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1 : olson 1.30 #
2 :     # Copyright (c) 2003-2006 University of Chicago and Fellowship
3 :     # for Interpretations of Genomes. All Rights Reserved.
4 :     #
5 :     # This file is part of the SEED Toolkit.
6 : parrello 1.61 #
7 : olson 1.30 # The SEED Toolkit is free software. You can redistribute
8 :     # it and/or modify it under the terms of the SEED Toolkit
9 : parrello 1.61 # Public License.
10 : olson 1.30 #
11 :     # You should have received a copy of the SEED Toolkit Public License
12 :     # along with this program; if not write to the University of Chicago
13 :     # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14 :     # Genomes at veronika@thefig.info or download a copy from
15 :     # http://www.theseed.org/LICENSE.TXT.
16 :     #
17 :    
18 : olson 1.1 package Tracer;
19 :    
20 : parrello 1.12 require Exporter;
21 :     @ISA = ('Exporter');
22 : parrello 1.72 @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);
23 : parrello 1.12 @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);
24 :     use strict;
25 :     use Carp qw(longmess croak);
26 :     use CGI;
27 : parrello 1.47 use Cwd;
28 : parrello 1.12 use FIG_Config;
29 : parrello 1.9 use PageBuilder;
30 : parrello 1.21 use Digest::MD5;
31 : parrello 1.36 use File::Basename;
32 : parrello 1.37 use File::Path;
33 : parrello 1.48 use File::stat;
34 : parrello 1.59 use LWP::UserAgent;
35 : parrello 1.64 use Time::HiRes 'gettimeofday';
36 : parrello 1.65 use URI::Escape;
37 : parrello 1.74 use Time::Local;
38 : olson 1.1
39 :     =head1 Tracing and Debugging Helpers
40 :    
41 : parrello 1.72 =head2 Tracing
42 : olson 1.1
43 :     This package provides simple tracing for debugging and reporting purposes. To use it simply call the
44 : parrello 1.72 L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
45 :     L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
46 :     each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
47 :     level is less than or equal to the setup trace level and whose category is activated will
48 : parrello 1.2 be written. Thus, a higher trace level on a message indicates that the message
49 : parrello 1.72 is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
50 :     appear.
51 : olson 1.1
52 : parrello 1.72 =head3 Putting Trace Messages in Your Code
53 :    
54 :     To generate a trace message, use the following syntax.
55 :    
56 :     Trace($message) if T(errors => 4);
57 : olson 1.1
58 : parrello 1.2 This statement will produce a trace message if the trace level is 4 or more and the C<errors>
59 : parrello 1.72 category is active. There is a special category C<main> that is always active, so
60 : olson 1.1
61 : parrello 1.72 Trace($message) if T(main => 4);
62 : olson 1.1
63 :     will trace if the trace level is 4 or more.
64 :    
65 :     If the category name is the same as the package name, all you need is the number. So, if the
66 :     following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
67 :     active and the trace level is 2 or more.
68 :    
69 : parrello 1.72 Trace($message) if T(2);
70 :    
71 :     In scripts, where no package name is available, the category defaults to C<main>.
72 :    
73 :     =head3 Custom Tracing
74 :    
75 :     Many programs have customized tracing configured using the L</TSetup> method. This is no longer
76 :     the preferred method, but a knowledge of how custom tracing works can make the more modern
77 :     L</Emergency Tracing> easier to understand.
78 : olson 1.1
79 : parrello 1.72 To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
80 :     a list of category names, and a destination. The trace level and list of category names are
81 : olson 1.1 specified as a space-delimited string. Thus
82 :    
83 : parrello 1.72 TSetup('3 errors Sprout ERDB', 'TEXT');
84 : olson 1.1
85 : parrello 1.7 sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
86 : parrello 1.72 specifies that messages should be sent to the standard output.
87 : parrello 1.12
88 :     To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
89 :     level 3 and writes the output to the standard error output. This sort of thing might be
90 :     useful in a CGI environment.
91 :    
92 : parrello 1.72 TSetup('3 *', 'WARN');
93 : olson 1.1
94 : parrello 1.72 In addition standard error and file output for trace messages, you can specify that the trace messages
95 : olson 1.1 be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
96 :     is useful if you are building a web page. Instead of having the trace messages interspersed with
97 :     the page output, they can be gathered together and displayed at the end of the page. This makes
98 :     it easier to debug page formatting problems.
99 :    
100 : parrello 1.72 Finally, you can specify that all trace messages be emitted to a file, or the standard output and
101 :     a file at the same time. To trace to a file, specify the filename with an output character in front
102 :     of it.
103 :    
104 :     TSetup('4 SQL', ">$fileName");
105 :    
106 :     To trace to the standard output and a file at the same time, put a C<+> in front of the angle
107 :     bracket.
108 :    
109 :     TSetup('3 *', "+>$fileName");
110 : parrello 1.4
111 : olson 1.1 The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
112 :     Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
113 :     Thus, debugging information is available and easily retrieved even when the application is
114 :     being used out in the field.
115 :    
116 : parrello 1.72 =head3 Trace Levels
117 :    
118 : parrello 1.10 There is no hard and fast rule on how to use trace levels. The following is therefore only
119 :     a suggestion.
120 :    
121 :     =over 4
122 :    
123 : parrello 1.32 =item Error 0
124 : parrello 1.10
125 :     Message indicates an error that may lead to incorrect results or that has stopped the
126 :     application entirely.
127 :    
128 : parrello 1.32 =item Warning 1
129 : parrello 1.10
130 :     Message indicates something that is unexpected but that probably did not interfere
131 :     with program execution.
132 :    
133 : parrello 1.32 =item Notice 2
134 : parrello 1.10
135 :     Message indicates the beginning or end of a major task.
136 :    
137 : parrello 1.32 =item Information 3
138 : parrello 1.10
139 :     Message indicates a subtask. In the FIG system, a subtask generally relates to a single
140 :     genome. This would be a big loop that is not expected to execute more than 500 times or so.
141 :    
142 : parrello 1.32 =item Detail 4
143 : parrello 1.10
144 :     Message indicates a low-level loop iteration.
145 :    
146 :     =back
147 :    
148 : parrello 1.69 The format of trace messages is important because some utilities analyze trace files.
149 : parrello 1.72 There are three fields-- the time stamp, the category name, and the text.
150 :     The time stamp is between square brackets and the category name between angle brackets.
151 :     After the category name there is a colon (C<:>) followed by the message text.
152 :     If the square brackets or angle brackets are missing, then the trace management
153 :     utilities assume that they are encountering a set of pre-formatted lines.
154 :    
155 :     Note, however, that this formatting is done automatically by the tracing functions. You
156 :     only need to know about it if you want to parse a trace file.
157 :    
158 :     =head3 Emergency Tracing
159 :    
160 :     Sometimes, you need a way for tracing to happen automatically without putting parameters
161 :     in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
162 :     from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.
163 :     Emergency tracing requires you specify a tracing key. For command-line tools, the key is
164 :     taken from the C<TRACING> environment variable. For web services, the key is taken from
165 :     a cookie. Either way, the key tells the tracing facility who you are, so that you control
166 :     the tracing in your environment without stepping on other users.
167 :    
168 :     The key can be anything you want. If you don't have a key, the C<SetPassword> page will
169 :     generate one for you.
170 :    
171 :     You can activate and de-activate emergency tracing from the debugging control panel, as
172 :     well as display the trace file itself.
173 :    
174 :     To enable emergency tracing in your code, call
175 :    
176 :     ETracing($cgi)
177 :    
178 :     from a web script and
179 :    
180 :     ETracing()
181 :    
182 :     from a command-line script.
183 :    
184 :     The web script will look for the tracing key in the cookies, and the command-line
185 :     script will look for it in the C<TRACING> environment variable. If you are
186 :     using the L</StandardScript> or L</StandardSetup> methods, emergency tracing
187 :     will be configured automatically.
188 :    
189 : parrello 1.84 NOTE: to configure emergency tracing from the command line instead of the Debugging
190 :     Control Panel (see below), use the C<trace.pl> script.
191 :    
192 : parrello 1.72 =head3 Debugging Control Panel
193 :    
194 :     The debugging control panel provides several tools to assist in development of
195 :     SEED and Sprout software. You access the debugging control panel from the URL
196 :     C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,
197 :     for example, the panel access point for the development NMPDR system is
198 :     C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to
199 :     find out what the password is. From this page, you can also specify a tracing
200 :     key. If you don't specify a key, one will be generated for you.
201 :    
202 :     =head4 Emergency Tracing Form
203 :    
204 :     At the bottom of the debugging control panel is a form that allows you to
205 :     specify a trace level and tracing categories. Special and common categories
206 :     are listed with check boxes. You can hold your mouse over a check box to see
207 :     what its category does. In general, however, a category name is the same as
208 :     the name of the package in which the trace message occurs.
209 :    
210 :     Additional categories can be entered in an input box, delimited by spaces or commas.
211 :    
212 :     The B<Activate> button turns on Emergency tracing at the level you specify with the
213 :     specified categories active. The B<Terminate> button turns tracing off. The
214 :     B<Show File> button displays the current contents of the trace file. The tracing
215 :     form at the bottom of the control panel is designed for emergency tracing, so it
216 :     will only affect programs that call L</ETracing>, L</StandardScript>,
217 :     or L</StandardSetup>.
218 :    
219 :     =head4 Script Form
220 :    
221 :     The top form of the debugging control panel allows you to enter a tiny script and
222 :     have the output generated in a formatted table. Certain object variables are
223 :     predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),
224 :     and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.
225 :    
226 :     The last line of the script must be a scalar, but it can be a reference to a hash,
227 :     a list, a list of lists, and various other combinations. If you select the appropriate
228 :     data type in the dropdown box, the output will be formatted accordingly. The form
229 :     also has controls for specifying tracing. These controls override any emergency
230 :     tracing in effect.
231 :    
232 :     =head4 Database Query Forms
233 :    
234 :     The forms between the script form and the emergency tracing form allow you to
235 :     make queries against the database. The FIG query form allows simple queries against
236 :     a single FIG table. The Sprout query form uses the B<GetAll> method to do a
237 :     multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>
238 :     package, and it takes five parameters.
239 :    
240 :     GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
241 :    
242 :     Each of the five parameters corresponds to a text box on the query form:
243 :    
244 :     =over 4
245 :    
246 :     =item Objects
247 :    
248 :     Comma-separated list containing the names of the entity and relationship objects to be retrieved.
249 :    
250 :     =item Filter
251 :    
252 :     WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
253 :     be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
254 :     B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a
255 :     field, I<objectName> is the name of the entity or relationship object containing the field, and
256 :     I<number> is the 1-based position of the object in the object list. Any parameters
257 :     specified in the filter clause should be specified in the B<Params> field.
258 :     The fields in a filter clause can come from primary entity relations,
259 :     relationship relations, or secondary entity relations; however, all of the
260 :     entities and relationships involved must be included in the list of object names.
261 :    
262 :     =item Params
263 :    
264 :     List of the parameters to be substituted in for the parameters marks in the filter clause. This
265 :     is a comma-separated list without any quoting or escaping.
266 :    
267 :     =item fields
268 :    
269 :     Comma-separated list of the fields to be returned in each element of the list returned. Fields
270 :     are specified in the same manner as in the filter clause.
271 :    
272 :     =item count
273 :    
274 :     Maximum number of records to return. If omitted or 0, all available records will be returned.
275 :    
276 :     =back
277 :    
278 :     B<GetAll> automatically joins together the entities and relationships listed in the object
279 :     names. This simplifies the coding of the filter clause, but it means that some queries are
280 :     not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation
281 :     that has yet to be addressed.
282 : parrello 1.69
283 : olson 1.1 =cut
284 : parrello 1.2
285 : olson 1.1 # Declare the configuration variables.
286 :    
287 : parrello 1.12 my $Destination = "NONE"; # Description of where to send the trace output.
288 :     my $TeeFlag = 0; # TRUE if output is going to a file and to the
289 :     # standard output
290 : parrello 1.3 my %Categories = ( main => 1 );
291 : parrello 1.12 # hash of active category names
292 :     my $TraceLevel = 0; # trace level; a higher trace level produces more
293 :     # messages
294 :     my @Queue = (); # queued list of trace messages.
295 : parrello 1.7 my $LastCategory = "main"; # name of the last category interrogated
296 : parrello 1.11 my $SetupCount = 0; # number of times TSetup called
297 : parrello 1.12 my $AllTrace = 0; # TRUE if we are tracing all categories.
298 : olson 1.1
299 :     =head2 Public Methods
300 :    
301 :     =head3 TSetup
302 :    
303 : parrello 1.92 TSetup($categoryList, $target);
304 : olson 1.1
305 :     This method is used to specify the trace options. The options are stored as package data
306 :     and interrogated by the L</Trace> and L</T> methods.
307 :    
308 :     =over 4
309 :    
310 :     =item categoryList
311 :    
312 :     A string specifying the trace level and the categories to be traced, separated by spaces.
313 :     The trace level must come first.
314 :    
315 :     =item target
316 :    
317 :     The destination for the trace output. To send the trace output to a file, specify the file
318 :     name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
319 : parrello 1.10 to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
320 :     symbol with a C<+> to echo output to a file AND to the standard output. In addition to
321 :     sending the trace messages to a file, you can specify a special destination. C<HTML> will
322 :     cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
323 : parrello 1.5 will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
324 : parrello 1.9 messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
325 : parrello 1.6 messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
326 : parrello 1.9 cause trace messages to be emitted as warnings using the B<warn> directive. C<NONE> will
327 : parrello 1.6 cause tracing to be suppressed.
328 : olson 1.1
329 :     =back
330 :    
331 :     =cut
332 :    
333 :     sub TSetup {
334 : parrello 1.12 # Get the parameters.
335 :     my ($categoryList, $target) = @_;
336 :     # Parse the category list.
337 :     my @categoryData = split /\s+/, $categoryList;
338 :     # Extract the trace level.
339 :     $TraceLevel = shift @categoryData;
340 :     # Presume category-based tracing until we learn otherwise.
341 :     $AllTrace = 0;
342 :     # Build the category hash. Note that if we find a "*", we turn on non-category
343 : parrello 1.33 # tracing. We must also clear away any pre-existing data.
344 : parrello 1.34 %Categories = ( main => 1 );
345 : parrello 1.12 for my $category (@categoryData) {
346 :     if ($category eq '*') {
347 :     $AllTrace = 1;
348 :     } else {
349 : parrello 1.13 $Categories{lc $category} = 1;
350 : parrello 1.12 }
351 :     }
352 :     # Now we need to process the destination information. The most important special
353 :     # cases are the single ">", which requires we clear the file first, and the
354 :     # "+" prefix which indicates a double echo.
355 :     if ($target =~ m/^\+?>>?/) {
356 :     if ($target =~ m/^\+/) {
357 :     $TeeFlag = 1;
358 :     $target = substr($target, 1);
359 :     }
360 :     if ($target =~ m/^>[^>]/) {
361 :     open TRACEFILE, $target;
362 : parrello 1.69 print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";
363 : parrello 1.12 close TRACEFILE;
364 :     $Destination = ">$target";
365 :     } else {
366 :     $Destination = $target;
367 :     }
368 :     } else {
369 :     $Destination = uc($target);
370 :     }
371 :     # Increment the setup counter.
372 :     $SetupCount++;
373 : parrello 1.11 }
374 :    
375 : parrello 1.31 =head3 StandardSetup
376 :    
377 : parrello 1.92 my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
378 : parrello 1.31
379 :     This method performs standard command-line parsing and tracing setup. The return
380 :     values are a hash of the command-line options and a list of the positional
381 :     parameters. Tracing is automatically set up and the command-line options are
382 :     validated.
383 :    
384 :     This is a complex method that does a lot of grunt work. The parameters can
385 :     be more easily understood, however, once they are examined individually.
386 :    
387 :     The I<categories> parameter is the most obtuse. It is a reference to a list of
388 :     special-purpose tracing categories. Most tracing categories are PERL package
389 :     names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
390 :     B<ERDB>, and B<SproutLoad> packages, you would specify the categories
391 :    
392 :     ["Sprout", "SproutLoad", "ERDB"]
393 :    
394 :     This would cause trace messages in the specified three packages to appear in
395 : parrello 1.69 the output. There are two special tracing categories that are automatically
396 : parrello 1.31 handled by this method. In other words, if you used L</TSetup> you would need
397 :     to include these categories manually, but if you use this method they are turned
398 :     on automatically.
399 :    
400 :     =over 4
401 :    
402 :     =item SQL
403 :    
404 :     Traces SQL commands and activity.
405 :    
406 :     =item Tracer
407 :    
408 :     Traces error messages and call stacks.
409 :    
410 :     =back
411 :    
412 :     C<SQL> is only turned on if the C<-sql> option is specified in the command line.
413 :     The trace level is specified using the C<-trace> command-line option. For example,
414 :     the following command line for C<TransactFeatures> turns on SQL tracing and runs
415 :     all tracing at level 3.
416 :    
417 :     TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
418 :    
419 :     Standard tracing is output to the standard output and echoed to the file
420 : parrello 1.38 C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
421 :     process ID. You can also specify the C<user> parameter to put a user ID
422 :     instead of a process ID in the trace file name. So, for example
423 : parrello 1.31
424 : parrello 1.35 The default trace level is 2. To get all messages, specify a trace level of 4.
425 :     For a genome-by-genome update, use 3.
426 : parrello 1.31
427 : parrello 1.38 TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
428 :    
429 :     would send the trace output to C<traceBruce.log> in the temporary directory.
430 :    
431 : parrello 1.31 The I<options> parameter is a reference to a hash containing the command-line
432 : parrello 1.36 options, their default values, and an explanation of what they mean. Command-line
433 :     options may be in the form of switches or keywords. In the case of a switch, the
434 :     option value is 1 if it is specified and 0 if it is not specified. In the case
435 :     of a keyword, the value is separated from the option name by an equal sign. You
436 :     can see this last in the command-line example above.
437 : parrello 1.31
438 : parrello 1.42 You can specify a different default trace level by setting C<$options->{trace}>
439 :     prior to calling this method.
440 :    
441 : parrello 1.31 An example at this point would help. Consider, for example, the command-line utility
442 :     C<TransactFeatures>. It accepts a list of positional parameters plus the options
443 :     C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
444 :     the following code.
445 :    
446 :     my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
447 : parrello 1.36 { safe => [0, "use database transactions"],
448 :     noAlias => [0, "do not expect aliases in CHANGE transactions"],
449 :     start => [' ', "start with this genome"],
450 :     tblFiles => [0, "output TBL files containing the corrected IDs"] },
451 : parrello 1.84 "<command> <transactionDirectory> <IDfile>",
452 : parrello 1.36 @ARGV);
453 : parrello 1.31
454 :    
455 :     The call to C<ParseCommand> specifies the default values for the options and
456 :     stores the actual options in a hash that is returned as C<$options>. The
457 : parrello 1.61 positional parameters are returned in C<@parameters>.
458 : parrello 1.31
459 :     The following is a sample command line for C<TransactFeatures>.
460 :    
461 :     TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
462 :    
463 : parrello 1.84 Single and double hyphens are equivalent. So, you could also code the
464 :     above command as
465 :    
466 :     TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
467 :    
468 : parrello 1.31 In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
469 :     parameters, and would find themselves in I<@parameters> after executing the
470 :     above code fragment. The tracing would be set to level 2, and the categories
471 : parrello 1.69 would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
472 : parrello 1.31 and C<DocUtils> was included because it came in within the first parameter
473 :     to this method. The I<$options> hash would be
474 :    
475 :     { trace => 2, sql => 0, safe => 0,
476 :     noAlias => 1, start => ' ', tblFiles => 0 }
477 :    
478 :     Use of C<StandardSetup> in this way provides a simple way of performing
479 :     standard tracing setup and command-line parsing. Note that the caller is
480 :     not even aware of the command-line switches C<-trace> and C<-sql>, which
481 :     are used by this method to control the tracing. If additional tracing features
482 :     need to be added in the future, they can be processed by this method without
483 :     upsetting the command-line utilities.
484 :    
485 : parrello 1.42 If the C<background> option is specified on the command line, then the
486 :     standard and error outputs will be directed to files in the temporary
487 :     directory, using the same suffix as the trace file. So, if the command
488 :     line specified
489 :    
490 :     -user=Bruce -background
491 :    
492 :     then the trace output would go to C<traceBruce.log>, the standard output to
493 :     C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
494 :     simplify starting a command in the background.
495 :    
496 : parrello 1.72 The user name is also used as the tracing key for L</Emergency Tracing>.
497 :     Specifying a value of C<E> for the trace level causes emergency tracing to
498 :     be used instead of custom tracing. If the user name is not specified,
499 :     the tracing key is taken from the C<Tracing> environment variable. If there
500 :     is no value for that variable, the tracing key will be computed from the PID.
501 :    
502 : parrello 1.84 Finally, if the special option C<-help> is specified, the option
503 :     names will be traced at level 0 and the program will exit without processing.
504 : parrello 1.36 This provides a limited help capability. For example, if the user enters
505 :    
506 : parrello 1.84 TransactFeatures -help
507 : parrello 1.36
508 :     he would see the following output.
509 :    
510 : parrello 1.84 TransactFeatures [options] <command> <transactionDirectory> <IDfile>
511 : parrello 1.72 -trace tracing level (default E)
512 : parrello 1.36 -sql trace SQL commands
513 :     -safe use database transactions
514 :     -noAlias do not expect aliases in CHANGE transactions
515 :     -start start with this genome
516 :     -tblFiles output TBL files containing the corrected IDs
517 :    
518 : parrello 1.44 The caller has the option of modifying the tracing scheme by placing a value
519 :     for C<trace> in the incoming options hash. The default value can be overridden,
520 :     or the tracing to the standard output can be turned off by suffixing a minus
521 : parrello 1.61 sign to the trace level. So, for example,
522 : parrello 1.44
523 :     { trace => [0, "tracing level (default 0)"],
524 :     ...
525 :    
526 : parrello 1.72 would set the default trace level to 0 instead of E, while
527 : parrello 1.44
528 :     { trace => ["2-", "tracing level (default 2)"],
529 :     ...
530 :    
531 : parrello 1.72 would set the default to 2, but trace only to the log file, not to the
532 : parrello 1.44 standard output.
533 :    
534 : parrello 1.31 The parameters to this method are as follows.
535 :    
536 :     =over 4
537 :    
538 :     =item categories
539 :    
540 :     Reference to a list of tracing category names. These should be names of
541 :     packages whose internal workings will need to be debugged to get the
542 :     command working.
543 :    
544 :     =item options
545 :    
546 :     Reference to a hash containing the legal options for the current command mapped
547 : parrello 1.36 to their default values and descriptions. The user can override the defaults
548 :     by specifying the options as command-line switches prefixed by a hyphen.
549 :     Tracing-related options may be added to this hash. If the C<-h> option is
550 :     specified on the command line, the option descriptions will be used to
551 : parrello 1.44 explain the options. To turn off tracing to the standard output, add a
552 :     minus sign to the value for C<trace> (see above).
553 : parrello 1.36
554 :     =item parmHelp
555 :    
556 :     A string that vaguely describes the positional parameters. This is used
557 :     if the user specifies the C<-h> option.
558 : parrello 1.31
559 : parrello 1.44 =item argv
560 : parrello 1.31
561 :     List of command line parameters, including the option switches, which must
562 :     precede the positional parameters and be prefixed by a hyphen.
563 :    
564 :     =item RETURN
565 :    
566 :     Returns a list. The first element of the list is the reference to a hash that
567 :     maps the command-line option switches to their values. These will either be the
568 :     default values or overrides specified on the command line. The remaining
569 :     elements of the list are the position parameters, in order.
570 :    
571 :     =back
572 :    
573 :     =cut
574 :    
575 :     sub StandardSetup {
576 :     # Get the parameters.
577 : parrello 1.36 my ($categories, $options, $parmHelp, @argv) = @_;
578 : parrello 1.72 # Get the default tracing key.
579 :     my $tkey = EmergencyKey();
580 : parrello 1.31 # Add the tracing options.
581 : parrello 1.41 if (! exists $options->{trace}) {
582 : parrello 1.85 $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
583 : parrello 1.41 }
584 : parrello 1.36 $options->{sql} = [0, "turn on SQL tracing"];
585 : parrello 1.84 $options->{help} = [0, "display command-line options"];
586 : parrello 1.72 $options->{user} = [$tkey, "tracing key"];
587 : parrello 1.42 $options->{background} = [0, "spool standard and error output"];
588 : parrello 1.36 # Create a parsing hash from the options hash. The parsing hash
589 :     # contains the default values rather than the default value
590 :     # and the description. While we're at it, we'll memorize the
591 :     # length of the longest option name.
592 :     my $longestName = 0;
593 :     my %parseOptions = ();
594 :     for my $key (keys %{$options}) {
595 :     if (length $key > $longestName) {
596 :     $longestName = length $key;
597 :     }
598 :     $parseOptions{$key} = $options->{$key}->[0];
599 :     }
600 : parrello 1.31 # Parse the command line.
601 : parrello 1.36 my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
602 : parrello 1.42 # Get the logfile suffix.
603 :     my $suffix = $retOptions->{user};
604 :     # Check for background mode.
605 :     if ($retOptions->{background}) {
606 :     my $outFileName = "$FIG_Config::temp/out$suffix.log";
607 :     my $errFileName = "$FIG_Config::temp/err$suffix.log";
608 :     open STDOUT, ">$outFileName";
609 :     open STDERR, ">$errFileName";
610 : parrello 1.92 # Check for phone support. If we have phone support and a phone number,
611 :     # we want to turn it on.
612 :     if ($ENV{PHONE} && defined($FIG_Config::phone)) {
613 :     $retOptions->{phone} = $ENV{PHONE};
614 :     }
615 : parrello 1.42 }
616 : parrello 1.72 # Now we want to set up tracing. First, we need to know if the user
617 :     # wants emergency tracing.
618 :     if ($retOptions->{trace} eq 'E') {
619 :     ETracing($retOptions->{user});
620 : parrello 1.44 } else {
621 : parrello 1.72 # Here the tracing is controlled from the command line.
622 :     my @cats = @{$categories};
623 :     if ($retOptions->{sql}) {
624 :     push @cats, "SQL";
625 :     }
626 :     # Add the default categories.
627 :     push @cats, "Tracer";
628 :     # Next, we create the category string by joining the categories.
629 :     my $cats = join(" ", @cats);
630 :     # Check to determine whether or not the caller wants to turn off tracing
631 :     # to the standard output.
632 :     my $traceLevel = $retOptions->{trace};
633 :     my $textOKFlag = 1;
634 :     if ($traceLevel =~ /^(.)-/) {
635 :     $traceLevel = $1;
636 :     $textOKFlag = 0;
637 :     }
638 :     # Now we set up the trace mode.
639 :     my $traceMode;
640 :     # Verify that we can open a file in the FIG temporary directory.
641 :     my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
642 :     if (open TESTTRACE, ">$traceFileName") {
643 :     # Here we can trace to a file.
644 :     $traceMode = ">$traceFileName";
645 :     if ($textOKFlag) {
646 :     # Echo to standard output if the text-OK flag is set.
647 :     $traceMode = "+$traceMode";
648 :     }
649 :     # Close the test file.
650 :     close TESTTRACE;
651 : parrello 1.44 } else {
652 : parrello 1.72 # Here we can't trace to a file. We trace to the standard output if it's
653 :     # okay, and the error log otherwise.
654 :     if ($textOKFlag) {
655 :     $traceMode = "TEXT";
656 :     } else {
657 :     $traceMode = "WARN";
658 :     }
659 : parrello 1.44 }
660 : parrello 1.72 # Now set up the tracing.
661 :     TSetup("$traceLevel $cats", $traceMode);
662 : parrello 1.40 }
663 : parrello 1.92 # Check for the "help" option. If it is specified, dump the command-line
664 : parrello 1.36 # options and exit the program.
665 : parrello 1.84 if ($retOptions->{help}) {
666 : parrello 1.36 $0 =~ m#[/\\](\w+)(\.pl)?$#i;
667 : parrello 1.69 print "$1 [options] $parmHelp\n";
668 : parrello 1.36 for my $key (sort keys %{$options}) {
669 :     my $name = Pad($key, $longestName, 0, ' ');
670 :     my $desc = $options->{$key}->[1];
671 :     if ($options->{$key}->[0]) {
672 :     $desc .= " (default " . $options->{$key}->[0] . ")";
673 :     }
674 : parrello 1.69 print " $name $desc\n";
675 : parrello 1.36 }
676 :     exit(0);
677 :     }
678 : parrello 1.83 # Trace the options, if applicable.
679 :     if (T(3)) {
680 :     my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
681 :     Trace("Selected options: " . join(", ", sort @parms) . ".");
682 :     }
683 : parrello 1.31 # Return the parsed parameters.
684 :     return ($retOptions, @retParameters);
685 :     }
686 :    
687 : parrello 1.11 =head3 Setups
688 :    
689 : parrello 1.92 my $count = Tracer::Setups();
690 : parrello 1.11
691 :     Return the number of times L</TSetup> has been called.
692 :    
693 :     This method allows for the creation of conditional tracing setups where, for example, we
694 :     may want to set up tracing if nobody else has done it before us.
695 :    
696 :     =cut
697 :    
698 :     sub Setups {
699 : parrello 1.12 return $SetupCount;
700 : olson 1.1 }
701 :    
702 : parrello 1.10 =head3 Open
703 :    
704 : parrello 1.92 my $handle = Open($fileHandle, $fileSpec, $message);
705 : parrello 1.10
706 : parrello 1.11 Open a file.
707 : parrello 1.10
708 :     The I<$fileSpec> is essentially the second argument of the PERL C<open>
709 :     function. The mode is specified using Unix-like shell information. So, for
710 :     example,
711 :    
712 : parrello 1.12 Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
713 : parrello 1.10
714 :     would open for output appended to the specified file, and
715 :    
716 : parrello 1.12 Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
717 : parrello 1.10
718 :     would open a pipe that sorts the records written and removes duplicates. Note
719 : parrello 1.11 the use of file handle syntax in the Open call. To use anonymous file handles,
720 :     code as follows.
721 : parrello 1.10
722 : parrello 1.12 my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
723 : parrello 1.10
724 : parrello 1.11 The I<$message> parameter is used if the open fails. If it is set to C<0>, then
725 :     the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
726 :     failed open will throw an exception and the third parameter will be used to construct
727 :     an error message. If the parameter is omitted, a standard message is constructed
728 :     using the file spec.
729 : parrello 1.10
730 : parrello 1.12 Could not open "/usr/spool/news/twitlog"
731 : parrello 1.10
732 :     Note that the mode characters are automatically cleaned from the file name.
733 :     The actual error message from the file system will be captured and appended to the
734 :     message in any case.
735 :    
736 : parrello 1.12 Could not open "/usr/spool/news/twitlog": file not found.
737 : parrello 1.10
738 :     In some versions of PERL the only error message we get is a number, which
739 :     corresponds to the C++ C<errno> value.
740 :    
741 : parrello 1.12 Could not open "/usr/spool/news/twitlog": 6.
742 : parrello 1.10
743 :     =over 4
744 :    
745 :     =item fileHandle
746 :    
747 :     File handle. If this parameter is C<undef>, a file handle will be generated
748 :     and returned as the value of this method.
749 :    
750 :     =item fileSpec
751 :    
752 :     File name and mode, as per the PERL C<open> function.
753 :    
754 :     =item message (optional)
755 :    
756 :     Error message to use if the open fails. If omitted, a standard error message
757 :     will be generated. In either case, the error information from the file system
758 : parrello 1.11 is appended to the message. To specify a conditional open that does not throw
759 :     an error if it fails, use C<0>.
760 : parrello 1.10
761 :     =item RETURN
762 :    
763 : parrello 1.11 Returns the name of the file handle assigned to the file, or C<undef> if the
764 :     open failed.
765 : parrello 1.10
766 :     =back
767 :    
768 :     =cut
769 :    
770 :     sub Open {
771 : parrello 1.12 # Get the parameters.
772 :     my ($fileHandle, $fileSpec, $message) = @_;
773 :     # Attempt to open the file.
774 :     my $rv = open $fileHandle, $fileSpec;
775 :     # If the open failed, generate an error message.
776 :     if (! $rv) {
777 :     # Save the system error message.
778 :     my $sysMessage = $!;
779 :     # See if we need a default message.
780 :     if (!$message) {
781 :     # Clean any obvious mode characters and leading spaces from the
782 :     # filename.
783 :     my ($fileName) = FindNamePart($fileSpec);
784 :     $message = "Could not open \"$fileName\"";
785 :     }
786 :     # Terminate with an error using the supplied message and the
787 :     # error message from the file system.
788 :     Confess("$message: $!");
789 :     }
790 :     # Return the file handle.
791 :     return $fileHandle;
792 : parrello 1.10 }
793 :    
794 : parrello 1.11 =head3 FindNamePart
795 :    
796 : parrello 1.92 my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
797 : parrello 1.11
798 :     Extract the portion of a file specification that contains the file name.
799 :    
800 :     A file specification is the string passed to an C<open> call. It specifies the file
801 :     mode and name. In a truly complex situation, it can specify a pipe sequence. This
802 :     method assumes that the file name is whatever follows the first angle bracket
803 :     sequence. So, for example, in the following strings the file name is
804 :     C</usr/fig/myfile.txt>.
805 :    
806 :     >>/usr/fig/myfile.txt
807 :     </usr/fig/myfile.txt
808 :     | sort -u > /usr/fig/myfile.txt
809 :    
810 :     If the method cannot find a file name using its normal methods, it will return the
811 :     whole incoming string.
812 :    
813 :     =over 4
814 :    
815 :     =item fileSpec
816 :    
817 :     File specification string from which the file name is to be extracted.
818 :    
819 :     =item RETURN
820 :    
821 :     Returns a three-element list. The first element contains the file name portion of
822 :     the specified string, or the whole string if a file name cannot be found via normal
823 :     methods. The second element contains the start position of the file name portion and
824 :     the third element contains the length.
825 :    
826 :     =back
827 :    
828 :     =cut
829 :     #: Return Type $;
830 :     sub FindNamePart {
831 :     # Get the parameters.
832 :     my ($fileSpec) = @_;
833 : parrello 1.12 # Default to the whole input string.
834 :     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
835 : parrello 1.11 # Parse out the file name if we can.
836 : parrello 1.12 if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
837 :     $retVal = $2;
838 :     $len = length $retVal;
839 :     $pos = (length $fileSpec) - (length $3) - $len;
840 :     }
841 : parrello 1.11 # Return the result.
842 :     return ($retVal, $pos, $len);
843 :     }
844 :    
845 :     =head3 OpenDir
846 :    
847 : parrello 1.92 my @files = OpenDir($dirName, $filtered, $flag);
848 : parrello 1.11
849 :     Open a directory and return all the file names. This function essentially performs
850 :     the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
851 : parrello 1.31 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
852 : parrello 1.33 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
853 :     filtered out of the return list. If the directory does not open and I<$flag> is not
854 :     set, an exception is thrown. So, for example,
855 : parrello 1.11
856 : parrello 1.12 my @files = OpenDir("/Volumes/fig/contigs", 1);
857 : parrello 1.29
858 : parrello 1.11 is effectively the same as
859 :    
860 : parrello 1.12 opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
861 : parrello 1.33 my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
862 : parrello 1.11
863 :     Similarly, the following code
864 :    
865 : parrello 1.31 my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
866 : parrello 1.29
867 : parrello 1.11 Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
868 : parrello 1.31 automatically returns an empty list if the directory fails to open.
869 : parrello 1.11
870 :     =over 4
871 :    
872 :     =item dirName
873 :    
874 :     Name of the directory to open.
875 :    
876 :     =item filtered
877 :    
878 :     TRUE if files whose names begin with a period (C<.>) should be automatically removed
879 :     from the list, else FALSE.
880 :    
881 : parrello 1.31 =item flag
882 :    
883 :     TRUE if a failure to open is okay, else FALSE
884 :    
885 : parrello 1.11 =back
886 :    
887 :     =cut
888 :     #: Return Type @;
889 :     sub OpenDir {
890 :     # Get the parameters.
891 : parrello 1.31 my ($dirName, $filtered, $flag) = @_;
892 : parrello 1.11 # Declare the return variable.
893 : parrello 1.31 my @retVal = ();
894 : parrello 1.12 # Open the directory.
895 :     if (opendir(my $dirHandle, $dirName)) {
896 :     # The directory opened successfully. Get the appropriate list according to the
897 :     # strictures of the filter parameter.
898 :     if ($filtered) {
899 : parrello 1.33 @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
900 : parrello 1.12 } else {
901 :     @retVal = readdir $dirHandle;
902 :     }
903 : parrello 1.31 } elsif (! $flag) {
904 :     # Here the directory would not open and it's considered an error.
905 : parrello 1.12 Confess("Could not open directory $dirName.");
906 :     }
907 : parrello 1.11 # Return the result.
908 :     return @retVal;
909 :     }
910 :    
911 : parrello 1.6 =head3 SetLevel
912 :    
913 : parrello 1.92 Tracer::SetLevel($newLevel);
914 : parrello 1.6
915 :     Modify the trace level. A higher trace level will cause more messages to appear.
916 :    
917 :     =over 4
918 :    
919 :     =item newLevel
920 :    
921 :     Proposed new trace level.
922 :    
923 :     =back
924 :    
925 :     =cut
926 :    
927 :     sub SetLevel {
928 :     $TraceLevel = $_[0];
929 :     }
930 :    
931 : olson 1.1 =head3 Now
932 :    
933 : parrello 1.92 my $string = Tracer::Now();
934 : olson 1.1
935 :     Return a displayable time stamp containing the local time.
936 :    
937 :     =cut
938 :    
939 :     sub Now {
940 : parrello 1.12 my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
941 :     my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
942 :     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
943 :     return $retVal;
944 : olson 1.1 }
945 :    
946 :     # Pad a number to 2 digits.
947 :     sub _p2 {
948 : parrello 1.12 my ($value) = @_;
949 :     $value = "0$value" if ($value < 10);
950 :     return $value;
951 : olson 1.1 }
952 :    
953 : parrello 1.74 =head3 ParseTraceDate
954 :    
955 : parrello 1.92 my $time = Tracer::ParseTraceDate($dateString);
956 : parrello 1.74
957 :     Convert a date from the trace file into a PERL timestamp.
958 :    
959 :     =over 4
960 :    
961 :     =item dateString
962 :    
963 :     The date string from the trace file. The format of the string is determined by the
964 :     L</Now> method.
965 :    
966 :     =item RETURN
967 :    
968 :     Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
969 :     the time string is invalid.
970 :    
971 : parrello 1.78 =back
972 :    
973 : parrello 1.74 =cut
974 :    
975 :     sub ParseTraceDate {
976 :     # Get the parameters.
977 :     my ($dateString) = @_;
978 :     # Declare the return variable.
979 :     my $retVal;
980 :     # Parse the date.
981 :     if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {
982 : parrello 1.76 # Create a time object. Note we need to convert the day, month,
983 :     # and year to a different base. Years count from 1900, and
984 :     # the internal month value is relocated to January = 0.
985 :     $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);
986 : parrello 1.74 }
987 :     # Return the result.
988 :     return $retVal;
989 :     }
990 :    
991 : olson 1.1 =head3 LogErrors
992 :    
993 : parrello 1.92 Tracer::LogErrors($fileName);
994 : olson 1.1
995 :     Route the standard error output to a log file.
996 :    
997 :     =over 4
998 :    
999 :     =item fileName
1000 :    
1001 :     Name of the file to receive the error output.
1002 :    
1003 :     =back
1004 :    
1005 :     =cut
1006 :    
1007 :     sub LogErrors {
1008 : parrello 1.12 # Get the file name.
1009 :     my ($fileName) = @_;
1010 :     # Open the file as the standard error output.
1011 :     open STDERR, '>', $fileName;
1012 : olson 1.1 }
1013 :    
1014 : parrello 1.5 =head3 ReadOptions
1015 :    
1016 : parrello 1.92 my %options = Tracer::ReadOptions($fileName);
1017 : parrello 1.5
1018 :     Read a set of options from a file. Each option is encoded in a line of text that has the
1019 :     format
1020 :    
1021 :     I<optionName>C<=>I<optionValue>C<; >I<comment>
1022 :    
1023 :     The option name must consist entirely of letters, digits, and the punctuation characters
1024 : parrello 1.9 C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1025 :     character is a semi-colon will be ignored. The return hash will map each option name to
1026 : parrello 1.5 the corresponding option value.
1027 :    
1028 :     =over 4
1029 :    
1030 :     =item fileName
1031 :    
1032 :     Name of the file containing the option data.
1033 :    
1034 :     =item RETURN
1035 :    
1036 :     Returns a hash mapping the option names specified in the file to their corresponding option
1037 :     value.
1038 :    
1039 :     =back
1040 :    
1041 :     =cut
1042 :    
1043 :     sub ReadOptions {
1044 : parrello 1.12 # Get the parameters.
1045 :     my ($fileName) = @_;
1046 :     # Open the file.
1047 :     (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1048 :     # Count the number of records read.
1049 :     my ($records, $comments) = 0;
1050 :     # Create the return hash.
1051 :     my %retVal = ();
1052 :     # Loop through the file, accumulating key-value pairs.
1053 :     while (my $line = <CONFIGFILE>) {
1054 :     # Denote we've read a line.
1055 :     $records++;
1056 :     # Determine the line type.
1057 :     if ($line =~ /^\s*[\n\r]/) {
1058 :     # A blank line is a comment.
1059 :     $comments++;
1060 :     } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1061 :     # Here we have an option assignment.
1062 :     retVal{$1} = $2;
1063 :     } elsif ($line =~ /^\s*;/) {
1064 :     # Here we have a text comment.
1065 :     $comments++;
1066 :     } else {
1067 :     # Here we have an invalid line.
1068 :     Trace("Invalid option statement in record $records.") if T(0);
1069 :     }
1070 :     }
1071 :     # Return the hash created.
1072 :     return %retVal;
1073 : parrello 1.5 }
1074 :    
1075 : olson 1.1 =head3 GetOptions
1076 :    
1077 : parrello 1.92 Tracer::GetOptions(\%defaults, \%options);
1078 : olson 1.1
1079 :     Merge a specified set of options into a table of defaults. This method takes two hash references
1080 :     as input and uses the data from the second to update the first. If the second does not exist,
1081 :     there will be no effect. An error will be thrown if one of the entries in the second hash does not
1082 :     exist in the first.
1083 :    
1084 :     Consider the following example.
1085 :    
1086 : parrello 1.92 my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1087 : olson 1.1
1088 :     In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1089 :     B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1090 :     B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1091 :     the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1092 :     will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1093 :    
1094 : parrello 1.92 {databaseType => 'Oracle'}
1095 : olson 1.1
1096 :     an error will occur because the B<databaseType> option does not exist.
1097 :    
1098 :     =over 4
1099 :    
1100 :     =item defaults
1101 :    
1102 :     Table of default option values.
1103 :    
1104 :     =item options
1105 :    
1106 :     Table of overrides, if any.
1107 :    
1108 :     =item RETURN
1109 :    
1110 :     Returns a reference to the default table passed in as the first parameter.
1111 :    
1112 :     =back
1113 :    
1114 :     =cut
1115 :    
1116 :     sub GetOptions {
1117 : parrello 1.12 # Get the parameters.
1118 :     my ($defaults, $options) = @_;
1119 :     # Check for overrides.
1120 :     if ($options) {
1121 :     # Loop through the overrides.
1122 :     while (my ($option, $setting) = each %{$options}) {
1123 :     # Insure this override exists.
1124 :     if (!exists $defaults->{$option}) {
1125 :     croak "Unrecognized option $option encountered.";
1126 :     } else {
1127 :     # Apply the override.
1128 :     $defaults->{$option} = $setting;
1129 :     }
1130 :     }
1131 :     }
1132 :     # Return the merged table.
1133 :     return $defaults;
1134 : olson 1.1 }
1135 :    
1136 :     =head3 MergeOptions
1137 :    
1138 : parrello 1.92 Tracer::MergeOptions(\%table, \%defaults);
1139 : olson 1.1
1140 :     Merge default values into a hash table. This method looks at the key-value pairs in the
1141 :     second (default) hash, and if a matching key is not found in the first hash, the default
1142 :     pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1143 :     checking and no return value.
1144 :    
1145 :     =over 4
1146 :    
1147 :     =item table
1148 :    
1149 :     Hash table to be updated with the default values.
1150 :    
1151 :     =item defaults
1152 :    
1153 :     Default values to be merged into the first hash table if they are not already present.
1154 :    
1155 :     =back
1156 :    
1157 :     =cut
1158 :    
1159 :     sub MergeOptions {
1160 : parrello 1.12 # Get the parameters.
1161 :     my ($table, $defaults) = @_;
1162 :     # Loop through the defaults.
1163 :     while (my ($key, $value) = each %{$defaults}) {
1164 :     if (!exists $table->{$key}) {
1165 :     $table->{$key} = $value;
1166 :     }
1167 :     }
1168 : olson 1.1 }
1169 :    
1170 :     =head3 Trace
1171 :    
1172 : parrello 1.92 Trace($message);
1173 : olson 1.1
1174 :     Write a trace message to the target location specified in L</TSetup>. If there has not been
1175 :     any prior call to B<TSetup>.
1176 :    
1177 :     =over 4
1178 :    
1179 :     =item message
1180 :    
1181 :     Message to write.
1182 :    
1183 :     =back
1184 :    
1185 :     =cut
1186 :    
1187 :     sub Trace {
1188 : parrello 1.12 # Get the parameters.
1189 :     my ($message) = @_;
1190 :     # Get the timestamp.
1191 :     my $timeStamp = Now();
1192 :     # Format the message. Note we strip off any line terminators at the end.
1193 : parrello 1.90 my $prefix = "[$timeStamp] <$LastCategory>: ";
1194 :     my $formatted = $prefix . Strip($message);
1195 : parrello 1.12 # Process according to the destination.
1196 :     if ($Destination eq "TEXT") {
1197 :     # Write the message to the standard output.
1198 :     print "$formatted\n";
1199 :     } elsif ($Destination eq "ERROR") {
1200 :     # Write the message to the error output.
1201 :     print STDERR "$formatted\n";
1202 :     } elsif ($Destination eq "QUEUE") {
1203 :     # Push the message into the queue.
1204 :     push @Queue, "$formatted";
1205 :     } elsif ($Destination eq "HTML") {
1206 :     # Convert the message to HTML and write it to the standard output.
1207 :     my $escapedMessage = CGI::escapeHTML($message);
1208 : parrello 1.90 print "<p>$timeStamp $LastCategory: $escapedMessage</p>\n";
1209 : parrello 1.4 } elsif ($Destination eq "WARN") {
1210 :     # Emit the message as a warning.
1211 :     warn $message;
1212 : parrello 1.12 } elsif ($Destination =~ m/^>>/) {
1213 :     # Write the trace message to an output file.
1214 : parrello 1.14 (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
1215 : parrello 1.12 print TRACING "$formatted\n";
1216 :     close TRACING;
1217 :     # If the Tee flag is on, echo it to the standard output.
1218 :     if ($TeeFlag) {
1219 :     print "$formatted\n";
1220 :     }
1221 :     }
1222 : olson 1.1 }
1223 :    
1224 :     =head3 T
1225 :    
1226 : parrello 1.92 my $switch = T($category, $traceLevel);
1227 : olson 1.1
1228 : parrello 1.12 or
1229 : parrello 1.2
1230 : parrello 1.92 my $switch = T($traceLevel);
1231 : olson 1.1
1232 :     Return TRUE if the trace level is at or above a specified value and the specified category
1233 :     is active, else FALSE. If no category is specified, the caller's package name is used.
1234 :    
1235 :     =over 4
1236 :    
1237 :     =item category
1238 :    
1239 :     Category to which the message belongs. If not specified, the caller's package name is
1240 :     used.
1241 :    
1242 :     =item traceLevel
1243 :    
1244 :     Relevant tracing level.
1245 :    
1246 :     =item RETURN
1247 :    
1248 :     TRUE if a message at the specified trace level would appear in the trace, else FALSE.
1249 :    
1250 :     =back
1251 :    
1252 :     =cut
1253 :    
1254 :     sub T {
1255 : parrello 1.12 # Declare the return variable.
1256 :     my $retVal = 0;
1257 :     # Only proceed if tracing is turned on.
1258 :     if ($Destination ne "NONE") {
1259 :     # Get the parameters.
1260 :     my ($category, $traceLevel) = @_;
1261 :     if (!defined $traceLevel) {
1262 :     # Here we have no category, so we need to get the calling package.
1263 :     # The calling package is normally the first parameter. If it is
1264 :     # omitted, the first parameter will be the tracelevel. So, the
1265 :     # first thing we do is shift the so-called category into the
1266 :     # $traceLevel variable where it belongs.
1267 :     $traceLevel = $category;
1268 :     my ($package, $fileName, $line) = caller;
1269 : parrello 1.3 # If there is no calling package, we default to "main".
1270 : parrello 1.12 if (!$package) {
1271 : parrello 1.3 $category = "main";
1272 : parrello 1.12 } else {
1273 : parrello 1.87 my @cats = split /::/, $package;
1274 :     $category = $cats[$#cats];
1275 : parrello 1.12 }
1276 :     }
1277 : parrello 1.7 # Save the category name.
1278 :     $LastCategory = $category;
1279 : parrello 1.13 # Convert it to lower case before we hash it.
1280 :     $category = lc $category;
1281 : parrello 1.12 # Use the category and tracelevel to compute the result.
1282 : parrello 1.36 if (ref $traceLevel) {
1283 :     Confess("Bad trace level.");
1284 :     } elsif (ref $TraceLevel) {
1285 :     Confess("Bad trace config.");
1286 :     }
1287 : parrello 1.12 $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
1288 : parrello 1.3 }
1289 : parrello 1.12 # Return the computed result.
1290 : parrello 1.3 return $retVal;
1291 : olson 1.1 }
1292 :    
1293 :     =head3 ParseCommand
1294 :    
1295 : parrello 1.92 my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1296 : olson 1.1
1297 :     Parse a command line consisting of a list of parameters. The initial parameters may be option
1298 : parrello 1.2 specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1299 :     off and merged into a table of default options. The remainder of the command line is
1300 : olson 1.1 returned as a list of positional arguments. For example, consider the following invocation.
1301 :    
1302 : parrello 1.92 my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1303 : olson 1.1
1304 : parrello 1.84 In this case, the list @words will be treated as a command line and there are two options available,
1305 : olson 1.1 B<errors> and B<logFile>. If @words has the following format
1306 :    
1307 : parrello 1.92 -logFile=error.log apple orange rutabaga
1308 : olson 1.1
1309 :     then at the end of the invocation, C<$options> will be
1310 :    
1311 : parrello 1.92 { errors => 0, logFile => 'error.log' }
1312 : olson 1.1
1313 :     and C<@arguments> will contain
1314 :    
1315 : parrello 1.92 apple orange rutabaga
1316 : olson 1.1
1317 : parrello 1.2 The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1318 : parrello 1.84 support for quote characters. Options can be specified with single or double hyphens.
1319 : olson 1.1
1320 :     =over 4
1321 :    
1322 :     =item optionTable
1323 :    
1324 :     Table of default options.
1325 :    
1326 :     =item inputList
1327 :    
1328 :     List of words on the command line.
1329 :    
1330 :     =item RETURN
1331 :    
1332 :     Returns a reference to the option table and a list of the positional arguments.
1333 :    
1334 :     =back
1335 :    
1336 :     =cut
1337 :    
1338 :     sub ParseCommand {
1339 : parrello 1.12 # Get the parameters.
1340 :     my ($optionTable, @inputList) = @_;
1341 :     # Process any options in the input list.
1342 :     my %overrides = ();
1343 : parrello 1.84 while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1344 : parrello 1.12 # Get the current option.
1345 :     my $arg = shift @inputList;
1346 :     # Pull out the option name.
1347 : parrello 1.84 $arg =~ /^--?([^=]*)/g;
1348 : parrello 1.12 my $name = $1;
1349 :     # Check for an option value.
1350 :     if ($arg =~ /\G=(.*)$/g) {
1351 :     # Here we have a value for the option.
1352 :     $overrides{$name} = UnEscape($1);
1353 :     } else {
1354 :     # Here there is no value, so we use 1.
1355 :     $overrides{$name} = 1;
1356 :     }
1357 :     }
1358 :     # Merge the options into the defaults.
1359 :     GetOptions($optionTable, \%overrides);
1360 :     # Translate the remaining parameters.
1361 :     my @retVal = ();
1362 :     for my $inputParm (@inputList) {
1363 :     push @retVal, UnEscape($inputParm);
1364 :     }
1365 :     # Return the results.
1366 :     return ($optionTable, @retVal);
1367 : olson 1.1 }
1368 :    
1369 : parrello 1.9 =head3 Escape
1370 :    
1371 : parrello 1.92 my $codedString = Tracer::Escape($realString);
1372 : parrello 1.9
1373 : parrello 1.25 Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines
1374 : parrello 1.28 replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
1375 :     result is to reverse the effect of L</UnEscape>.
1376 : parrello 1.9
1377 :     =over 4
1378 :    
1379 :     =item realString
1380 :    
1381 :     String to escape.
1382 :    
1383 :     =item RETURN
1384 :    
1385 :     Escaped equivalent of the real string.
1386 :    
1387 :     =back
1388 :    
1389 :     =cut
1390 :    
1391 :     sub Escape {
1392 : parrello 1.12 # Get the parameter.
1393 :     my ($realString) = @_;
1394 :     # Initialize the return variable.
1395 :     my $retVal = "";
1396 :     # Loop through the parameter string, looking for sequences to escape.
1397 :     while (length $realString > 0) {
1398 :     # Look for the first sequence to escape.
1399 : parrello 1.27 if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1400 : parrello 1.12 # Here we found it. The text preceding the sequence is in $1. The sequence
1401 :     # itself is in $2. First, move the clear text to the return variable.
1402 :     $retVal .= $1;
1403 : parrello 1.14 # Strip the processed section off the real string.
1404 :     $realString = substr $realString, (length $2) + (length $1);
1405 : parrello 1.28 # Get the matched character.
1406 : parrello 1.12 my $char = $2;
1407 : parrello 1.28 # If we have a CR, we are done.
1408 :     if ($char ne "\r") {
1409 :     # It's not a CR, so encode the escape sequence.
1410 :     $char =~ tr/\t\n/tn/;
1411 :     $retVal .= "\\" . $char;
1412 :     }
1413 : parrello 1.12 } else {
1414 :     # Here there are no more escape sequences. The rest of the string is
1415 :     # transferred unmodified.
1416 :     $retVal .= $realString;
1417 :     $realString = "";
1418 :     }
1419 :     }
1420 :     # Return the result.
1421 :     return $retVal;
1422 : parrello 1.9 }
1423 :    
1424 : olson 1.1 =head3 UnEscape
1425 :    
1426 : parrello 1.92 my $realString = Tracer::UnEscape($codedString);
1427 : olson 1.1
1428 : parrello 1.25 Replace escape sequences with their actual equivalents. C<\t> will be replaced by
1429 : parrello 1.28 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
1430 :     be deleted.
1431 : olson 1.1
1432 :     =over 4
1433 :    
1434 :     =item codedString
1435 :    
1436 :     String to un-escape.
1437 :    
1438 :     =item RETURN
1439 :    
1440 :     Returns a copy of the original string with the escape sequences converted to their actual
1441 :     values.
1442 :    
1443 :     =back
1444 :    
1445 :     =cut
1446 :    
1447 :     sub UnEscape {
1448 : parrello 1.12 # Get the parameter.
1449 :     my ($codedString) = @_;
1450 :     # Initialize the return variable.
1451 :     my $retVal = "";
1452 :     # Only proceed if the incoming string is nonempty.
1453 :     if (defined $codedString) {
1454 :     # Loop through the parameter string, looking for escape sequences. We can't do
1455 : parrello 1.25 # translating because it causes problems with the escaped slash. ("\\t" becomes
1456 :     # "\<tab>" no matter what we do.)
1457 : parrello 1.12 while (length $codedString > 0) {
1458 :     # Look for the first escape sequence.
1459 : parrello 1.27 if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
1460 : parrello 1.12 # Here we found it. The text preceding the sequence is in $1. The sequence
1461 :     # itself is in $2. First, move the clear text to the return variable.
1462 :     $retVal .= $1;
1463 :     $codedString = substr $codedString, (2 + length $1);
1464 : parrello 1.28 # Get the escape value.
1465 : parrello 1.12 my $char = $2;
1466 : parrello 1.28 # If we have a "\r", we are done.
1467 :     if ($char ne 'r') {
1468 :     # Here it's not an 'r', so we convert it.
1469 :     $char =~ tr/\\tn/\\\t\n/;
1470 :     $retVal .= $char;
1471 :     }
1472 : parrello 1.12 } else {
1473 :     # Here there are no more escape sequences. The rest of the string is
1474 :     # transferred unmodified.
1475 :     $retVal .= $codedString;
1476 :     $codedString = "";
1477 :     }
1478 :     }
1479 :     }
1480 :     # Return the result.
1481 :     return $retVal;
1482 : olson 1.1 }
1483 :    
1484 :     =head3 ParseRecord
1485 :    
1486 : parrello 1.92 my @fields = Tracer::ParseRecord($line);
1487 : olson 1.1
1488 :     Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1489 :     and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1490 :     These will automatically be converted.
1491 :    
1492 :     =over 4
1493 :    
1494 :     =item line
1495 :    
1496 :     Line of data containing the tab-delimited fields.
1497 :    
1498 :     =item RETURN
1499 :    
1500 :     Returns a list of the fields found in the data line.
1501 :    
1502 :     =back
1503 :    
1504 :     =cut
1505 :    
1506 :     sub ParseRecord {
1507 : parrello 1.12 # Get the parameter.
1508 :     my ($line) = @_;
1509 :     # Remove the trailing new-line, if any.
1510 :     chomp $line;
1511 :     # Split the line read into pieces using the tab character.
1512 :     my @retVal = split /\t/, $line;
1513 :     # Trim and fix the escapes in each piece.
1514 :     for my $value (@retVal) {
1515 :     # Trim leading whitespace.
1516 :     $value =~ s/^\s+//;
1517 :     # Trim trailing whitespace.
1518 :     $value =~ s/\s+$//;
1519 :     # Delete the carriage returns.
1520 :     $value =~ s/\r//g;
1521 :     # Convert the escapes into their real values.
1522 :     $value =~ s/\\t/"\t"/ge;
1523 :     $value =~ s/\\n/"\n"/ge;
1524 :     }
1525 :     # Return the result.
1526 :     return @retVal;
1527 : olson 1.1 }
1528 :    
1529 :     =head3 Merge
1530 :    
1531 : parrello 1.92 my @mergedList = Tracer::Merge(@inputList);
1532 : olson 1.1
1533 :     Sort a list of strings and remove duplicates.
1534 :    
1535 :     =over 4
1536 :    
1537 :     =item inputList
1538 :    
1539 :     List of scalars to sort and merge.
1540 :    
1541 :     =item RETURN
1542 :    
1543 :     Returns a list containing the same elements sorted in ascending order with duplicates
1544 :     removed.
1545 :    
1546 :     =back
1547 :    
1548 :     =cut
1549 :    
1550 :     sub Merge {
1551 : parrello 1.12 # Get the input list in sort order.
1552 :     my @inputList = sort @_;
1553 :     # Only proceed if the list has at least two elements.
1554 :     if (@inputList > 1) {
1555 :     # Now we want to move through the list splicing out duplicates.
1556 :     my $i = 0;
1557 :     while ($i < @inputList) {
1558 :     # Get the current entry.
1559 :     my $thisEntry = $inputList[$i];
1560 :     # Find out how many elements duplicate the current entry.
1561 :     my $j = $i + 1;
1562 :     my $dup1 = $i + 1;
1563 :     while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
1564 :     # If the number is nonzero, splice out the duplicates found.
1565 :     if ($j > $dup1) {
1566 :     splice @inputList, $dup1, $j - $dup1;
1567 :     }
1568 :     # Now the element at position $dup1 is different from the element before it
1569 :     # at position $i. We push $i forward one position and start again.
1570 :     $i++;
1571 :     }
1572 :     }
1573 :     # Return the merged list.
1574 :     return @inputList;
1575 : olson 1.1 }
1576 :    
1577 : parrello 1.54 =head3 Percent
1578 :    
1579 : parrello 1.92 my $percent = Tracer::Percent($number, $base);
1580 : parrello 1.54
1581 :     Returns the percent of the base represented by the given number. If the base
1582 :     is zero, returns zero.
1583 :    
1584 :     =over 4
1585 :    
1586 :     =item number
1587 :    
1588 :     Percent numerator.
1589 :    
1590 :     =item base
1591 :    
1592 :     Percent base.
1593 :    
1594 :     =item RETURN
1595 :    
1596 :     Returns the percentage of the base represented by the numerator.
1597 :    
1598 :     =back
1599 :    
1600 :     =cut
1601 :    
1602 :     sub Percent {
1603 :     # Get the parameters.
1604 :     my ($number, $base) = @_;
1605 :     # Declare the return variable.
1606 :     my $retVal = 0;
1607 :     # Compute the percent.
1608 :     if ($base != 0) {
1609 :     $retVal = $number * 100 / $base;
1610 :     }
1611 :     # Return the result.
1612 :     return $retVal;
1613 :     }
1614 :    
1615 : olson 1.1 =head3 GetFile
1616 :    
1617 : parrello 1.92 my @fileContents = Tracer::GetFile($fileName);
1618 : olson 1.1
1619 : parrello 1.35 or
1620 :    
1621 : parrello 1.92 my $fileContents = Tracer::GetFile($fileName);
1622 : parrello 1.35
1623 :     Return the entire contents of a file. In list context, line-ends are removed and
1624 :     each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1625 : olson 1.1
1626 :     =over 4
1627 :    
1628 :     =item fileName
1629 :    
1630 :     Name of the file to read.
1631 :    
1632 :     =item RETURN
1633 :    
1634 : parrello 1.6 In a list context, returns the entire file as a list with the line terminators removed.
1635 : parrello 1.39 In a scalar context, returns the entire file as a string. If an error occurs opening
1636 :     the file, an empty list will be returned.
1637 : olson 1.1
1638 :     =back
1639 :    
1640 :     =cut
1641 :    
1642 :     sub GetFile {
1643 : parrello 1.12 # Get the parameters.
1644 :     my ($fileName) = @_;
1645 :     # Declare the return variable.
1646 :     my @retVal = ();
1647 :     # Open the file for input.
1648 : parrello 1.60 my $handle = Open(undef, "<$fileName");
1649 :     # Read the whole file into the return variable, stripping off any terminator
1650 :     # characters.
1651 :     my $lineCount = 0;
1652 :     while (my $line = <$handle>) {
1653 :     $lineCount++;
1654 :     $line = Strip($line);
1655 :     push @retVal, $line;
1656 :     }
1657 :     # Close it.
1658 :     close $handle;
1659 :     my $actualLines = @retVal;
1660 : parrello 1.77 Trace("$actualLines lines read from file $fileName.") if T(File => 2);
1661 : parrello 1.12 # Return the file's contents in the desired format.
1662 : parrello 1.9 if (wantarray) {
1663 : parrello 1.12 return @retVal;
1664 : parrello 1.6 } else {
1665 :     return join "\n", @retVal;
1666 :     }
1667 : olson 1.1 }
1668 :    
1669 : parrello 1.60 =head3 PutFile
1670 :    
1671 : parrello 1.92 Tracer::PutFile($fileName, \@lines);
1672 : parrello 1.60
1673 :     Write out a file from a list of lines of text.
1674 :    
1675 :     =over 4
1676 :    
1677 :     =item fileName
1678 :    
1679 :     Name of the output file.
1680 :    
1681 :     =item lines
1682 :    
1683 :     Reference to a list of text lines. The lines will be written to the file in order, with trailing
1684 : parrello 1.66 new-line characters. Alternatively, may be a string, in which case the string will be written without
1685 :     modification.
1686 : parrello 1.60
1687 :     =back
1688 :    
1689 :     =cut
1690 :    
1691 :     sub PutFile {
1692 :     # Get the parameters.
1693 :     my ($fileName, $lines) = @_;
1694 :     # Open the output file.
1695 :     my $handle = Open(undef, ">$fileName");
1696 : parrello 1.77 # Count the lines written.
1697 : parrello 1.66 if (ref $lines ne 'ARRAY') {
1698 :     # Here we have a scalar, so we write it raw.
1699 :     print $handle $lines;
1700 : parrello 1.77 Trace("Scalar put to file $fileName.") if T(File => 3);
1701 : parrello 1.66 } else {
1702 :     # Write the lines one at a time.
1703 : parrello 1.77 my $count = 0;
1704 : parrello 1.66 for my $line (@{$lines}) {
1705 :     print $handle "$line\n";
1706 : parrello 1.77 $count++;
1707 : parrello 1.66 }
1708 : parrello 1.77 Trace("$count lines put to file $fileName.") if T(File => 3);
1709 : parrello 1.60 }
1710 :     # Close the output file.
1711 :     close $handle;
1712 :     }
1713 :    
1714 : olson 1.1 =head3 QTrace
1715 :    
1716 : parrello 1.92 my $data = QTrace($format);
1717 : olson 1.1
1718 :     Return the queued trace data in the specified format.
1719 :    
1720 :     =over 4
1721 :    
1722 :     =item format
1723 :    
1724 :     C<html> to format the data as an HTML list, C<text> to format it as straight text.
1725 :    
1726 :     =back
1727 :    
1728 :     =cut
1729 :    
1730 :     sub QTrace {
1731 : parrello 1.12 # Get the parameter.
1732 :     my ($format) = @_;
1733 :     # Create the return variable.
1734 :     my $retVal = "";
1735 : parrello 1.14 # Only proceed if there is an actual queue.
1736 :     if (@Queue) {
1737 :     # Process according to the format.
1738 :     if ($format =~ m/^HTML$/i) {
1739 :     # Convert the queue into an HTML list.
1740 :     $retVal = "<ul>\n";
1741 :     for my $line (@Queue) {
1742 :     my $escapedLine = CGI::escapeHTML($line);
1743 :     $retVal .= "<li>$escapedLine</li>\n";
1744 :     }
1745 :     $retVal .= "</ul>\n";
1746 :     } elsif ($format =~ m/^TEXT$/i) {
1747 :     # Convert the queue into a list of text lines.
1748 :     $retVal = join("\n", @Queue) . "\n";
1749 :     }
1750 :     # Clear the queue.
1751 :     @Queue = ();
1752 : parrello 1.12 }
1753 :     # Return the formatted list.
1754 :     return $retVal;
1755 : olson 1.1 }
1756 :    
1757 :     =head3 Confess
1758 :    
1759 : parrello 1.92 Confess($message);
1760 : olson 1.1
1761 : parrello 1.22 Trace the call stack and abort the program with the specified message. When used with
1762 : parrello 1.9 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
1763 : parrello 1.6 So, for example
1764 : olson 1.1
1765 : parrello 1.92 Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
1766 : olson 1.1
1767 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
1768 :    
1769 :     =over 4
1770 :    
1771 :     =item message
1772 :    
1773 :     Message to include in the trace.
1774 :    
1775 :     =back
1776 :    
1777 :     =cut
1778 :    
1779 :     sub Confess {
1780 : parrello 1.12 # Get the parameters.
1781 :     my ($message) = @_;
1782 : parrello 1.87 if (! defined($FIG_Config::no_tool_hdr)) {
1783 :     # Here we have a tool header. Display its length so that the user can adjust the line numbers.
1784 : parrello 1.90 my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
1785 : parrello 1.89 # Only proceed if the tool header file is actually present.
1786 :     if (-f $toolHeaderFile) {
1787 :     my @lines = GetFile($toolHeaderFile);
1788 :     Trace("Tool header has " . scalar(@lines) . " lines.");
1789 :     }
1790 : parrello 1.87 }
1791 : parrello 1.12 # Trace the call stack.
1792 : parrello 1.22 Cluck($message);
1793 : parrello 1.12 # Abort the program.
1794 :     croak(">>> $message");
1795 : olson 1.1 }
1796 :    
1797 : parrello 1.6 =head3 Assert
1798 :    
1799 : parrello 1.92 Assert($condition1, $condition2, ... $conditionN);
1800 : parrello 1.6
1801 :     Return TRUE if all the conditions are true. This method can be used in conjunction with
1802 : parrello 1.29 the OR operator and the L</Confess> method as a debugging assert.
1803 : parrello 1.6 So, for example
1804 :    
1805 : parrello 1.92 Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
1806 : parrello 1.6
1807 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
1808 :    
1809 :     =cut
1810 :     sub Assert {
1811 :     my $retVal = 1;
1812 :     LOOP: for my $condition (@_) {
1813 :     if (! $condition) {
1814 :     $retVal = 0;
1815 :     last LOOP;
1816 :     }
1817 :     }
1818 :     return $retVal;
1819 :     }
1820 :    
1821 : olson 1.1 =head3 Cluck
1822 :    
1823 : parrello 1.92 Cluck($message);
1824 : olson 1.1
1825 :     Trace the call stack. Note that for best results, you should qualify the call with a
1826 :     trace condition. For example,
1827 :    
1828 : parrello 1.92 Cluck("Starting record parse.") if T(3);
1829 : olson 1.1
1830 :     will only trace the stack if the trace level for the package is 3 or more.
1831 :    
1832 :     =over 4
1833 :    
1834 :     =item message
1835 :    
1836 :     Message to include in the trace.
1837 :    
1838 :     =back
1839 :    
1840 :     =cut
1841 :    
1842 :     sub Cluck {
1843 : parrello 1.12 # Get the parameters.
1844 :     my ($message) = @_;
1845 : parrello 1.5 # Trace what's happening.
1846 :     Trace("Stack trace for event: $message");
1847 : parrello 1.12 my $confession = longmess($message);
1848 :     # Convert the confession to a series of trace messages. Note we skip any
1849 : parrello 1.5 # messages relating to calls into Tracer.
1850 : parrello 1.12 for my $line (split /\s*\n/, $confession) {
1851 :     Trace($line) if ($line !~ /Tracer\.pm/);
1852 :     }
1853 : olson 1.1 }
1854 :    
1855 : parrello 1.5 =head3 Min
1856 :    
1857 : parrello 1.92 my $min = Min($value1, $value2, ... $valueN);
1858 : parrello 1.5
1859 :     Return the minimum argument. The arguments are treated as numbers.
1860 :    
1861 :     =over 4
1862 :    
1863 :     =item $value1, $value2, ... $valueN
1864 :    
1865 :     List of numbers to compare.
1866 :    
1867 :     =item RETURN
1868 :    
1869 :     Returns the lowest number in the list.
1870 :    
1871 :     =back
1872 :    
1873 :     =cut
1874 :    
1875 :     sub Min {
1876 : parrello 1.12 # Get the parameters. Note that we prime the return value with the first parameter.
1877 :     my ($retVal, @values) = @_;
1878 :     # Loop through the remaining parameters, looking for the lowest.
1879 :     for my $value (@values) {
1880 :     if ($value < $retVal) {
1881 :     $retVal = $value;
1882 :     }
1883 :     }
1884 :     # Return the minimum found.
1885 :     return $retVal;
1886 : parrello 1.5 }
1887 :    
1888 :     =head3 Max
1889 :    
1890 : parrello 1.92 my $max = Max($value1, $value2, ... $valueN);
1891 : parrello 1.5
1892 :     Return the maximum argument. The arguments are treated as numbers.
1893 :    
1894 :     =over 4
1895 :    
1896 :     =item $value1, $value2, ... $valueN
1897 :    
1898 :     List of numbers to compare.
1899 :    
1900 :     =item RETURN
1901 :    
1902 :     Returns the highest number in the list.
1903 :    
1904 :     =back
1905 :    
1906 :     =cut
1907 :    
1908 :     sub Max {
1909 : parrello 1.12 # Get the parameters. Note that we prime the return value with the first parameter.
1910 :     my ($retVal, @values) = @_;
1911 :     # Loop through the remaining parameters, looking for the highest.
1912 :     for my $value (@values) {
1913 :     if ($value > $retVal) {
1914 :     $retVal = $value;
1915 :     }
1916 :     }
1917 :     # Return the maximum found.
1918 :     return $retVal;
1919 : parrello 1.5 }
1920 :    
1921 :     =head3 AddToListMap
1922 :    
1923 : parrello 1.92 Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN);
1924 : parrello 1.5
1925 :     Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list
1926 :     is created for the key. Otherwise, the new value is pushed onto the list.
1927 :    
1928 :     =over 4
1929 :    
1930 :     =item hash
1931 :    
1932 :     Reference to the target hash.
1933 :    
1934 :     =item key
1935 :    
1936 :     Key for which the value is to be added.
1937 :    
1938 : parrello 1.53 =item value1, value2, ... valueN
1939 : parrello 1.5
1940 : parrello 1.53 List of values to add to the key's value list.
1941 : parrello 1.5
1942 :     =back
1943 :    
1944 :     =cut
1945 :    
1946 :     sub AddToListMap {
1947 :     # Get the parameters.
1948 : parrello 1.53 my ($hash, $key, @values) = @_;
1949 : parrello 1.5 # Process according to whether or not the key already has a value.
1950 :     if (! exists $hash->{$key}) {
1951 : parrello 1.53 $hash->{$key} = [@values];
1952 : parrello 1.5 } else {
1953 : parrello 1.53 push @{$hash->{$key}}, @values;
1954 : parrello 1.5 }
1955 :     }
1956 : olson 1.1
1957 : parrello 1.7 =head3 DebugMode
1958 :    
1959 : parrello 1.92 if (Tracer::DebugMode) { ...code... }
1960 : parrello 1.7
1961 : parrello 1.69 Return TRUE if debug mode has been turned on, else abort.
1962 : parrello 1.7
1963 :     Certain CGI scripts are too dangerous to exist in the production
1964 :     environment. This method provides a simple way to prevent them
1965 : parrello 1.21 from working unless they are explicitly turned on by creating a password
1966 :     cookie via the B<SetPassword> script. If debugging mode
1967 : parrello 1.69 is not turned on, an error will occur.
1968 : parrello 1.7
1969 :     =cut
1970 :    
1971 :     sub DebugMode {
1972 : parrello 1.12 # Declare the return variable.
1973 : parrello 1.21 my $retVal = 0;
1974 : parrello 1.12 # Check the debug configuration.
1975 : parrello 1.21 my $password = CGI::cookie("DebugMode");
1976 :     my $encrypted = Digest::MD5::md5_hex($password);
1977 :     if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1978 : parrello 1.12 $retVal = 1;
1979 :     } else {
1980 : parrello 1.69 # Here debug mode is off, so we generate an error.
1981 :     Confess("Cannot use this facility without logging in.");
1982 : parrello 1.12 }
1983 :     # Return the determination indicator.
1984 : parrello 1.18 return $retVal;
1985 : parrello 1.9 }
1986 :    
1987 :     =head3 Strip
1988 :    
1989 : parrello 1.92 my $string = Tracer::Strip($line);
1990 : parrello 1.9
1991 :     Strip all line terminators off a string. This is necessary when dealing with files
1992 :     that may have been transferred back and forth several times among different
1993 :     operating environments.
1994 :    
1995 :     =over 4
1996 :    
1997 :     =item line
1998 :    
1999 :     Line of text to be stripped.
2000 :    
2001 :     =item RETURN
2002 :    
2003 :     The same line of text with all the line-ending characters chopped from the end.
2004 :    
2005 :     =back
2006 :    
2007 :     =cut
2008 :    
2009 :     sub Strip {
2010 : parrello 1.12 # Get a copy of the parameter string.
2011 :     my ($string) = @_;
2012 : parrello 1.29 my $retVal = (defined $string ? $string : "");
2013 : parrello 1.9 # Strip the line terminator characters.
2014 :     $retVal =~ s/(\r|\n)+$//g;
2015 : parrello 1.12 # Return the result.
2016 :     return $retVal;
2017 : parrello 1.9 }
2018 :    
2019 :     =head3 Pad
2020 :    
2021 : parrello 1.92 my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
2022 : parrello 1.9
2023 :     Pad a string to a specified length. The pad character will be a
2024 :     space, and the padding will be on the right side unless specified
2025 :     in the third parameter.
2026 :    
2027 :     =over 4
2028 :    
2029 :     =item string
2030 :    
2031 :     String to be padded.
2032 :    
2033 :     =item len
2034 :    
2035 :     Desired length of the padded string.
2036 :    
2037 :     =item left (optional)
2038 :    
2039 :     TRUE if the string is to be left-padded; otherwise it will be padded on the right.
2040 :    
2041 :     =item padChar (optional)
2042 :    
2043 : parrello 1.22 Character to use for padding. The default is a space.
2044 :    
2045 : parrello 1.9 =item RETURN
2046 :    
2047 : parrello 1.22 Returns a copy of the original string with the pad character added to the
2048 :     specified end so that it achieves the desired length.
2049 : parrello 1.9
2050 :     =back
2051 :    
2052 :     =cut
2053 :    
2054 :     sub Pad {
2055 : parrello 1.12 # Get the parameters.
2056 :     my ($string, $len, $left, $padChar) = @_;
2057 :     # Compute the padding character.
2058 :     if (! defined $padChar) {
2059 :     $padChar = " ";
2060 :     }
2061 :     # Compute the number of spaces needed.
2062 :     my $needed = $len - length $string;
2063 :     # Copy the string into the return variable.
2064 :     my $retVal = $string;
2065 :     # Only proceed if padding is needed.
2066 :     if ($needed > 0) {
2067 :     # Create the pad string.
2068 :     my $pad = $padChar x $needed;
2069 :     # Affix it to the return value.
2070 :     if ($left) {
2071 :     $retVal = $pad . $retVal;
2072 :     } else {
2073 :     $retVal .= $pad;
2074 :     }
2075 :     }
2076 :     # Return the result.
2077 :     return $retVal;
2078 : parrello 1.7 }
2079 :    
2080 : parrello 1.29 =head3 EOF
2081 :    
2082 :     This is a constant that is lexically greater than any useful string.
2083 :    
2084 :     =cut
2085 :    
2086 :     sub EOF {
2087 :     return "\xFF\xFF\xFF\xFF\xFF";
2088 :     }
2089 :    
2090 : parrello 1.15 =head3 TICK
2091 :    
2092 : parrello 1.92 my @results = TICK($commandString);
2093 : parrello 1.15
2094 :     Perform a back-tick operation on a command. If this is a Windows environment, any leading
2095 :     dot-slash (C<./> will be removed. So, for example, if you were doing
2096 :    
2097 :     `./protein.cgi`
2098 :    
2099 :     from inside a CGI script, it would work fine in Unix, but would issue an error message
2100 :     in Windows complaining that C<'.'> is not a valid command. If instead you code
2101 :    
2102 :     TICK("./protein.cgi")
2103 :    
2104 :     it will work correctly in both environments.
2105 :    
2106 :     =over 4
2107 :    
2108 :     =item commandString
2109 :    
2110 :     The command string to pass to the system.
2111 :    
2112 :     =item RETURN
2113 :    
2114 :     Returns the standard output from the specified command, as a list.
2115 :    
2116 :     =back
2117 :    
2118 :     =cut
2119 :     #: Return Type @;
2120 :     sub TICK {
2121 :     # Get the parameters.
2122 :     my ($commandString) = @_;
2123 :     # Chop off the dot-slash if this is Windows.
2124 :     if ($FIG_Config::win_mode) {
2125 :     $commandString =~ s!^\./!!;
2126 :     }
2127 :     # Activate the command and return the result.
2128 :     return `$commandString`;
2129 :     }
2130 :    
2131 : parrello 1.35 =head3 ScriptSetup
2132 :    
2133 : parrello 1.92 my ($cgi, $varHash) = ScriptSetup($noTrace);
2134 : parrello 1.35
2135 :     Perform standard tracing and debugging setup for scripts. The value returned is
2136 : parrello 1.81 the CGI object followed by a pre-built variable hash. At the end of the script,
2137 :     the client should call L</ScriptFinish> to output the web page.
2138 : parrello 1.35
2139 : parrello 1.81 This method calls L</ETracing> to configure tracing, which allows the tracing
2140 :     to be configured via the emergency tracing form on the debugging control panel.
2141 : parrello 1.72 Tracing will then be turned on automatically for all programs that use the L</ETracing>
2142 :     method, which includes every program that uses this method or L</StandardSetup>.
2143 : parrello 1.69
2144 :     =over 4
2145 :    
2146 :     =item noTrace (optional)
2147 :    
2148 :     If specified, tracing will be suppressed. This is useful if the script wants to set up
2149 :     tracing manually.
2150 :    
2151 :     =item RETURN
2152 :    
2153 :     Returns a two-element list consisting of a CGI query object and a variable hash for
2154 :     the output page.
2155 :    
2156 :     =back
2157 : parrello 1.35
2158 :     =cut
2159 :    
2160 :     sub ScriptSetup {
2161 : parrello 1.69 # Get the parameters.
2162 :     my ($noTrace) = @_;
2163 : parrello 1.35 # Get the CGI query object.
2164 : parrello 1.69 my $cgi = CGI->new();
2165 :     # Set up tracing if it's not suppressed.
2166 : parrello 1.72 ETracing($cgi) unless $noTrace;
2167 : parrello 1.69 # Create the variable hash.
2168 :     my $varHash = { results => '' };
2169 :     # Return the query object and variable hash.
2170 :     return ($cgi, $varHash);
2171 :     }
2172 :    
2173 : parrello 1.72 =head3 ETracing
2174 : parrello 1.69
2175 : parrello 1.92 ETracing($parameter);
2176 : parrello 1.69
2177 : parrello 1.72 Set up emergency tracing. Emergency tracing is tracing that is turned
2178 :     on automatically for any program that calls this method. The emergency
2179 :     tracing parameters are stored in a a file identified by a tracing key.
2180 :     If this method is called with a CGI object, then the tracing key is
2181 :     taken from a cookie. If it is called with no parameters, then the tracing
2182 :     key is taken from an environment variable. If it is called with a string,
2183 :     the tracing key is that string.
2184 : parrello 1.69
2185 :     =over 4
2186 :    
2187 : parrello 1.72 =item parameter
2188 : parrello 1.69
2189 : parrello 1.72 A parameter from which the tracing key is computed. If it is a scalar,
2190 :     that scalar is used as the tracing key. If it is a CGI object, the
2191 :     tracing key is taken from the C<IP> cookie. If it is omitted, the
2192 :     tracing key is taken from the C<TRACING> environment variable. If it
2193 :     is a CGI object and emergency tracing is not on, the C<Trace> and
2194 :     C<TF> parameters will be used to determine the type of tracing.
2195 : parrello 1.69
2196 :     =back
2197 :    
2198 :     =cut
2199 :    
2200 : parrello 1.72 sub ETracing {
2201 :     # Get the parameter.
2202 :     my ($parameter) = @_;
2203 :     # Check for CGI mode.
2204 :     my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
2205 : parrello 1.69 # Default to no tracing except errors.
2206 :     my ($tracing, $dest) = ("0", "WARN");
2207 :     # Check for emergency tracing.
2208 : parrello 1.72 my $tkey = EmergencyKey($parameter);
2209 :     my $emergencyFile = EmergencyFileName($tkey);
2210 : parrello 1.69 if (-e $emergencyFile) {
2211 :     # We have the file. Read in the data.
2212 :     my @tracing = GetFile($emergencyFile);
2213 :     # Pull off the time limit.
2214 :     my $expire = shift @tracing;
2215 :     # Convert it to seconds.
2216 :     $expire *= 3600;
2217 :     # Check the file data.
2218 :     my $stat = stat($emergencyFile);
2219 :     my ($now) = gettimeofday;
2220 :     if ($now - $stat->mtime > $expire) {
2221 :     # Delete the expired file.
2222 :     unlink $emergencyFile;
2223 :     } else {
2224 :     # Emergency tracing is on. Pull off the destination and
2225 :     # the trace level;
2226 :     $dest = shift @tracing;
2227 :     my $level = shift @tracing;
2228 :     # Convert the destination to a real tracing destination.
2229 :     # temp directory.
2230 : parrello 1.72 $dest = EmergencyTracingDest($tkey, $dest);
2231 : parrello 1.69 # Insure Tracer is specified.
2232 :     my %moduleHash = map { $_ => 1 } @tracing;
2233 :     $moduleHash{Tracer} = 1;
2234 :     # Set the trace parameter.
2235 :     $tracing = join(" ", $level, sort keys %moduleHash);
2236 : parrello 1.72 }
2237 :     } elsif (defined $cgi) {
2238 :     # There's no emergency tracing, but we have a CGI object, so check
2239 :     # for tracing from the form parameters.
2240 :     if ($cgi->param('Trace')) {
2241 :     # Here the user has requested tracing via a form.
2242 :     $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
2243 :     $tracing = $cgi->param('Trace') . " Tracer";
2244 :     }
2245 :     }
2246 : parrello 1.69 # Setup the tracing we've determined from all the stuff above.
2247 :     TSetup($tracing, $dest);
2248 : parrello 1.72 # If we're a web script, trace the parameter and environment data.
2249 :     if (defined $cgi) {
2250 :     TraceParms($cgi);
2251 :     }
2252 : parrello 1.69 }
2253 :    
2254 :     =head3 EmergencyFileName
2255 :    
2256 : parrello 1.92 my $fileName = Tracer::EmergencyFileName($tkey);
2257 : parrello 1.69
2258 :     Return the emergency tracing file name. This is the file that specifies
2259 :     the tracing information.
2260 :    
2261 :     =over 4
2262 :    
2263 : parrello 1.72 =item tkey
2264 : parrello 1.69
2265 : parrello 1.72 Tracing key for the current program.
2266 : parrello 1.69
2267 :     =item RETURN
2268 :    
2269 :     Returns the name of the file to contain the emergency tracing information.
2270 :    
2271 :     =back
2272 :    
2273 :     =cut
2274 :    
2275 :     sub EmergencyFileName {
2276 :     # Get the parameters.
2277 : parrello 1.72 my ($tkey) = @_;
2278 : parrello 1.69 # Compute the emergency tracing file name.
2279 : parrello 1.72 return "$FIG_Config::temp/Emergency$tkey.txt";
2280 : parrello 1.69 }
2281 :    
2282 :     =head3 EmergencyFileTarget
2283 :    
2284 : parrello 1.92 my $fileName = Tracer::EmergencyFileTarget($tkey);
2285 : parrello 1.69
2286 :     Return the emergency tracing target file name. This is the file that receives
2287 :     the tracing output for file-based tracing.
2288 :    
2289 :     =over 4
2290 :    
2291 : parrello 1.72 =item tkey
2292 : parrello 1.69
2293 : parrello 1.72 Tracing key for the current program.
2294 : parrello 1.69
2295 :     =item RETURN
2296 :    
2297 : parrello 1.72 Returns the name of the file to contain the trace output.
2298 : parrello 1.69
2299 :     =back
2300 :    
2301 :     =cut
2302 :    
2303 :     sub EmergencyFileTarget {
2304 :     # Get the parameters.
2305 : parrello 1.72 my ($tkey) = @_;
2306 : parrello 1.69 # Compute the emergency tracing file name.
2307 : parrello 1.72 return "$FIG_Config::temp/trace$tkey.log";
2308 : parrello 1.69 }
2309 :    
2310 :     =head3 EmergencyTracingDest
2311 :    
2312 : parrello 1.92 my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
2313 : parrello 1.69
2314 :     This method converts an emergency tracing destination to a real
2315 :     tracing destination. The main difference is that if the
2316 :     destination is C<FILE> or C<APPEND>, we convert it to file
2317 : parrello 1.84 output. If the destination is C<DUAL>, we convert it to file
2318 :     and standard output.
2319 : parrello 1.69
2320 :     =over 4
2321 :    
2322 : parrello 1.72 =item tkey
2323 : parrello 1.69
2324 : parrello 1.72 Tracing key for this environment.
2325 : parrello 1.69
2326 :     =item myDest
2327 :    
2328 :     Destination from the emergency tracing file.
2329 :    
2330 :     =item RETURN
2331 :    
2332 :     Returns a destination that can be passed into L</TSetup>.
2333 :    
2334 :     =back
2335 :    
2336 :     =cut
2337 :    
2338 :     sub EmergencyTracingDest {
2339 :     # Get the parameters.
2340 : parrello 1.72 my ($tkey, $myDest) = @_;
2341 : parrello 1.69 # Declare the return variable.
2342 : parrello 1.86 my $retVal = $myDest;
2343 : parrello 1.69 # Process according to the destination value.
2344 :     if ($myDest eq 'FILE') {
2345 : parrello 1.72 $retVal = ">" . EmergencyFileTarget($tkey);
2346 : parrello 1.69 } elsif ($myDest eq 'APPEND') {
2347 : parrello 1.72 $retVal = ">>" . EmergencyFileTarget($tkey);
2348 : parrello 1.84 } elsif ($myDest eq 'DUAL') {
2349 :     $retVal = "+>" . EmergencyFileTarget($tkey);
2350 : parrello 1.35 }
2351 : parrello 1.69 # Return the result.
2352 :     return $retVal;
2353 :     }
2354 :    
2355 :     =head3 Emergency
2356 :    
2357 : parrello 1.92 Emergency($key, $hours, $dest, $level, @modules);
2358 : parrello 1.69
2359 : parrello 1.84 Turn on emergency tracing. This method is normally invoked over the web from
2360 :     a debugging console, but it can also be called by the C<trace.pl> script.
2361 :     The caller specifies the duration of the emergency in hours, the desired tracing
2362 :     destination, the trace level, and a list of the trace modules to activate.
2363 :     For the length of the duration, when a program in an environment with the
2364 :     specified tracing key active invokes a Sprout CGI script, tracing will be
2365 :     turned on automatically. See L</TSetup> for more about tracing setup and
2366 :     L</ETracing> for more about emergency tracing.
2367 : parrello 1.69
2368 :     =over 4
2369 :    
2370 : parrello 1.72 =item tkey
2371 : parrello 1.69
2372 : parrello 1.72 The tracing key. This is used to identify the control file and the trace file.
2373 : parrello 1.69
2374 :     =item hours
2375 :    
2376 :     Number of hours to keep emergency tracing alive.
2377 :    
2378 :     =item dest
2379 :    
2380 :     Tracing destination. If no path information is specified for a file
2381 :     destination, it is put in the FIG temporary directory.
2382 :    
2383 :     =item level
2384 :    
2385 :     Tracing level. A higher level means more trace messages.
2386 :    
2387 :     =item modules
2388 :    
2389 :     A list of the tracing modules to activate.
2390 :    
2391 :     =back
2392 :    
2393 :     =cut
2394 :    
2395 :     sub Emergency {
2396 :     # Get the parameters.
2397 : parrello 1.72 my ($tkey, $hours, $dest, $level, @modules) = @_;
2398 : parrello 1.69 # Create the emergency file.
2399 : parrello 1.72 my $specFile = EmergencyFileName($tkey);
2400 : parrello 1.69 my $outHandle = Open(undef, ">$specFile");
2401 : parrello 1.71 print $outHandle join("\n", $hours, $dest, $level, @modules, "");
2402 : parrello 1.69 }
2403 :    
2404 : parrello 1.72 =head3 EmergencyKey
2405 : parrello 1.69
2406 : parrello 1.92 my $tkey = EmergencyKey($parameter);
2407 : parrello 1.69
2408 : parrello 1.72 Return the Key to be used for emergency tracing. This could be an IP address,
2409 :     a session ID, or a user name, depending on the environment.
2410 : parrello 1.69
2411 :     =over 4
2412 :    
2413 : parrello 1.72 =item parameter
2414 : parrello 1.69
2415 : parrello 1.72 Parameter defining the method for finding the tracing key. If it is a scalar,
2416 :     then it is presumed to be the tracing key itself. If it is a CGI object, then
2417 :     the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
2418 :     taken from the C<TRACING> environment variable.
2419 : parrello 1.69
2420 :     =item RETURN
2421 :    
2422 : parrello 1.72 Returns the key to be used for labels in emergency tracing.
2423 : parrello 1.69
2424 :     =back
2425 :    
2426 :     =cut
2427 :    
2428 : parrello 1.72 sub EmergencyKey {
2429 : parrello 1.69 # Get the parameters.
2430 : parrello 1.72 my ($parameter) = @_;
2431 :     # Declare the return variable.
2432 :     my $retVal;
2433 :     # Determine the parameter type.
2434 :     if (! defined $parameter) {
2435 :     # Here we're supposed to check the environment.
2436 :     $retVal = $ENV{TRACING};
2437 :     } else {
2438 :     my $ptype = ref $parameter;
2439 :     if ($ptype eq 'CGI') {
2440 :     # Here we were invoked from a web page. Look for a cookie.
2441 :     $retVal = $parameter->cookie('IP');
2442 :     } elsif (! $ptype) {
2443 :     # Here the key was passed in.
2444 :     $retVal = $parameter;
2445 :     }
2446 :     }
2447 :     # If no luck finding a key, use the PID.
2448 :     if (! defined $retVal) {
2449 :     $retVal = $$;
2450 :     }
2451 : parrello 1.69 # Return the result.
2452 : parrello 1.70 return $retVal;
2453 : parrello 1.35 }
2454 :    
2455 : parrello 1.69
2456 : parrello 1.65 =head3 TraceParms
2457 :    
2458 : parrello 1.92 Tracer::TraceParms($cgi);
2459 : parrello 1.65
2460 :     Trace the CGI parameters at trace level CGI => 3 and the environment variables
2461 :     at level CGI => 4.
2462 :    
2463 :     =over 4
2464 :    
2465 : parrello 1.69 =item cgi
2466 : parrello 1.65
2467 :     CGI query object containing the parameters to trace.
2468 :    
2469 :     =back
2470 :    
2471 :     =cut
2472 :    
2473 :     sub TraceParms {
2474 :     # Get the parameters.
2475 : parrello 1.69 my ($cgi) = @_;
2476 : parrello 1.65 if (T(CGI => 3)) {
2477 :     # Here we want to trace the parameter data.
2478 : parrello 1.69 my @names = $cgi->param;
2479 : parrello 1.65 for my $parmName (sort @names) {
2480 : parrello 1.68 # Note we skip the Trace parameters, which are for our use only.
2481 :     if ($parmName ne 'Trace' && $parmName ne 'TF') {
2482 : parrello 1.69 my @values = $cgi->param($parmName);
2483 : parrello 1.65 Trace("CGI: $parmName = " . join(", ", @values));
2484 :     }
2485 :     }
2486 : parrello 1.67 # Display the request method.
2487 : parrello 1.69 my $method = $cgi->request_method();
2488 : parrello 1.67 Trace("Method: $method");
2489 : parrello 1.65 }
2490 :     if (T(CGI => 4)) {
2491 :     # Here we want the environment data too.
2492 :     for my $envName (sort keys %ENV) {
2493 :     Trace("ENV: $envName = $ENV{$envName}");
2494 :     }
2495 :     }
2496 :     }
2497 :    
2498 : parrello 1.35 =head3 ScriptFinish
2499 :    
2500 : parrello 1.92 ScriptFinish($webData, $varHash);
2501 : parrello 1.35
2502 :     Output a web page at the end of a script. Either the string to be output or the
2503 :     name of a template file can be specified. If the second parameter is omitted,
2504 :     it is assumed we have a string to be output; otherwise, it is assumed we have the
2505 :     name of a template file. The template should have the variable C<DebugData>
2506 :     specified in any form that invokes a standard script. If debugging mode is turned
2507 :     on, a form field will be put in that allows the user to enter tracing data.
2508 :     Trace messages will be placed immediately before the terminal C<BODY> tag in
2509 :     the output, formatted as a list.
2510 :    
2511 :     A typical standard script would loook like the following.
2512 :    
2513 :     BEGIN {
2514 :     # Print the HTML header.
2515 :     print "CONTENT-TYPE: text/html\n\n";
2516 :     }
2517 :     use Tracer;
2518 :     use CGI;
2519 :     use FIG;
2520 :     # ... more uses ...
2521 : parrello 1.61
2522 : parrello 1.69 my ($cgi, $varHash) = ScriptSetup();
2523 : parrello 1.35 eval {
2524 : parrello 1.69 # ... get data from $cgi, put it in $varHash ...
2525 : parrello 1.35 };
2526 :     if ($@) {
2527 :     Trace("Script Error: $@") if T(0);
2528 :     }
2529 :     ScriptFinish("Html/MyTemplate.html", $varHash);
2530 :    
2531 :     The idea here is that even if the script fails, you'll see trace messages and
2532 :     useful output.
2533 :    
2534 :     =over 4
2535 :    
2536 :     =item webData
2537 :    
2538 :     A string containing either the full web page to be written to the output or the
2539 :     name of a template file from which the page is to be constructed. If the name
2540 :     of a template file is specified, then the second parameter must be present;
2541 :     otherwise, it must be absent.
2542 :    
2543 :     =item varHash (optional)
2544 :    
2545 :     If specified, then a reference to a hash mapping variable names for a template
2546 :     to their values. The template file will be read into memory, and variable markers
2547 :     will be replaced by data in this hash reference.
2548 :    
2549 : parrello 1.37 =back
2550 :    
2551 : parrello 1.35 =cut
2552 :    
2553 :     sub ScriptFinish {
2554 :     # Get the parameters.
2555 :     my ($webData, $varHash) = @_;
2556 :     # Check for a template file situation.
2557 :     my $outputString;
2558 :     if (defined $varHash) {
2559 : parrello 1.64 # Here we have a template file. We need to determine the template type.
2560 :     my $template;
2561 :     if ($FIG_Config::template_url && $webData =~ /\.php$/) {
2562 :     $template = "$FIG_Config::template_url/$webData";
2563 :     } else {
2564 :     $template = "<<$webData";
2565 :     }
2566 :     $outputString = PageBuilder::Build($template, $varHash, "Html");
2567 : parrello 1.35 } else {
2568 :     # Here the user gave us a raw string.
2569 :     $outputString = $webData;
2570 :     }
2571 :     # Check for trace messages.
2572 : parrello 1.68 if ($Destination ne "NONE" && $TraceLevel > 0) {
2573 : parrello 1.35 # We have trace messages, so we want to put them at the end of the body. This
2574 :     # is either at the end of the whole string or at the beginning of the BODY
2575 :     # end-tag.
2576 :     my $pos = length $outputString;
2577 :     if ($outputString =~ m#</body>#gi) {
2578 :     $pos = (pos $outputString) - 7;
2579 :     }
2580 : parrello 1.68 # If the trace messages were queued, we unroll them. Otherwise, we display the
2581 :     # destination.
2582 :     my $traceHtml;
2583 :     if ($Destination eq "QUEUE") {
2584 :     $traceHtml = QTrace('Html');
2585 :     } elsif ($Destination =~ /^>>(.+)$/) {
2586 :     # Here the tracing output it to a file. We code it as a hyperlink so the user
2587 :     # can copy the file name into the clipboard easily.
2588 :     my $actualDest = $1;
2589 : parrello 1.73 $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
2590 : parrello 1.68 } else {
2591 :     # Here we have one of the special destinations.
2592 :     $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
2593 :     }
2594 :     substr $outputString, $pos, 0, $traceHtml;
2595 : parrello 1.35 }
2596 :     # Write the output string.
2597 :     print $outputString;
2598 :     }
2599 :    
2600 : parrello 1.37 =head3 Insure
2601 :    
2602 : parrello 1.92 Insure($dirName, $chmod);
2603 : parrello 1.37
2604 :     Insure a directory is present.
2605 :    
2606 :     =over 4
2607 :    
2608 :     =item dirName
2609 :    
2610 :     Name of the directory to check. If it does not exist, it will be created.
2611 :    
2612 : parrello 1.91 =item chmod (optional)
2613 :    
2614 :     Security privileges to be given to the directory if it is created.
2615 :    
2616 : parrello 1.37 =back
2617 :    
2618 :     =cut
2619 :    
2620 :     sub Insure {
2621 : parrello 1.91 my ($dirName, $chmod) = @_;
2622 : parrello 1.37 if (! -d $dirName) {
2623 : parrello 1.91 Trace("Creating $dirName directory.") if T(2);
2624 :     eval {
2625 :     mkpath $dirName;
2626 :     # If we have permissions specified, set them here.
2627 :     if (defined($chmod)) {
2628 :     chmod $chmod, $dirName;
2629 :     }
2630 :     };
2631 : parrello 1.43 if ($@) {
2632 :     Confess("Error creating $dirName: $@");
2633 :     }
2634 :     }
2635 :     }
2636 :    
2637 :     =head3 ChDir
2638 :    
2639 : parrello 1.92 ChDir($dirName);
2640 : parrello 1.43
2641 :     Change to the specified directory.
2642 :    
2643 :     =over 4
2644 :    
2645 :     =item dirName
2646 :    
2647 :     Name of the directory to which we want to change.
2648 :    
2649 :     =back
2650 :    
2651 :     =cut
2652 :    
2653 :     sub ChDir {
2654 :     my ($dirName) = @_;
2655 :     if (! -d $dirName) {
2656 :     Confess("Cannot change to directory $dirName: no such directory.");
2657 :     } else {
2658 : parrello 1.77 Trace("Changing to directory $dirName.") if T(File => 4);
2659 : parrello 1.43 my $okFlag = chdir $dirName;
2660 :     if (! $okFlag) {
2661 :     Confess("Error switching to directory $dirName.");
2662 :     }
2663 : parrello 1.37 }
2664 :     }
2665 :    
2666 : parrello 1.59 =head3 SendSMS
2667 :    
2668 : parrello 1.92 my $msgID = Tracer::SendSMS($phoneNumber, $msg);
2669 : parrello 1.59
2670 :     Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
2671 :     user name, password, and API ID for the relevant account in the hash reference variable
2672 :     I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
2673 :     example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
2674 :     is C<2561022>, then the FIG_Config file must contain
2675 :    
2676 :     $phone = { user => 'BruceTheHumanPet',
2677 :     password => 'silly',
2678 :     api_id => '2561022' };
2679 :    
2680 :     The original purpose of this method was to insure Bruce would be notified immediately when the
2681 :     Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
2682 :     when you call this method.
2683 :    
2684 :     The message ID will be returned if successful, and C<undef> if an error occurs.
2685 :    
2686 :     =over 4
2687 :    
2688 :     =item phoneNumber
2689 :    
2690 :     Phone number to receive the message, in international format. A United States phone number
2691 :     would be prefixed by "1". A British phone number would be prefixed by "44".
2692 :    
2693 :     =item msg
2694 :    
2695 :     Message to send to the specified phone.
2696 :    
2697 :     =item RETURN
2698 :    
2699 :     Returns the message ID if successful, and C<undef> if the message could not be sent.
2700 :    
2701 :     =back
2702 :    
2703 :     =cut
2704 :    
2705 :     sub SendSMS {
2706 :     # Get the parameters.
2707 :     my ($phoneNumber, $msg) = @_;
2708 :     # Declare the return variable. If we do not change it, C<undef> will be returned.
2709 :     my $retVal;
2710 :     # Only proceed if we have phone support.
2711 :     if (! defined $FIG_Config::phone) {
2712 :     Trace("Phone support not present in FIG_Config.") if T(1);
2713 :     } else {
2714 :     # Get the phone data.
2715 :     my $parms = $FIG_Config::phone;
2716 :     # Get the Clickatell URL.
2717 :     my $url = "http://api.clickatell.com/http/";
2718 :     # Create the user agent.
2719 :     my $ua = LWP::UserAgent->new;
2720 :     # Request a Clickatell session.
2721 :     my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
2722 :     password => $parms->{password},
2723 :     api_id => $parms->{api_id},
2724 :     to => $phoneNumber,
2725 :     text => $msg});
2726 :     # Check for an error.
2727 :     if (! $resp->is_success) {
2728 :     Trace("Alert failed.") if T(1);
2729 :     } else {
2730 :     # Get the message ID.
2731 :     my $rstring = $resp->content;
2732 :     if ($rstring =~ /^ID:\s+(.*)$/) {
2733 :     $retVal = $1;
2734 :     } else {
2735 :     Trace("Phone attempt failed with $rstring") if T(1);
2736 :     }
2737 :     }
2738 :     }
2739 :     # Return the result.
2740 :     return $retVal;
2741 :     }
2742 :    
2743 : parrello 1.55 =head3 CommaFormat
2744 :    
2745 : parrello 1.92 my $formatted = Tracer::CommaFormat($number);
2746 : parrello 1.55
2747 :     Insert commas into a number.
2748 :    
2749 :     =over 4
2750 :    
2751 :     =item number
2752 :    
2753 :     A sequence of digits.
2754 :    
2755 :     =item RETURN
2756 :    
2757 :     Returns the same digits with commas strategically inserted.
2758 :    
2759 :     =back
2760 :    
2761 :     =cut
2762 :    
2763 :     sub CommaFormat {
2764 :     # Get the parameters.
2765 :     my ($number) = @_;
2766 :     # Pad the length up to a multiple of three.
2767 :     my $padded = "$number";
2768 :     $padded = " " . $padded while length($padded) % 3 != 0;
2769 :     # This is a fancy PERL trick. The parentheses in the SPLIT pattern
2770 :     # cause the delimiters to be included in the output stream. The
2771 :     # GREP removes the empty strings in between the delimiters.
2772 :     my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
2773 :     # Clean out the spaces.
2774 :     $retVal =~ s/ //g;
2775 :     # Return the result.
2776 :     return $retVal;
2777 :     }
2778 : parrello 1.46 =head3 SetPermissions
2779 :    
2780 : parrello 1.92 Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2781 : parrello 1.46
2782 :     Set the permissions for a directory and all the files and folders inside it.
2783 :     In addition, the group ownership will be changed to the specified value.
2784 :    
2785 :     This method is more vulnerable than most to permission and compatability
2786 :     problems, so it does internal error recovery.
2787 :    
2788 :     =over 4
2789 :    
2790 :     =item dirName
2791 :    
2792 :     Name of the directory to process.
2793 :    
2794 :     =item group
2795 :    
2796 :     Name of the group to be assigned.
2797 :    
2798 :     =item mask
2799 :    
2800 :     Permission mask. Bits that are C<1> in this mask will be ORed into the
2801 :     permission bits of any file or directory that does not already have them
2802 :     set to 1.
2803 :    
2804 : parrello 1.49 =item otherMasks
2805 :    
2806 :     Map of search patterns to permission masks. If a directory name matches
2807 :     one of the patterns, that directory and all its members and subdirectories
2808 :     will be assigned the new pattern. For example, the following would
2809 :     assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2810 :    
2811 :     Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2812 :    
2813 :     The list is ordered, so the following would use 0777 for C<tmp1> and
2814 :     0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2815 :    
2816 :     Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2817 :     '^tmp' => 0666);
2818 :    
2819 :     Note that the pattern matches are all case-insensitive, and only directory
2820 :     names are matched, not file names.
2821 :    
2822 : parrello 1.46 =back
2823 :    
2824 :     =cut
2825 :    
2826 :     sub SetPermissions {
2827 :     # Get the parameters.
2828 : parrello 1.49 my ($dirName, $group, $mask, @otherMasks) = @_;
2829 : parrello 1.46 # Set up for error recovery.
2830 :     eval {
2831 : parrello 1.49 # Switch to the specified directory.
2832 : parrello 1.46 ChDir($dirName);
2833 :     # Get the group ID.
2834 :     my $gid = getgrnam($group);
2835 : parrello 1.50 # Get the mask for tracing.
2836 : parrello 1.51 my $traceMask = sprintf("%04o", $mask) . "($mask)";
2837 : parrello 1.77 Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2838 : parrello 1.46 my $fixCount = 0;
2839 :     my $lookCount = 0;
2840 :     # @dirs will be a stack of directories to be processed.
2841 :     my @dirs = (getcwd());
2842 :     while (scalar(@dirs) > 0) {
2843 :     # Get the current directory.
2844 :     my $dir = pop @dirs;
2845 : parrello 1.49 # Check for a match to one of the specified directory names. To do
2846 :     # that, we need to pull the individual part of the name off of the
2847 :     # whole path.
2848 :     my $simpleName = $dir;
2849 : parrello 1.57 if ($dir =~ m!/([^/]+)$!) {
2850 : parrello 1.49 $simpleName = $1;
2851 :     }
2852 : parrello 1.77 Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2853 : parrello 1.49 # Search for a match.
2854 :     my $match = 0;
2855 :     my $i;
2856 :     for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2857 :     my $pattern = $otherMasks[$i];
2858 :     if ($simpleName =~ /$pattern/i) {
2859 :     $match = 1;
2860 : parrello 1.46 }
2861 : parrello 1.49 }
2862 : parrello 1.52 # Check for a match. Note we use $i-1 because the loop added 2
2863 :     # before terminating due to the match.
2864 :     if ($match && $otherMasks[$i-1] != $mask) {
2865 : parrello 1.49 # This directory matches one of the incoming patterns, and it's
2866 :     # a different mask, so we process it recursively with that mask.
2867 : parrello 1.52 SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2868 : parrello 1.49 } else {
2869 :     # Here we can process normally. Get all of the non-hidden members.
2870 :     my @submems = OpenDir($dir, 1);
2871 :     for my $submem (@submems) {
2872 :     # Get the full name.
2873 :     my $thisMem = "$dir/$submem";
2874 :     Trace("Checking member $thisMem.") if T(4);
2875 :     $lookCount++;
2876 :     if ($lookCount % 1000 == 0) {
2877 : parrello 1.77 Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2878 : parrello 1.49 }
2879 :     # Fix the group.
2880 :     chown -1, $gid, $thisMem;
2881 :     # Insure this member is not a symlink.
2882 :     if (! -l $thisMem) {
2883 :     # Get its info.
2884 :     my $fileInfo = stat $thisMem;
2885 :     # Only proceed if we got the info. Otherwise, it's a hard link
2886 :     # and we want to skip it anyway.
2887 :     if ($fileInfo) {
2888 :     my $fileMode = $fileInfo->mode;
2889 : parrello 1.58 if (($fileMode & $mask) != $mask) {
2890 : parrello 1.49 # Fix this member.
2891 :     $fileMode |= $mask;
2892 :     chmod $fileMode, $thisMem;
2893 :     $fixCount++;
2894 :     }
2895 :     # If it's a subdirectory, stack it.
2896 :     if (-d $thisMem) {
2897 :     push @dirs, $thisMem;
2898 :     }
2899 : parrello 1.46 }
2900 :     }
2901 :     }
2902 :     }
2903 :     }
2904 : parrello 1.77 Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2905 : parrello 1.46 };
2906 :     # Check for an error.
2907 :     if ($@) {
2908 :     Confess("SetPermissions error: $@");
2909 :     }
2910 :     }
2911 :    
2912 : parrello 1.62 =head3 CompareLists
2913 :    
2914 : parrello 1.92 my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
2915 : parrello 1.62
2916 :     Compare two lists of tuples, and return a hash analyzing the differences. The lists
2917 :     are presumed to be sorted alphabetically by the value in the $keyIndex column.
2918 :     The return value contains a list of items that are only in the new list
2919 :     (inserted) and only in the old list (deleted).
2920 :    
2921 :     =over 4
2922 :    
2923 :     =item newList
2924 :    
2925 :     Reference to a list of new tuples.
2926 :    
2927 :     =item oldList
2928 :    
2929 :     Reference to a list of old tuples.
2930 :    
2931 :     =item keyIndex (optional)
2932 :    
2933 :     Index into each tuple of its key field. The default is 0.
2934 :    
2935 :     =item RETURN
2936 :    
2937 :     Returns a 2-tuple consisting of a reference to the list of items that are only in the new
2938 :     list (inserted) followed by a reference to the list of items that are only in the old
2939 :     list (deleted).
2940 :    
2941 :     =back
2942 :    
2943 :     =cut
2944 :    
2945 :     sub CompareLists {
2946 :     # Get the parameters.
2947 :     my ($newList, $oldList, $keyIndex) = @_;
2948 :     if (! defined $keyIndex) {
2949 :     $keyIndex = 0;
2950 :     }
2951 :     # Declare the return variables.
2952 :     my ($inserted, $deleted) = ([], []);
2953 :     # Loop through the two lists simultaneously.
2954 :     my ($newI, $oldI) = (0, 0);
2955 :     my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
2956 :     while ($newI < $newN || $oldI < $oldN) {
2957 :     # Get the current object in each list. Note that if one
2958 :     # of the lists is past the end, we'll get undef.
2959 :     my $newItem = $newList->[$newI];
2960 :     my $oldItem = $oldList->[$oldI];
2961 : parrello 1.63 if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
2962 : parrello 1.62 # The old item is not in the new list, so mark it deleted.
2963 :     push @{$deleted}, $oldItem;
2964 :     $oldI++;
2965 :     } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
2966 :     # The new item is not in the old list, so mark it inserted.
2967 :     push @{$inserted}, $newItem;
2968 :     $newI++;
2969 :     } else {
2970 :     # The item is in both lists, so push forward.
2971 :     $oldI++;
2972 :     $newI++;
2973 :     }
2974 :     }
2975 :     # Return the result.
2976 :     return ($inserted, $deleted);
2977 :     }
2978 :    
2979 : parrello 1.65 =head3 GetLine
2980 :    
2981 : parrello 1.92 my @data = Tracer::GetLine($handle);
2982 : parrello 1.65
2983 :     Read a line of data from a tab-delimited file.
2984 :    
2985 :     =over 4
2986 :    
2987 :     =item handle
2988 :    
2989 :     Open file handle from which to read.
2990 :    
2991 :     =item RETURN
2992 :    
2993 :     Returns a list of the fields in the record read. The fields are presumed to be
2994 :     tab-delimited. If we are at the end of the file, then an empty list will be
2995 :     returned. If an empty line is read, a single list item consisting of a null
2996 :     string will be returned.
2997 :    
2998 :     =back
2999 :    
3000 :     =cut
3001 :    
3002 :     sub GetLine {
3003 :     # Get the parameters.
3004 :     my ($handle) = @_;
3005 :     # Declare the return variable.
3006 :     my @retVal = ();
3007 : parrello 1.92 Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
3008 : parrello 1.65 # Read from the file.
3009 :     my $line = <$handle>;
3010 :     # Only proceed if we found something.
3011 :     if (defined $line) {
3012 : parrello 1.80 # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
3013 :     # upload control and have a nonstandard EOL combination.
3014 :     $line =~ s/(\r|\n)+$//;
3015 :     # Here we do some fancy tracing to help in debugging complicated EOL marks.
3016 :     if (T(File => 4)) {
3017 :     my $escapedLine = $line;
3018 :     $escapedLine =~ s/\n/\\n/g;
3019 :     $escapedLine =~ s/\r/\\r/g;
3020 :     $escapedLine =~ s/\t/\\t/g;
3021 :     Trace("Line read: -->$escapedLine<--");
3022 :     }
3023 : parrello 1.65 # If the line is empty, return a single empty string; otherwise, parse
3024 :     # it into fields.
3025 :     if ($line eq "") {
3026 :     push @retVal, "";
3027 :     } else {
3028 :     push @retVal, split /\t/,$line;
3029 :     }
3030 : parrello 1.77 } else {
3031 :     # Trace the reason the read failed.
3032 :     Trace("End of file: $!") if T(File => 3);
3033 : parrello 1.65 }
3034 :     # Return the result.
3035 :     return @retVal;
3036 :     }
3037 :    
3038 :     =head3 PutLine
3039 :    
3040 : parrello 1.92 Tracer::PutLine($handle, \@fields, $eol);
3041 : parrello 1.65
3042 :     Write a line of data to a tab-delimited file. The specified field values will be
3043 :     output in tab-separated form, with a trailing new-line.
3044 :    
3045 :     =over 4
3046 :    
3047 :     =item handle
3048 :    
3049 :     Output file handle.
3050 :    
3051 :     =item fields
3052 :    
3053 :     List of field values.
3054 :    
3055 : parrello 1.82 =item eol (optional)
3056 :    
3057 :     End-of-line character (default is "\n").
3058 :    
3059 : parrello 1.65 =back
3060 :    
3061 :     =cut
3062 :    
3063 :     sub PutLine {
3064 :     # Get the parameters.
3065 : parrello 1.82 my ($handle, $fields, $eol) = @_;
3066 : parrello 1.65 # Write the data.
3067 : parrello 1.82 print $handle join("\t", @{$fields}) . ($eol || "\n");
3068 : parrello 1.65 }
3069 :    
3070 :     =head3 GenerateURL
3071 :    
3072 : parrello 1.92 my $queryUrl = Tracer::GenerateURL($page, %parameters);
3073 : parrello 1.65
3074 :     Generate a GET-style URL for the specified page with the specified parameter
3075 :     names and values. The values will be URL-escaped automatically. So, for
3076 :     example
3077 :    
3078 :     Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3079 :    
3080 :     would return
3081 :    
3082 : parrello 1.79 form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3083 : parrello 1.65
3084 :     =over 4
3085 :    
3086 :     =item page
3087 :    
3088 :     Page URL.
3089 :    
3090 :     =item parameters
3091 :    
3092 :     Hash mapping parameter names to parameter values.
3093 :    
3094 :     =item RETURN
3095 :    
3096 :     Returns a GET-style URL that goes to the specified page and passes in the
3097 :     specified parameters and values.
3098 :    
3099 :     =back
3100 :    
3101 :     =cut
3102 :    
3103 :     sub GenerateURL {
3104 :     # Get the parameters.
3105 :     my ($page, %parameters) = @_;
3106 :     # Prime the return variable with the page URL.
3107 :     my $retVal = $page;
3108 :     # Loop through the parameters, creating parameter elements in a list.
3109 :     my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3110 :     # If the list is nonempty, tack it on.
3111 :     if (@parmList) {
3112 : parrello 1.79 $retVal .= "?" . join(";", @parmList);
3113 : parrello 1.65 }
3114 :     # Return the result.
3115 :     return $retVal;
3116 :     }
3117 :    
3118 : parrello 1.78 =head3 ApplyURL
3119 :    
3120 : parrello 1.92 Tracer::ApplyURL($table, $target, $url);
3121 : parrello 1.78
3122 :     Run through a two-dimensional table (or more accurately, a list of lists), converting the
3123 :     I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3124 :     URL column will be deleted by this process and the target column will be HTML-escaped.
3125 :    
3126 :     This provides a simple way to process the results of a database query into something
3127 :     displayable by combining a URL with text.
3128 :    
3129 :     =over 4
3130 :    
3131 :     =item table
3132 :    
3133 :     Reference to a list of lists. The elements in the containing list will be updated by
3134 :     this method.
3135 :    
3136 :     =item target
3137 :    
3138 :     The index of the column to be converted into HTML.
3139 :    
3140 :     =item url
3141 :    
3142 :     The index of the column containing the URL. Note that the URL must have a recognizable
3143 :     C<http:> at the beginning.
3144 :    
3145 :     =back
3146 :    
3147 :     =cut
3148 :    
3149 :     sub ApplyURL {
3150 :     # Get the parameters.
3151 :     my ($table, $target, $url) = @_;
3152 :     # Loop through the table.
3153 :     for my $row (@{$table}) {
3154 :     # Apply the URL to the target cell.
3155 :     $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3156 :     # Delete the URL from the row.
3157 :     delete $row->[$url];
3158 :     }
3159 :     }
3160 :    
3161 :     =head3 CombineURL
3162 :    
3163 : parrello 1.92 my $combinedHtml = Tracer::CombineURL($text, $url);
3164 : parrello 1.78
3165 :     This method will convert the specified text into HTML hyperlinked to the specified
3166 :     URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3167 :     is defined and begins with an C<http:> header.
3168 :    
3169 :     =over 4
3170 :    
3171 :     =item text
3172 :    
3173 :     Text to return. This will be HTML-escaped automatically.
3174 :    
3175 :     =item url
3176 :    
3177 :     A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3178 :     will be returned without any hyperlinking.
3179 :    
3180 :     =item RETURN
3181 :    
3182 :     Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3183 :     doesn't look right, the HTML-escaped text will be returned without any further
3184 :     modification.
3185 :    
3186 :     =back
3187 :    
3188 :     =cut
3189 :    
3190 :     sub CombineURL {
3191 :     # Get the parameters.
3192 :     my ($text, $url) = @_;
3193 :     # Declare the return variable.
3194 :     my $retVal = CGI::escapeHTML($text);
3195 :     # Verify the URL.
3196 :     if (defined($url) && $url =~ m!http://!i) {
3197 :     # It's good, so we apply it to the text.
3198 :     $retVal = "<a href=\"$url\">$retVal</a>";
3199 :     }
3200 :     # Return the result.
3201 :     return $retVal;
3202 :     }
3203 :    
3204 : parrello 1.87
3205 : olson 1.88 1;

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