Filename | /Users/ap13/perl5/lib/perl5/Bio/Root/Exception.pm |
Statements | Executed 13 statements in 1.14ms |
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1 | 1 | 1 | 22µs | 49µs | BEGIN@2 | Bio::Root::Exception::
0 | 0 | 0 | 0s | 0s | _reformat_stacktrace | Bio::Root::Exception::
0 | 0 | 0 | 0s | 0s | new | Bio::Root::Exception::
0 | 0 | 0 | 0s | 0s | pretty_format | Bio::Root::Exception::
0 | 0 | 0 | 0s | 0s | stringify | Bio::Root::Exception::
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1 | package Bio::Root::Exception; | ||||
2 | 2 | 1.09ms | 2 | 76µs | # spent 49µs (22+27) within Bio::Root::Exception::BEGIN@2 which was called:
# once (22µs+27µs) by Bio::Root::Root::BEGIN@146 at line 2 # spent 49µs making 1 call to Bio::Root::Exception::BEGIN@2
# spent 27µs making 1 call to strict::import |
3 | |||||
4 | # ABSTRACT: generic exception objects for Bioperl | ||||
5 | # AUTHOR: Steve Chervitz <sac@bioperl.org> | ||||
6 | # OWNER: 2001 Steve Chervitz | ||||
7 | # LICENSE: Perl_5 | ||||
8 | |||||
9 | =head1 SYNOPSIS | ||||
10 | |||||
11 | =head2 Throwing exceptions using L<Error.pm throw|Error::throw>: | ||||
12 | |||||
13 | use Bio::Root::Exception; | ||||
14 | use Error; | ||||
15 | |||||
16 | # Set Error::Debug to include stack trace data in the error messages | ||||
17 | $Error::Debug = 1; | ||||
18 | |||||
19 | $file = shift; | ||||
20 | open my $IN, '<', $file | ||||
21 | or Bio::Root::FileOpenException->throw("Could not read file '$file': $!"); | ||||
22 | |||||
23 | =head2 Throwing exceptions using L<Bioperl throw|Bio::Root::Root/throw>: | ||||
24 | |||||
25 | # Here we have an object that ISA Bio::Root::Root, so it inherits throw(). | ||||
26 | |||||
27 | open my $IN, '<', $file | ||||
28 | or $object->throw(-class => 'Bio::Root::FileOpenException', | ||||
29 | -text => "Could not read file '$file'", | ||||
30 | -value => $!); | ||||
31 | |||||
32 | =head2 Catching and handling exceptions using L<Error.pm try|Error/try>: | ||||
33 | |||||
34 | use Bio::Root::Exception; | ||||
35 | use Error qw(:try); | ||||
36 | |||||
37 | # Note that we need to import the 'try' tag from Error.pm | ||||
38 | |||||
39 | # Set Error::Debug to include stack trace data in the error messages | ||||
40 | $Error::Debug = 1; | ||||
41 | |||||
42 | my $file = shift; | ||||
43 | my $IN; | ||||
44 | try { | ||||
45 | open $IN, '<', $file | ||||
46 | or Bio::Root::FileOpenException->throw("Could not read file '$file': $!"); | ||||
47 | } | ||||
48 | catch Bio::Root::FileOpenException with { | ||||
49 | my $err = shift; | ||||
50 | print STDERR "Using default input file: $default_file\n"; | ||||
51 | open $IN, '<', $default_file or die "Could not read file '$default_file': $!"; | ||||
52 | } | ||||
53 | otherwise { | ||||
54 | my $err = shift; | ||||
55 | print STDERR "An unexpected exception occurred: \n$err"; | ||||
56 | |||||
57 | # By placing an the error object reference within double quotes, | ||||
58 | # you're invoking its stringify() method. | ||||
59 | } | ||||
60 | finally { | ||||
61 | # Any code that you want to execute regardless of whether or not | ||||
62 | # an exception occurred. | ||||
63 | }; | ||||
64 | # the ending semicolon is essential! | ||||
65 | |||||
66 | |||||
67 | =head2 Defining a new Exception type as a subclass of Bio::Root::Exception: | ||||
68 | |||||
69 | @Bio::TestException::ISA = qw( Bio::Root::Exception ); | ||||
70 | |||||
71 | =head1 DESCRIPTION | ||||
72 | |||||
73 | =head2 Exceptions defined in L<Bio::Root::Exception> | ||||
74 | |||||
75 | These are generic exceptions for typical problem situations that could arise | ||||
76 | in any module or script. | ||||
77 | |||||
78 | =for :list | ||||
79 | * C<Bio::Root::Exception()> | ||||
80 | * C<Bio::Root::NotImplemented()> | ||||
81 | * C<Bio::Root::IOException()> | ||||
82 | * C<Bio::Root::FileOpenException()> | ||||
83 | * C<Bio::Root::SystemException()> | ||||
84 | * C<Bio::Root::BadParameter()> | ||||
85 | * C<Bio::Root::OutOfRange()> | ||||
86 | * C<Bio::Root::NoSuchThing()> | ||||
87 | |||||
88 | Using defined exception classes like these is a good idea because it | ||||
89 | indicates the basic nature of what went wrong in a convenient, | ||||
90 | computable way. | ||||
91 | |||||
92 | If there is a type of exception that you want to throw | ||||
93 | that is not covered by the classes listed above, it is easy to define | ||||
94 | a new one that fits your needs. Just write a line like the following | ||||
95 | in your module or script where you want to use it (or put it somewhere | ||||
96 | that is accessible to your code): | ||||
97 | |||||
98 | @NoCanDoException::ISA = qw( Bio::Root::Exception ); | ||||
99 | |||||
100 | All of the exceptions defined in this module inherit from a common | ||||
101 | base class exception, Bio::Root::Exception. This allows a user to | ||||
102 | write a handler for all Bioperl-derived exceptions as follows: | ||||
103 | |||||
104 | use Bio::Whatever; | ||||
105 | use Error qw(:try); | ||||
106 | |||||
107 | try { | ||||
108 | # some code that depends on Bioperl | ||||
109 | } | ||||
110 | catch Bio::Root::Exception with { | ||||
111 | my $err = shift; | ||||
112 | print "A Bioperl exception occurred:\n$err\n"; | ||||
113 | }; | ||||
114 | |||||
115 | So if you do create your own exceptions, just be sure they inherit | ||||
116 | from Bio::Root::Exception directly, or indirectly by inheriting from a | ||||
117 | Bio::Root::Exception subclass. | ||||
118 | |||||
119 | The exceptions in Bio::Root::Exception are extensions of Graham Barr's | ||||
120 | L<Error> module available from CPAN. Despite this dependency, the | ||||
121 | L<Bio::Root::Exception> module does not explicitly C<require Error>. | ||||
122 | This permits Bio::Root::Exception to be loaded even when | ||||
123 | Error.pm is not available. | ||||
124 | |||||
125 | =head2 Throwing exceptions within Bioperl modules | ||||
126 | |||||
127 | Error.pm is not part of the Bioperl distibution, and may not be | ||||
128 | present within any given perl installation. So, when you want to | ||||
129 | throw an exception in a Bioperl module, the safe way to throw it | ||||
130 | is to use L<Bio::Root::Root/throw> which can use Error.pm | ||||
131 | when it's available. See documentation in Bio::Root::Root for details. | ||||
132 | |||||
133 | =head1 SEE ALSO | ||||
134 | |||||
135 | See the C<examples/exceptions> directory of the Bioperl distribution for | ||||
136 | working demo code. | ||||
137 | |||||
138 | L<Bio::Root::Root/throw> for information about throwing | ||||
139 | L<Bio::Root::Exception>-based exceptions. | ||||
140 | |||||
141 | L<Error> (available from CPAN, author: GBARR) | ||||
142 | |||||
143 | Error.pm is helping to guide the design of exception handling in Perl 6. | ||||
144 | See these RFC's: | ||||
145 | |||||
146 | http://dev.perl.org/rfc/63.pod | ||||
147 | |||||
148 | http://dev.perl.org/rfc/88.pod | ||||
149 | |||||
150 | =head1 EXCEPTIONS | ||||
151 | |||||
152 | =cut | ||||
153 | |||||
154 | 1 | 500ns | my $debug = $Error::Debug; # Prevents the "used only once" warning. | ||
155 | 1 | 600ns | my $DEFAULT_VALUE = "__DUMMY__"; # Permits eval{} based handlers to work | ||
156 | |||||
157 | =head2 L<Bio::Root::Exception> | ||||
158 | |||||
159 | Purpose : A generic base class for all BioPerl exceptions. | ||||
160 | By including a "catch Bio::Root::Exception" block, you | ||||
161 | should be able to trap all BioPerl exceptions. | ||||
162 | Example : throw Bio::Root::Exception("A generic exception", $!); | ||||
163 | |||||
164 | =cut | ||||
165 | |||||
166 | #--------------------------------------------------------- | ||||
167 | 1 | 8µs | @Bio::Root::Exception::ISA = qw( Error ); | ||
168 | #--------------------------------------------------------- | ||||
169 | |||||
170 | =head1 Methods defined by Bio::Root::Exception | ||||
171 | |||||
172 | =head2 new | ||||
173 | |||||
174 | Purpose : Guarantees that -value is set properly before | ||||
175 | calling Error::new(). | ||||
176 | |||||
177 | Arguments: key-value style arguments same as for Error::new() | ||||
178 | |||||
179 | You can also specify plain arguments as ($message, $value) | ||||
180 | where $value is optional. | ||||
181 | |||||
182 | -value, if defined, must be non-zero and not an empty string | ||||
183 | in order for eval{}-based exception handlers to work. | ||||
184 | These require that if($@) evaluates to true, which will not | ||||
185 | be the case if the Error has no value (Error overloads | ||||
186 | numeric operations to the Error::value() method). | ||||
187 | |||||
188 | It is OK to create Bio::Root::Exception objects without | ||||
189 | specifying -value. In this case, an invisible dummy value is used. | ||||
190 | |||||
191 | If you happen to specify a -value of zero (0), it will | ||||
192 | be replaced by the string "The number zero (0)". | ||||
193 | |||||
194 | If you happen to specify a -value of empty string (""), it will | ||||
195 | be replaced by the string "An empty string ("")". | ||||
196 | |||||
197 | =cut | ||||
198 | |||||
199 | sub new { | ||||
200 | my ($class, @args) = @_; | ||||
201 | my ($value, %params); | ||||
202 | if( @args % 2 == 0 && $args[0] =~ /^-/) { | ||||
203 | %params = @args; | ||||
204 | $value = $params{'-value'}; | ||||
205 | } | ||||
206 | else { | ||||
207 | $params{-text} = $args[0]; | ||||
208 | $value = $args[1]; | ||||
209 | } | ||||
210 | |||||
211 | if( defined $value ) { | ||||
212 | $value = "The number zero (0)" if $value =~ /^\d+$/ && $value == 0; | ||||
213 | $value = "An empty string (\"\")" if $value eq ""; | ||||
214 | } | ||||
215 | else { | ||||
216 | $value ||= $DEFAULT_VALUE; | ||||
217 | } | ||||
218 | $params{-value} = $value; | ||||
219 | |||||
220 | my $self = $class->SUPER::new( %params ); | ||||
221 | return $self; | ||||
222 | } | ||||
223 | |||||
224 | =head2 pretty_format() | ||||
225 | |||||
226 | Purpose : Get a nicely formatted string containing information about the | ||||
227 | exception. Format is similar to that produced by | ||||
228 | Bio::Root::Root::throw(), with the addition of the name of | ||||
229 | the exception class in the EXCEPTION line and some other | ||||
230 | data available via the Error object. | ||||
231 | Example : print $error->pretty_format; | ||||
232 | |||||
233 | =cut | ||||
234 | |||||
235 | sub pretty_format { | ||||
236 | my $self = shift; | ||||
237 | my $msg = $self->text; | ||||
238 | my $stack = ''; | ||||
239 | if( $Error::Debug ) { | ||||
240 | $stack = $self->_reformat_stacktrace(); | ||||
241 | } | ||||
242 | my $value_string = $self->value ne $DEFAULT_VALUE ? "VALUE: ".$self->value."\n" : ""; | ||||
243 | my $class = ref($self); | ||||
244 | |||||
245 | my $title = "------------- EXCEPTION: $class -------------"; | ||||
246 | my $footer = "\n" . '-' x CORE::length($title); | ||||
247 | my $out = "\n$title\n" | ||||
248 | . "MSG: $msg\n". $value_string. $stack. $footer . "\n"; | ||||
249 | return $out; | ||||
250 | } | ||||
251 | |||||
252 | |||||
253 | =head2 _reformat_stacktrace | ||||
254 | |||||
255 | Reformatting of the stack performed by _reformat_stacktrace: | ||||
256 | for :list | ||||
257 | 1. Shift the file:line data in line i to line i+1. | ||||
258 | 2. change xxx::__ANON__() to "try{} block" | ||||
259 | 3. skip the "require" and "Error::subs::try" stack entries (boring) | ||||
260 | |||||
261 | This means that the first line in the stack won't have any file:line data | ||||
262 | But this isn't a big issue since it's for a Bio::Root::-based method | ||||
263 | that doesn't vary from exception to exception. | ||||
264 | |||||
265 | =cut | ||||
266 | |||||
267 | sub _reformat_stacktrace { | ||||
268 | my $self = shift; | ||||
269 | my $msg = $self->text; | ||||
270 | my $stack = $self->stacktrace(); | ||||
271 | $stack =~ s/\Q$msg//; | ||||
272 | my @stack = split( /\n/, $stack); | ||||
273 | my @new_stack = (); | ||||
274 | my ($method, $file, $linenum, $prev_file, $prev_linenum); | ||||
275 | my $stack_count = 0; | ||||
276 | foreach my $i( 0..$#stack ) { | ||||
277 | # print "STACK-ORIG: $stack[$i]\n"; | ||||
278 | if( ($stack[$i] =~ /^\s*([^(]+)\s*\(.*\) called at (\S+) line (\d+)/) || | ||||
279 | ($stack[$i] =~ /^\s*(require 0) called at (\S+) line (\d+)/)) { | ||||
280 | ($method, $file, $linenum) = ($1, $2, $3); | ||||
281 | $stack_count++; | ||||
282 | } | ||||
283 | else{ | ||||
284 | next; | ||||
285 | } | ||||
286 | if( $stack_count == 1 ) { | ||||
287 | push @new_stack, "STACK: $method"; | ||||
288 | ($prev_file, $prev_linenum) = ($file, $linenum); | ||||
289 | next; | ||||
290 | } | ||||
291 | |||||
292 | if( $method =~ /__ANON__/ ) { | ||||
293 | $method = "try{} block"; | ||||
294 | } | ||||
295 | if( ($method =~ /^require/ and $file =~ /Error\.pm/ ) || | ||||
296 | ($method =~ /^Error::subs::try/ ) ) { | ||||
297 | last; | ||||
298 | } | ||||
299 | push @new_stack, "STACK: $method $prev_file:$prev_linenum"; | ||||
300 | ($prev_file, $prev_linenum) = ($file, $linenum); | ||||
301 | } | ||||
302 | push @new_stack, "STACK: $prev_file:$prev_linenum"; | ||||
303 | |||||
304 | return join "\n", @new_stack; | ||||
305 | } | ||||
306 | |||||
307 | =head2 stringify() | ||||
308 | |||||
309 | Purpose : Overrides Error::stringify() to call pretty_format(). | ||||
310 | This is called automatically when an exception object | ||||
311 | is placed between double quotes. | ||||
312 | Example : catch Bio::Root::Exception with { | ||||
313 | my $error = shift; | ||||
314 | print "$error"; | ||||
315 | } | ||||
316 | |||||
317 | See Also: L<pretty_format()|pretty_format> | ||||
318 | |||||
319 | =cut | ||||
320 | |||||
321 | sub stringify { | ||||
322 | my ($self, @args) = @_; | ||||
323 | return $self->pretty_format( @args ); | ||||
324 | } | ||||
325 | |||||
326 | =head1 Subclasses of Bio::Root::Exception | ||||
327 | |||||
328 | =head2 L<Bio::Root::NotImplemented> | ||||
329 | |||||
330 | Purpose : Indicates that a method has not been implemented. | ||||
331 | Example : throw Bio::Root::NotImplemented( | ||||
332 | -text => "Method \"foo\" not implemented in module FooBar.", | ||||
333 | -value => "foo" ); | ||||
334 | |||||
335 | =cut | ||||
336 | |||||
337 | #--------------------------------------------------------- | ||||
338 | 1 | 4µs | @Bio::Root::NotImplemented::ISA = qw( Bio::Root::Exception ); | ||
339 | #--------------------------------------------------------- | ||||
340 | |||||
341 | =head2 L<Bio::Root::IOException> | ||||
342 | |||||
343 | Purpose : Indicates that some input/output-related trouble has occurred. | ||||
344 | Example : throw Bio::Root::IOException( | ||||
345 | -text => "Can't save data to file $file.", | ||||
346 | -value => $! ); | ||||
347 | |||||
348 | =cut | ||||
349 | |||||
350 | #--------------------------------------------------------- | ||||
351 | 1 | 4µs | @Bio::Root::IOException::ISA = qw( Bio::Root::Exception ); | ||
352 | #--------------------------------------------------------- | ||||
353 | |||||
354 | |||||
355 | =head2 L<Bio::Root::FileOpenException> | ||||
356 | |||||
357 | Purpose : Indicates that a file could not be opened. | ||||
358 | Example : throw Bio::Root::FileOpenException( | ||||
359 | -text => "Can't open file $file for reading.", | ||||
360 | -value => $! ); | ||||
361 | |||||
362 | =cut | ||||
363 | |||||
364 | #--------------------------------------------------------- | ||||
365 | 1 | 4µs | @Bio::Root::FileOpenException::ISA = qw( Bio::Root::IOException ); | ||
366 | #--------------------------------------------------------- | ||||
367 | |||||
368 | |||||
369 | =head2 L<Bio::Root::SystemException> | ||||
370 | |||||
371 | Purpose : Indicates that a system call failed. | ||||
372 | Example : unlink($file) or throw Bio::Root::SystemException( | ||||
373 | -text => "Can't unlink file $file.", | ||||
374 | -value => $! ); | ||||
375 | |||||
376 | =cut | ||||
377 | |||||
378 | #--------------------------------------------------------- | ||||
379 | 1 | 4µs | @Bio::Root::SystemException::ISA = qw( Bio::Root::Exception ); | ||
380 | #--------------------------------------------------------- | ||||
381 | |||||
382 | |||||
383 | =head2 L<Bio::Root::BadParameter> | ||||
384 | |||||
385 | Purpose : Indicates that one or more parameters supplied to a method | ||||
386 | are invalid, unspecified, or conflicting. | ||||
387 | Example : throw Bio::Root::BadParameter( | ||||
388 | -text => "Required parameter \"-foo\" was not specified", | ||||
389 | -value => "-foo" ); | ||||
390 | |||||
391 | =cut | ||||
392 | |||||
393 | #--------------------------------------------------------- | ||||
394 | 1 | 3µs | @Bio::Root::BadParameter::ISA = qw( Bio::Root::Exception ); | ||
395 | #--------------------------------------------------------- | ||||
396 | |||||
397 | |||||
398 | =head2 L<Bio::Root::OutOfRange> | ||||
399 | |||||
400 | Purpose : Indicates that a specified (start,end) range or | ||||
401 | an index to an array is outside the permitted range. | ||||
402 | Example : throw Bio::Root::OutOfRange( | ||||
403 | -text => "Start coordinate ($start) cannot be less than zero.", | ||||
404 | -value => $start ); | ||||
405 | |||||
406 | =cut | ||||
407 | |||||
408 | #--------------------------------------------------------- | ||||
409 | 1 | 4µs | @Bio::Root::OutOfRange::ISA = qw( Bio::Root::Exception ); | ||
410 | #--------------------------------------------------------- | ||||
411 | |||||
412 | |||||
413 | =head2 L<Bio::Root::NoSuchThing> | ||||
414 | |||||
415 | Purpose : Indicates that a requested thing cannot be located | ||||
416 | and therefore could possibly be bogus. | ||||
417 | Example : throw Bio::Root::NoSuchThing( | ||||
418 | -text => "Accession M000001 could not be found.", | ||||
419 | -value => "M000001" ); | ||||
420 | |||||
421 | =cut | ||||
422 | |||||
423 | #--------------------------------------------------------- | ||||
424 | 1 | 3µs | @Bio::Root::NoSuchThing::ISA = qw( Bio::Root::Exception ); | ||
425 | #--------------------------------------------------------- | ||||
426 | |||||
427 | 1 | 13µs | 1; |