot-slash (C<./> will be removed. So, for example, if you were doing
2947 : parrello 1.59
2948 : parrello 1.93 `./protein.cgi`
2949 : parrello 1.59
2950 : parrello 1.93 from inside a CGI script, it would work fine in Unix, but would issue an error message
2951 :     in Windows complaining that C<'.'> is not a valid command. If instead you code
2952 : parrello 1.59
2953 : parrello 1.93 TICK("./protein.cgi")
2954 : parrello 1.59
2955 : parrello 1.93 it will work correctly in both environments.
2956 : parrello 1.59
2957 : parrello 1.93 =over 4
2958 : parrello 1.59
2959 : parrello 1.93 =item commandString
2960 : parrello 1.59
2961 : parrello 1.93 The command string to pass to the system.
2962 : parrello 1.59
2963 :     =item RETURN
2964 :    
2965 : parrello 1.93 Returns the standard output from the specified command, as a list.
2966 : parrello 1.59
2967 :     =back
2968 :    
2969 :     =cut
2970 : parrello 1.93 #: Return Type @;
2971 :     sub TICK {
2972 : parrello 1.59 # Get the parameters.
2973 : parrello 1.93 my ($commandString) = @_;
2974 :     # Chop off the dot-slash if this is Windows.
2975 :     if ($FIG_Config::win_mode) {
2976 :     $commandString =~ s!^\./!!;
2977 : parrello 1.59 }
2978 : parrello 1.93 # Activate the command and return the result.
2979 :     return `$commandString`;
2980 : parrello 1.59 }
2981 :    
2982 : parrello 1.93
2983 : parrello 1.55 =head3 CommaFormat
2984 :    
2985 : parrello 1.92 my $formatted = Tracer::CommaFormat($number);
2986 : parrello 1.55
2987 :     Insert commas into a number.
2988 :    
2989 :     =over 4
2990 :    
2991 :     =item number
2992 :    
2993 :     A sequence of digits.
2994 :    
2995 :     =item RETURN
2996 :    
2997 :     Returns the same digits with commas strategically inserted.
2998 :    
2999 :     =back
3000 :    
3001 :     =cut
3002 :    
3003 :     sub CommaFormat {
3004 :     # Get the parameters.
3005 :     my ($number) = @_;
3006 :     # Pad the length up to a multiple of three.
3007 :     my $padded = "$number";
3008 :     $padded = " " . $padded while length($padded) % 3 != 0;
3009 :     # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3010 :     # cause the delimiters to be included in the output stream. The
3011 :     # GREP removes the empty strings in between the delimiters.
3012 :     my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3013 :     # Clean out the spaces.
3014 :     $retVal =~ s/ //g;
3015 :     # Return the result.
3016 :     return $retVal;
3017 :     }
3018 : parrello 1.46
3019 :    
3020 : parrello 1.62 =head3 CompareLists
3021 :    
3022 : parrello 1.92 my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3023 : parrello 1.62
3024 :     Compare two lists of tuples, and return a hash analyzing the differences. The lists
3025 :     are presumed to be sorted alphabetically by the value in the $keyIndex column.
3026 :     The return value contains a list of items that are only in the new list
3027 :     (inserted) and only in the old list (deleted).
3028 :    
3029 :     =over 4
3030 :    
3031 :     =item newList
3032 :    
3033 :     Reference to a list of new tuples.
3034 :    
3035 :     =item oldList
3036 :    
3037 :     Reference to a list of old tuples.
3038 :    
3039 :     =item keyIndex (optional)
3040 :    
3041 :     Index into each tuple of its key field. The default is 0.
3042 :    
3043 :     =item RETURN
3044 :    
3045 :     Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3046 :     list (inserted) followed by a reference to the list of items that are only in the old
3047 :     list (deleted).
3048 :    
3049 :     =back
3050 :    
3051 :     =cut
3052 :    
3053 :     sub CompareLists {
3054 :     # Get the parameters.
3055 :     my ($newList, $oldList, $keyIndex) = @_;
3056 :     if (! defined $keyIndex) {
3057 :     $keyIndex = 0;
3058 :     }
3059 :     # Declare the return variables.
3060 :     my ($inserted, $deleted) = ([], []);
3061 :     # Loop through the two lists simultaneously.
3062 :     my ($newI, $oldI) = (0, 0);
3063 :     my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3064 :     while ($newI < $newN || $oldI < $oldN) {
3065 :     # Get the current object in each list. Note that if one
3066 :     # of the lists is past the end, we'll get undef.
3067 :     my $newItem = $newList->[$newI];
3068 :     my $oldItem = $oldList->[$oldI];
3069 : parrello 1.63 if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3070 : parrello 1.62 # The old item is not in the new list, so mark it deleted.
3071 :     push @{$deleted}, $oldItem;
3072 :     $oldI++;
3073 :     } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3074 :     # The new item is not in the old list, so mark it inserted.
3075 :     push @{$inserted}, $newItem;
3076 :     $newI++;
3077 :     } else {
3078 :     # The item is in both lists, so push forward.
3079 :     $oldI++;
3080 :     $newI++;
3081 :     }
3082 :     }
3083 :     # Return the result.
3084 :     return ($inserted, $deleted);
3085 :     }
3086 :    
3087 : parrello 1.65 =head3 GenerateURL
3088 :    
3089 : parrello 1.92 my $queryUrl = Tracer::GenerateURL($page, %parameters);
3090 : parrello 1.65
3091 :     Generate a GET-style URL for the specified page with the specified parameter
3092 :     names and values. The values will be URL-escaped automatically. So, for
3093 :     example
3094 :    
3095 :     Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3096 :    
3097 :     would return
3098 :    
3099 : parrello 1.79 form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3100 : parrello 1.65
3101 :     =over 4
3102 :    
3103 :     =item page
3104 :    
3105 :     Page URL.
3106 :    
3107 :     =item parameters
3108 :    
3109 :     Hash mapping parameter names to parameter values.
3110 :    
3111 :     =item RETURN
3112 :    
3113 :     Returns a GET-style URL that goes to the specified page and passes in the
3114 :     specified parameters and values.
3115 :    
3116 :     =back
3117 :    
3118 :     =cut
3119 :    
3120 :     sub GenerateURL {
3121 :     # Get the parameters.
3122 :     my ($page, %parameters) = @_;
3123 :     # Prime the return variable with the page URL.
3124 :     my $retVal = $page;
3125 :     # Loop through the parameters, creating parameter elements in a list.
3126 :     my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3127 :     # If the list is nonempty, tack it on.
3128 :     if (@parmList) {
3129 : parrello 1.79 $retVal .= "?" . join(";", @parmList);
3130 : parrello 1.65 }
3131 :     # Return the result.
3132 :     return $retVal;
3133 :     }
3134 :    
3135 : parrello 1.78 =head3 ApplyURL
3136 :    
3137 : parrello 1.92 Tracer::ApplyURL($table, $target, $url);
3138 : parrello 1.78
3139 :     Run through a two-dimensional table (or more accurately, a list of lists), converting the
3140 :     I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3141 :     URL column will be deleted by this process and the target column will be HTML-escaped.
3142 :    
3143 :     This provides a simple way to process the results of a database query into something
3144 :     displayable by combining a URL with text.
3145 :    
3146 :     =over 4
3147 :    
3148 :     =item table
3149 :    
3150 :     Reference to a list of lists. The elements in the containing list will be updated by
3151 :     this method.
3152 :    
3153 :     =item target
3154 :    
3155 :     The index of the column to be converted into HTML.
3156 :    
3157 :     =item url
3158 :    
3159 :     The index of the column containing the URL. Note that the URL must have a recognizable
3160 :     C<http:> at the beginning.
3161 :    
3162 :     =back
3163 :    
3164 :     =cut
3165 :    
3166 :     sub ApplyURL {
3167 :     # Get the parameters.
3168 :     my ($table, $target, $url) = @_;
3169 :     # Loop through the table.
3170 :     for my $row (@{$table}) {
3171 :     # Apply the URL to the target cell.
3172 :     $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3173 :     # Delete the URL from the row.
3174 :     delete $row->[$url];
3175 :     }
3176 :     }
3177 :    
3178 :     =head3 CombineURL
3179 :    
3180 : parrello 1.92 my $combinedHtml = Tracer::CombineURL($text, $url);
3181 : parrello 1.78
3182 :     This method will convert the specified text into HTML hyperlinked to the specified
3183 :     URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3184 :     is defined and begins with an C<http:> header.
3185 :    
3186 :     =over 4
3187 :    
3188 :     =item text
3189 :    
3190 :     Text to return. This will be HTML-escaped automatically.
3191 :    
3192 :     =item url
3193 :    
3194 :     A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3195 :     will be returned without any hyperlinking.
3196 :    
3197 :     =item RETURN
3198 :    
3199 :     Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3200 :     doesn't look right, the HTML-escaped text will be returned without any further
3201 :     modification.
3202 :    
3203 :     =back
3204 :    
3205 :     =cut
3206 :    
3207 :     sub CombineURL {
3208 :     # Get the parameters.
3209 :     my ($text, $url) = @_;
3210 :     # Declare the return variable.
3211 :     my $retVal = CGI::escapeHTML($text);
3212 :     # Verify the URL.
3213 :     if (defined($url) && $url =~ m!http://!i) {
3214 :     # It's good, so we apply it to the text.
3215 :     $retVal = "<a href=\"$url\">$retVal</a>";
3216 :     }
3217 :     # Return the result.
3218 :     return $retVal;
3219 :     }
3220 :    
3221 : parrello 1.93 =head3 Cmp
3222 :    
3223 :     my $cmp = Tracer::Cmp($a, $b);
3224 :    
3225 :     This method performs a universal sort comparison. Each value coming in is
3226 :     separated into a leading text part and a trailing number part. The text
3227 :     part is string compared, and if both parts are equal, then the number
3228 :     parts are compared numerically. A stream of just numbers or a stream of
3229 :     just strings will sort correctly, and a mixed stream will sort with the
3230 :     numbers first. Strings with a label and a number will sort in the
3231 :     expected manner instead of lexically.
3232 :    
3233 :     =over 4
3234 :    
3235 :     =item a
3236 :    
3237 :     First item to compare.
3238 :    
3239 :     =item b
3240 :    
3241 :     Second item to compare.
3242 :    
3243 :     =item RETURN
3244 :    
3245 :     Returns a negative number if the first item should sort first (is less), a positive
3246 :     number if the first item should sort second (is greater), and a zero if the items are
3247 :     equal.
3248 :    
3249 :     =back
3250 :    
3251 :     =cut
3252 :    
3253 :     sub Cmp {
3254 :     # Get the parameters.
3255 :     my ($a, $b) = @_;
3256 :     # Declare the return value.
3257 :     my $retVal;
3258 :     # Check for nulls.
3259 :     if (! defined($a)) {
3260 :     $retVal = (! defined($b) ? 0 : -1);
3261 :     } elsif (! defined($b)) {
3262 :     $retVal = 1;
3263 :     } else {
3264 :     # Here we have two real values. Parse the two strings.
3265 :     $a =~ /^(\D*)(\d*)$/;
3266 :     my $aParsed = [$1, $2];
3267 :     $b =~ /^(\D*)(\d*)$/;
3268 :     my $bParsed = [$1, $2];
3269 :     # Compare the string parts.
3270 :     $retVal = $aParsed->[0] cmp $bParsed->[0];
3271 :     if (! $retVal) {
3272 :     $retVal = $aParsed->[1] <=> $bParsed->[1];
3273 :     }
3274 :     }
3275 :     # Return the result.
3276 :     return $retVal;
3277 :     }
3278 :    
3279 : parrello 1.87
3280 : olson 1.88 1;

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