[Bio] / FigKernelPackages / Tracer.pm Repository:
ViewVC logotype

Diff of /FigKernelPackages/Tracer.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.9, Wed May 4 03:05:12 2005 UTC revision 1.37, Fri Feb 17 00:26:23 2006 UTC
# Line 1  Line 1 
1    #
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    #
7    # The SEED Toolkit is free software. You can redistribute
8    # it and/or modify it under the terms of the SEED Toolkit
9    # Public License.
10    #
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  package Tracer;  package Tracer;
19    
20          require Exporter;          require Exporter;
21          @ISA = ('Exporter');          @ISA = ('Exporter');
22          @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup ScriptSetup ScriptFinish Insure);
23          @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);          @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);
24          use strict;          use strict;
25          use Carp qw(longmess croak);          use Carp qw(longmess croak);
26          use CGI;          use CGI;
27          use FIG_Config;          use FIG_Config;
28      use PageBuilder;      use PageBuilder;
29        use Digest::MD5;
30        use File::Basename;
31        use File::Path;
32    
33  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
34    
# Line 20  Line 40 
40  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace
41  level is less than or equal to this package's trace level and whose category is activated will  level is less than or equal to this package's trace level and whose category is activated will
42  be written. Thus, a higher trace level on a message indicates that the message  be written. Thus, a higher trace level on a message indicates that the message
43  is less likely to be seen. A higher trace level passed to B<Setup> means more trace messages will  is less likely to be seen. A higher trace level passed to B<TSetup> means more trace messages will
44  appear. To generate a trace message, use the following syntax.  appear. To generate a trace message, use the following syntax.
45    
46  C<< Trace($message) if T(errors => 4); >>  C<< Trace($message) if T(errors => 4); >>
# Line 38  Line 58 
58    
59  C<< Trace($message) if T(2); >>  C<< Trace($message) if T(2); >>
60    
61  To set up tracing, you call the C</Setup> method. The method takes as input a trace level, a list  To set up tracing, you call the L</TSetup> method. The method takes as input a trace level, a list
62  of category names, and a set of options. The trace level and list of category names are  of category names, and a set of options. The trace level and list of category names are
63  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
64    
65  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>
66    
67  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
68  specifies that messages should be output as HTML paragraphs. The parameters are formatted  specifies that messages should be output as HTML paragraphs.
69  to make it easier to input tracing configuration on a web form.  
70    To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
71    level 3 and writes the output to the standard error output. This sort of thing might be
72    useful in a CGI environment.
73    
74    C<< TSetup('3 *', 'WARN'); >>
75    
76  In addition to HTML and file output for trace messages, you can specify that the trace messages  In addition to HTML and file output for trace messages, you can specify that the trace messages
77  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
# Line 61  Line 86 
86  Thus, debugging information is available and easily retrieved even when the application is  Thus, debugging information is available and easily retrieved even when the application is
87  being used out in the field.  being used out in the field.
88    
89    There is no hard and fast rule on how to use trace levels. The following is therefore only
90    a suggestion.
91    
92    =over 4
93    
94    =item Error 0
95    
96    Message indicates an error that may lead to incorrect results or that has stopped the
97    application entirely.
98    
99    =item Warning 1
100    
101    Message indicates something that is unexpected but that probably did not interfere
102    with program execution.
103    
104    =item Notice 2
105    
106    Message indicates the beginning or end of a major task.
107    
108    =item Information 3
109    
110    Message indicates a subtask. In the FIG system, a subtask generally relates to a single
111    genome. This would be a big loop that is not expected to execute more than 500 times or so.
112    
113    =item Detail 4
114    
115    Message indicates a low-level loop iteration.
116    
117    =back
118    
119  =cut  =cut
120    
121  # Declare the configuration variables.  # Declare the configuration variables.
122    
123  my $Destination = "NONE";       # Description of where to send the trace output.  my $Destination = "NONE";       # Description of where to send the trace output.
124    my $TeeFlag = 0;            # TRUE if output is going to a file and to the
125                                # standard output
126  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
127                                                          # hash of active category names                                                          # hash of active category names
128  my $TraceLevel = 0;                     # trace level; a higher trace level produces more  my $TraceLevel = 0;                     # trace level; a higher trace level produces more
129                                                          # messages                                                          # messages
130  my @Queue = ();                         # queued list of trace messages.  my @Queue = ();                         # queued list of trace messages.
131  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
132    my $SetupCount = 0;         # number of times TSetup called
133    my $AllTrace = 0;           # TRUE if we are tracing all categories.
134    
135  =head2 Public Methods  =head2 Public Methods
136    
# Line 93  Line 152 
152    
153  The destination for the trace output. To send the trace output to a file, specify the file  The destination for the trace output. To send the trace output to a file, specify the file
154  name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended  name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
155  to the file. Otherwise the file is cleared before tracing begins. In addition to sending  to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
156  the trace messages to a file, you can specify a special destination. C<HTML> will cause  symbol with a C<+> to echo output to a file AND to the standard output. In addition to
157  tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>  sending the trace messages to a file, you can specify a special destination. C<HTML> will
158    cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
159  will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace  will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
160  messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace  messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
161  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
# Line 113  Line 173 
173          my @categoryData = split /\s+/, $categoryList;          my @categoryData = split /\s+/, $categoryList;
174          # Extract the trace level.          # Extract the trace level.
175          $TraceLevel = shift @categoryData;          $TraceLevel = shift @categoryData;
176          # Build the category hash.      # Presume category-based tracing until we learn otherwise.
177        $AllTrace = 0;
178        # Build the category hash. Note that if we find a "*", we turn on non-category
179        # tracing. We must also clear away any pre-existing data.
180        %Categories = ( main => 1 );
181          for my $category (@categoryData) {          for my $category (@categoryData) {
182                  $Categories{$category} = 1;          if ($category eq '*') {
183                $AllTrace = 1;
184            } else {
185                $Categories{lc $category} = 1;
186            }
187          }          }
188          # Now we need to process the destination information. The most important special          # Now we need to process the destination information. The most important special
189          # case is the single ">", which requires we clear the file first. After doing      # cases are the single ">", which requires we clear the file first, and the
190          # so, we tack on another ">" sign so that future trace messages are appended.      # "+" prefix which indicates a double echo.
191        if ($target =~ m/^\+?>>?/) {
192            if ($target =~ m/^\+/) {
193                $TeeFlag = 1;
194                $target = substr($target, 1);
195            }
196          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
197                  open TRACEFILE, $target;                  open TRACEFILE, $target;
198                  print TRACEFILE Now() . " Tracing initialized.\n";                  print TRACEFILE Now() . " Tracing initialized.\n";
199                  close TRACEFILE;                  close TRACEFILE;
200                  $Destination = ">$target";                  $Destination = ">$target";
201          } else {          } else {
202                $Destination = $target;
203            }
204        } else {
205                  $Destination = uc($target);                  $Destination = uc($target);
206          }          }
207        # Increment the setup counter.
208        $SetupCount++;
209    }
210    
211    =head3 StandardSetup
212    
213    C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>
214    
215    This method performs standard command-line parsing and tracing setup. The return
216    values are a hash of the command-line options and a list of the positional
217    parameters. Tracing is automatically set up and the command-line options are
218    validated.
219    
220    This is a complex method that does a lot of grunt work. The parameters can
221    be more easily understood, however, once they are examined individually.
222    
223    The I<categories> parameter is the most obtuse. It is a reference to a list of
224    special-purpose tracing categories. Most tracing categories are PERL package
225    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
226    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
227    
228        ["Sprout", "SproutLoad", "ERDB"]
229    
230    This would cause trace messages in the specified three packages to appear in
231    the output. There are threer special tracing categories that are automatically
232    handled by this method. In other words, if you used L</TSetup> you would need
233    to include these categories manually, but if you use this method they are turned
234    on automatically.
235    
236    =over 4
237    
238    =item FIG
239    
240    Turns on trace messages inside the B<FIG> package.
241    
242    =item SQL
243    
244    Traces SQL commands and activity.
245    
246    =item Tracer
247    
248    Traces error messages and call stacks.
249    
250    =back
251    
252    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
253    The trace level is specified using the C<-trace> command-line option. For example,
254    the following command line for C<TransactFeatures> turns on SQL tracing and runs
255    all tracing at level 3.
256    
257        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
258    
259    Standard tracing is output to the standard output and echoed to the file
260    C<trace.log> in the FIG temporary directory.
261    
262    The default trace level is 2. To get all messages, specify a trace level of 4.
263    For a genome-by-genome update, use 3.
264    
265    The I<options> parameter is a reference to a hash containing the command-line
266    options, their default values, and an explanation of what they mean. Command-line
267    options may be in the form of switches or keywords. In the case of a switch, the
268    option value is 1 if it is specified and 0 if it is not specified. In the case
269    of a keyword, the value is separated from the option name by an equal sign. You
270    can see this last in the command-line example above.
271    
272    An example at this point would help. Consider, for example, the command-line utility
273    C<TransactFeatures>. It accepts a list of positional parameters plus the options
274    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
275    the following code.
276    
277        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
278                            { safe => [0, "use database transactions"],
279                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
280                              start => [' ', "start with this genome"],
281                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
282                            "command transactionDirectory IDfile",
283                          @ARGV);
284    
285    
286    The call to C<ParseCommand> specifies the default values for the options and
287    stores the actual options in a hash that is returned as C<$options>. The
288    positional parameters are returned in C<@parameters>.
289    
290    The following is a sample command line for C<TransactFeatures>.
291    
292        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
293    
294    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
295    parameters, and would find themselves in I<@parameters> after executing the
296    above code fragment. The tracing would be set to level 2, and the categories
297    would be C<FIG>, C<Tracer>, and <DocUtils>. C<FIG> and C<Tracer> are standard,
298    and C<DocUtils> was included because it came in within the first parameter
299    to this method. The I<$options> hash would be
300    
301        { trace => 2, sql => 0, safe => 0,
302          noAlias => 1, start => ' ', tblFiles => 0 }
303    
304    Use of C<StandardSetup> in this way provides a simple way of performing
305    standard tracing setup and command-line parsing. Note that the caller is
306    not even aware of the command-line switches C<-trace> and C<-sql>, which
307    are used by this method to control the tracing. If additional tracing features
308    need to be added in the future, they can be processed by this method without
309    upsetting the command-line utilities.
310    
311    Finally, if the special option C<-h> is specified, the option names will
312    be traced at level 0 and the program will exit without processing.
313    This provides a limited help capability. For example, if the user enters
314    
315        TransactFeatures -h
316    
317    he would see the following output.
318    
319        TransactFeatures [options] command transactionDirectory IDfile
320            -trace    tracing level (default 2)
321            -sql      trace SQL commands
322            -safe     use database transactions
323            -noAlias  do not expect aliases in CHANGE transactions
324            -start    start with this genome
325            -tblFiles output TBL files containing the corrected IDs
326    
327    The parameters to this method are as follows.
328    
329    =over 4
330    
331    =item categories
332    
333    Reference to a list of tracing category names. These should be names of
334    packages whose internal workings will need to be debugged to get the
335    command working.
336    
337    =item options
338    
339    Reference to a hash containing the legal options for the current command mapped
340    to their default values and descriptions. The user can override the defaults
341    by specifying the options as command-line switches prefixed by a hyphen.
342    Tracing-related options may be added to this hash. If the C<-h> option is
343    specified on the command line, the option descriptions will be used to
344    explain the options.
345    
346    =item parmHelp
347    
348    A string that vaguely describes the positional parameters. This is used
349    if the user specifies the C<-h> option.
350    
351    =item ARGV
352    
353    List of command line parameters, including the option switches, which must
354    precede the positional parameters and be prefixed by a hyphen.
355    
356    =item RETURN
357    
358    Returns a list. The first element of the list is the reference to a hash that
359    maps the command-line option switches to their values. These will either be the
360    default values or overrides specified on the command line. The remaining
361    elements of the list are the position parameters, in order.
362    
363    =back
364    
365    =cut
366    
367    sub StandardSetup {
368        # Get the parameters.
369        my ($categories, $options, $parmHelp, @argv) = @_;
370        # Add the tracing options.
371        $options->{trace} = [2, "tracing level"];
372        $options->{sql} = [0, "turn on SQL tracing"];
373        $options->{h} = [0, "display command-line options"];
374        # Create a parsing hash from the options hash. The parsing hash
375        # contains the default values rather than the default value
376        # and the description. While we're at it, we'll memorize the
377        # length of the longest option name.
378        my $longestName = 0;
379        my %parseOptions = ();
380        for my $key (keys %{$options}) {
381            if (length $key > $longestName) {
382                $longestName = length $key;
383            }
384            $parseOptions{$key} = $options->{$key}->[0];
385        }
386        # Parse the command line.
387        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
388        # Now we want to set up tracing. First, we need to know if SQL is to
389        # be traced.
390        my @cats = @{$categories};
391        if ($retOptions->{sql}) {
392            push @cats, "SQL";
393        }
394        # Add the default categories.
395        push @cats, "Tracer", "FIG";
396        # Next, we create the category string by prefixing the trace level
397        # and joining the categories.
398        my $cats = join(" ", $parseOptions{trace}, @cats);
399        # Now set up the tracing.
400        TSetup($cats, "+>$FIG_Config::temp/trace.log");
401        # Check for the "h" option. If it is specified, dump the command-line
402        # options and exit the program.
403        if ($retOptions->{h}) {
404            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
405            Trace("$1 [options] $parmHelp") if T(0);
406            for my $key (sort keys %{$options}) {
407                my $name = Pad($key, $longestName, 0, ' ');
408                my $desc = $options->{$key}->[1];
409                if ($options->{$key}->[0]) {
410                    $desc .= " (default " . $options->{$key}->[0] . ")";
411                }
412                Trace("  $name $desc") if T(0);
413            }
414            exit(0);
415        }
416        # Return the parsed parameters.
417        return ($retOptions, @retParameters);
418    }
419    
420    =head3 Setups
421    
422    C<< my $count = Tracer::Setups(); >>
423    
424    Return the number of times L</TSetup> has been called.
425    
426    This method allows for the creation of conditional tracing setups where, for example, we
427    may want to set up tracing if nobody else has done it before us.
428    
429    =cut
430    
431    sub Setups {
432        return $SetupCount;
433    }
434    
435    =head3 Open
436    
437    C<< my $handle = Open($fileHandle, $fileSpec, $message); >>
438    
439    Open a file.
440    
441    The I<$fileSpec> is essentially the second argument of the PERL C<open>
442    function. The mode is specified using Unix-like shell information. So, for
443    example,
444    
445        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
446    
447    would open for output appended to the specified file, and
448    
449        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
450    
451    would open a pipe that sorts the records written and removes duplicates. Note
452    the use of file handle syntax in the Open call. To use anonymous file handles,
453    code as follows.
454    
455        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
456    
457    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
458    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
459    failed open will throw an exception and the third parameter will be used to construct
460    an error message. If the parameter is omitted, a standard message is constructed
461    using the file spec.
462    
463        Could not open "/usr/spool/news/twitlog"
464    
465    Note that the mode characters are automatically cleaned from the file name.
466    The actual error message from the file system will be captured and appended to the
467    message in any case.
468    
469        Could not open "/usr/spool/news/twitlog": file not found.
470    
471    In some versions of PERL the only error message we get is a number, which
472    corresponds to the C++ C<errno> value.
473    
474        Could not open "/usr/spool/news/twitlog": 6.
475    
476    =over 4
477    
478    =item fileHandle
479    
480    File handle. If this parameter is C<undef>, a file handle will be generated
481    and returned as the value of this method.
482    
483    =item fileSpec
484    
485    File name and mode, as per the PERL C<open> function.
486    
487    =item message (optional)
488    
489    Error message to use if the open fails. If omitted, a standard error message
490    will be generated. In either case, the error information from the file system
491    is appended to the message. To specify a conditional open that does not throw
492    an error if it fails, use C<0>.
493    
494    =item RETURN
495    
496    Returns the name of the file handle assigned to the file, or C<undef> if the
497    open failed.
498    
499    =back
500    
501    =cut
502    
503    sub Open {
504        # Get the parameters.
505        my ($fileHandle, $fileSpec, $message) = @_;
506        # Attempt to open the file.
507        my $rv = open $fileHandle, $fileSpec;
508        # If the open failed, generate an error message.
509        if (! $rv) {
510            # Save the system error message.
511            my $sysMessage = $!;
512            # See if we need a default message.
513            if (!$message) {
514                # Clean any obvious mode characters and leading spaces from the
515                # filename.
516                my ($fileName) = FindNamePart($fileSpec);
517                $message = "Could not open \"$fileName\"";
518            }
519            # Terminate with an error using the supplied message and the
520            # error message from the file system.
521            Confess("$message: $!");
522        }
523        # Return the file handle.
524        return $fileHandle;
525    }
526    
527    =head3 FindNamePart
528    
529    C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>
530    
531    Extract the portion of a file specification that contains the file name.
532    
533    A file specification is the string passed to an C<open> call. It specifies the file
534    mode and name. In a truly complex situation, it can specify a pipe sequence. This
535    method assumes that the file name is whatever follows the first angle bracket
536    sequence.  So, for example, in the following strings the file name is
537    C</usr/fig/myfile.txt>.
538    
539        >>/usr/fig/myfile.txt
540        </usr/fig/myfile.txt
541        | sort -u > /usr/fig/myfile.txt
542    
543    If the method cannot find a file name using its normal methods, it will return the
544    whole incoming string.
545    
546    =over 4
547    
548    =item fileSpec
549    
550    File specification string from which the file name is to be extracted.
551    
552    =item RETURN
553    
554    Returns a three-element list. The first element contains the file name portion of
555    the specified string, or the whole string if a file name cannot be found via normal
556    methods. The second element contains the start position of the file name portion and
557    the third element contains the length.
558    
559    =back
560    
561    =cut
562    #: Return Type $;
563    sub FindNamePart {
564        # Get the parameters.
565        my ($fileSpec) = @_;
566        # Default to the whole input string.
567        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
568        # Parse out the file name if we can.
569        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
570            $retVal = $2;
571            $len = length $retVal;
572            $pos = (length $fileSpec) - (length $3) - $len;
573        }
574        # Return the result.
575        return ($retVal, $pos, $len);
576    }
577    
578    =head3 OpenDir
579    
580    C<< my @files = OpenDir($dirName, $filtered, $flag); >>
581    
582    Open a directory and return all the file names. This function essentially performs
583    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
584    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
585    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
586    filtered out of the return list. If the directory does not open and I<$flag> is not
587    set, an exception is thrown. So, for example,
588    
589        my @files = OpenDir("/Volumes/fig/contigs", 1);
590    
591    is effectively the same as
592    
593        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
594        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
595    
596    Similarly, the following code
597    
598        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
599    
600    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
601    automatically returns an empty list if the directory fails to open.
602    
603    =over 4
604    
605    =item dirName
606    
607    Name of the directory to open.
608    
609    =item filtered
610    
611    TRUE if files whose names begin with a period (C<.>) should be automatically removed
612    from the list, else FALSE.
613    
614    =item flag
615    
616    TRUE if a failure to open is okay, else FALSE
617    
618    =back
619    
620    =cut
621    #: Return Type @;
622    sub OpenDir {
623        # Get the parameters.
624        my ($dirName, $filtered, $flag) = @_;
625        # Declare the return variable.
626        my @retVal = ();
627        # Open the directory.
628        if (opendir(my $dirHandle, $dirName)) {
629            # The directory opened successfully. Get the appropriate list according to the
630            # strictures of the filter parameter.
631            if ($filtered) {
632                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
633            } else {
634                @retVal = readdir $dirHandle;
635            }
636        } elsif (! $flag) {
637            # Here the directory would not open and it's considered an error.
638            Confess("Could not open directory $dirName.");
639        }
640        # Return the result.
641        return @retVal;
642  }  }
643    
644  =head3 SetLevel  =head3 SetLevel
# Line 394  Line 905 
905         warn $message;         warn $message;
906          } elsif ($Destination =~ m/^>>/) {          } elsif ($Destination =~ m/^>>/) {
907                  # Write the trace message to an output file.                  # Write the trace message to an output file.
908                  open TRACING, $Destination;          (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
909                  print TRACING "$formatted\n";                  print TRACING "$formatted\n";
910                  close TRACING;                  close TRACING;
911            # If the Tee flag is on, echo it to the standard output.
912            if ($TeeFlag) {
913                print "$formatted\n";
914            }
915          }          }
916  }  }
917    
# Line 439  Line 954 
954                  my ($category, $traceLevel) = @_;                  my ($category, $traceLevel) = @_;
955                  if (!defined $traceLevel) {                  if (!defined $traceLevel) {
956                          # Here we have no category, so we need to get the calling package.                          # Here we have no category, so we need to get the calling package.
957                # The calling package is normally the first parameter. If it is
958                # omitted, the first parameter will be the tracelevel. So, the
959                # first thing we do is shift the so-called category into the
960                # $traceLevel variable where it belongs.
961                          $traceLevel = $category;                          $traceLevel = $category;
962                          my ($package, $fileName, $line) = caller;                          my ($package, $fileName, $line) = caller;
963              # If there is no calling package, we default to "main".              # If there is no calling package, we default to "main".
# Line 450  Line 969 
969                  }                  }
970          # Save the category name.          # Save the category name.
971          $LastCategory = $category;          $LastCategory = $category;
972            # Convert it to lower case before we hash it.
973            $category = lc $category;
974                  # Use the category and tracelevel to compute the result.                  # Use the category and tracelevel to compute the result.
975                  $retVal = ($traceLevel <= $TraceLevel && exists $Categories{$category});          if (ref $traceLevel) {
976                Confess("Bad trace level.");
977            } elsif (ref $TraceLevel) {
978                Confess("Bad trace config.");
979            }
980            $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
981      }      }
982          # Return the computed result.          # Return the computed result.
983      return $retVal;      return $retVal;
# Line 537  Line 1063 
1063    
1064  C<< my $codedString = Tracer::Escape($realString); >>  C<< my $codedString = Tracer::Escape($realString); >>
1065    
1066  Escape a string for use in a command length. Spaces will be replaced by C<\b>,  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines
1067  tabs replaced by C<\t>, new-lines replaced by C<\n>, and backslashes will be  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
1068  doubled. The effect is to exactly reverse the effect of L</UnEscape>.  result is to reverse the effect of L</UnEscape>.
1069    
1070  =over 4  =over 4
1071    
# Line 563  Line 1089 
1089          # Loop through the parameter string, looking for sequences to escape.          # Loop through the parameter string, looking for sequences to escape.
1090          while (length $realString > 0) {          while (length $realString > 0) {
1091                  # Look for the first sequence to escape.                  # Look for the first sequence to escape.
1092                  if ($realString =~ /^(.*?)([ \n\t\\])/) {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1093                          # Here we found it. The text preceding the sequence is in $1. The sequence                          # Here we found it. The text preceding the sequence is in $1. The sequence
1094                          # itself is in $2. First, move the clear text to the return variable.                          # itself is in $2. First, move the clear text to the return variable.
1095                          $retVal .= $1;                          $retVal .= $1;
1096                          $realString = substr $realString, (length $2 + length $1);              # Strip the processed section off the real string.
1097                          # Encode the escape sequence.              $realString = substr $realString, (length $2) + (length $1);
1098                # Get the matched character.
1099                          my $char = $2;                          my $char = $2;
1100                          $char =~ tr/ \t\n/btn/;              # If we have a CR, we are done.
1101                if ($char ne "\r") {
1102                    # It's not a CR, so encode the escape sequence.
1103                    $char =~ tr/\t\n/tn/;
1104                          $retVal .= "\\" . $char;                          $retVal .= "\\" . $char;
1105                }
1106                  } else {                  } else {
1107                          # Here there are no more escape sequences. The rest of the string is                          # Here there are no more escape sequences. The rest of the string is
1108                          # transferred unmodified.                          # transferred unmodified.
# Line 587  Line 1118 
1118    
1119  C<< my $realString = Tracer::UnEscape($codedString); >>  C<< my $realString = Tracer::UnEscape($codedString); >>
1120    
1121  Replace escape sequences with their actual equivalents. C<\b> will be replaced by a space,  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
1122  C<\t> by a tab, C<\n> by a new-line character, and C<\\> by a back-slash.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
1123    be deleted.
1124    
1125  =over 4  =over 4
1126    
# Line 613  Line 1145 
1145          # Only proceed if the incoming string is nonempty.          # Only proceed if the incoming string is nonempty.
1146          if (defined $codedString) {          if (defined $codedString) {
1147                  # Loop through the parameter string, looking for escape sequences. We can't do                  # Loop through the parameter string, looking for escape sequences. We can't do
1148                  # translating because it causes problems with the escaped slash. ("\\b" becomes          # translating because it causes problems with the escaped slash. ("\\t" becomes
1149                  # "\ " no matter what we do.)          # "\<tab>" no matter what we do.)
1150                  while (length $codedString > 0) {                  while (length $codedString > 0) {
1151                          # Look for the first escape sequence.                          # Look for the first escape sequence.
1152                          if ($codedString =~ /^(.*?)\\(\\|b|n|t)/) {              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
1153                                  # Here we found it. The text preceding the sequence is in $1. The sequence                                  # Here we found it. The text preceding the sequence is in $1. The sequence
1154                                  # itself is in $2. First, move the clear text to the return variable.                                  # itself is in $2. First, move the clear text to the return variable.
1155                                  $retVal .= $1;                                  $retVal .= $1;
1156                                  $codedString = substr $codedString, (2 + length $1);                                  $codedString = substr $codedString, (2 + length $1);
1157                                  # Decode the escape sequence.                  # Get the escape value.
1158                                  my $char = $2;                                  my $char = $2;
1159                                  $char =~ tr/\\btn/\\ \t\n/;                  # If we have a "\r", we are done.
1160                    if ($char ne 'r') {
1161                        # Here it's not an 'r', so we convert it.
1162                        $char =~ tr/\\tn/\\\t\n/;
1163                                  $retVal .= $char;                                  $retVal .= $char;
1164                    }
1165                          } else {                          } else {
1166                                  # Here there are no more escape sequences. The rest of the string is                                  # Here there are no more escape sequences. The rest of the string is
1167                                  # transferred unmodified.                                  # transferred unmodified.
# Line 735  Line 1271 
1271    
1272  C<< my @fileContents = Tracer::GetFile($fileName); >>  C<< my @fileContents = Tracer::GetFile($fileName); >>
1273    
1274  Return the entire contents of a file.      or
1275    
1276    C<< my $fileContents = Tracer::GetFile($fileName); >>
1277    
1278    Return the entire contents of a file. In list context, line-ends are removed and
1279    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1280    
1281  =over 4  =over 4
1282    
# Line 761  Line 1302 
1302          my $ok = open INPUTFILE, "<$fileName";          my $ok = open INPUTFILE, "<$fileName";
1303          if (!$ok) {          if (!$ok) {
1304                  # If we had an error, trace it. We will automatically return a null value.                  # If we had an error, trace it. We will automatically return a null value.
1305                  Trace("Could not open \"$fileName\" for input.") if T(0);          Trace("Could not open \"$fileName\" for input: $!") if T(0);
1306          } else {          } else {
1307                  # Read the whole file into the return variable, stripping off any terminator                  # Read the whole file into the return variable, stripping off any terminator
1308          # characters.          # characters.
# Line 774  Line 1315 
1315                  # Close it.                  # Close it.
1316                  close INPUTFILE;                  close INPUTFILE;
1317          my $actualLines = @retVal;          my $actualLines = @retVal;
         Trace("$lineCount lines read from $fileName. $actualLines processed.") if T(3);  
1318          }          }
1319          # Return the file's contents in the desired format.          # Return the file's contents in the desired format.
1320      if (wantarray) {      if (wantarray) {
# Line 805  Line 1345 
1345          my ($format) = @_;          my ($format) = @_;
1346          # Create the return variable.          # Create the return variable.
1347          my $retVal = "";          my $retVal = "";
1348        # Only proceed if there is an actual queue.
1349        if (@Queue) {
1350          # Process according to the format.          # Process according to the format.
1351          if ($format =~ m/^HTML$/i) {          if ($format =~ m/^HTML$/i) {
1352                  # Convert the queue into an HTML list.                  # Convert the queue into an HTML list.
# Line 820  Line 1362 
1362          }          }
1363          # Clear the queue.          # Clear the queue.
1364          @Queue = ();          @Queue = ();
1365        }
1366          # Return the formatted list.          # Return the formatted list.
1367          return $retVal;          return $retVal;
1368  }  }
# Line 828  Line 1371 
1371    
1372  C<< Confess($message); >>  C<< Confess($message); >>
1373    
1374  Trace the call stack and abort the program with the specified message. The stack  Trace the call stack and abort the program with the specified message. When used with
 trace will only appear if the trace level for this package is 1 or more. When used with  
1375  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
1376  So, for example  So, for example
1377    
# Line 851  Line 1393 
1393          # Get the parameters.          # Get the parameters.
1394          my ($message) = @_;          my ($message) = @_;
1395          # Trace the call stack.          # Trace the call stack.
1396          Cluck($message) if T(1);      Cluck($message);
1397          # Abort the program.          # Abort the program.
1398          croak(">>> $message");          croak(">>> $message");
1399  }  }
# Line 861  Line 1403 
1403  C<< Assert($condition1, $condition2, ... $conditionN); >>  C<< Assert($condition1, $condition2, ... $conditionN); >>
1404    
1405  Return TRUE if all the conditions are true. This method can be used in conjunction with  Return TRUE if all the conditions are true. This method can be used in conjunction with
1406  the OR operator and the L</Confess> method, B<Assert> can function as a debugging assert.  the OR operator and the L</Confess> method as a debugging assert.
1407  So, for example  So, for example
1408    
1409  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
# Line 1020  Line 1562 
1562    
1563  C<< if (Tracer::DebugMode) { ...code... } >>  C<< if (Tracer::DebugMode) { ...code... } >>
1564    
1565  Return TRUE if debug mode has been turned on in FIG_Config, else output  Return TRUE if debug mode has been turned on, else output an error
1566  an error page and return FALSE.  page and return FALSE.
1567    
1568  Certain CGI scripts are too dangerous to exist in the production  Certain CGI scripts are too dangerous to exist in the production
1569  environment. This method provides a simple way to prevent them  environment. This method provides a simple way to prevent them
1570  from working unless they are explicitly turned on in the configuration  from working unless they are explicitly turned on by creating a password
1571  file by setting C<$FIG_Config::debug_mode> to 1. If debugging mode  cookie via the B<SetPassword> script.  If debugging mode
1572  is not turned on, an error web page will be output.  is not turned on, an error web page will be output directing the
1573    user to enter in the correct password.
1574    
1575  =cut  =cut
1576    
1577  sub DebugMode {  sub DebugMode {
1578          # Declare the return variable.          # Declare the return variable.
1579          my $retVal;      my $retVal = 0;
1580          # Check the debug configuration.          # Check the debug configuration.
1581          if ($FIG_Config::debug_mode) {      my $password = CGI::cookie("DebugMode");
1582        my $encrypted = Digest::MD5::md5_hex($password);
1583        if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1584                  $retVal = 1;                  $retVal = 1;
1585          } else {          } else {
1586                  # Here debug mode is off, so we generate an error page.                  # Here debug mode is off, so we generate an error page.
# Line 1071  Line 1616 
1616  sub Strip {  sub Strip {
1617          # Get a copy of the parameter string.          # Get a copy of the parameter string.
1618          my ($string) = @_;          my ($string) = @_;
1619          my $retVal = $string;      my $retVal = (defined $string ? $string : "");
1620      # Strip the line terminator characters.      # Strip the line terminator characters.
1621      $retVal =~ s/(\r|\n)+$//g;      $retVal =~ s/(\r|\n)+$//g;
1622          # Return the result.          # Return the result.
# Line 1102  Line 1647 
1647    
1648  =item padChar (optional)  =item padChar (optional)
1649    
1650    Character to use for padding. The default is a space.
1651    
1652  =item RETURN  =item RETURN
1653    
1654  Returns a copy of the original string with the spaces added to the specified end so  Returns a copy of the original string with the pad character added to the
1655  that it achieves the desired length.  specified end so that it achieves the desired length.
1656    
1657  =back  =back
1658    
# Line 1137  Line 1684 
1684          return $retVal;          return $retVal;
1685  }  }
1686    
1687    =head3 EOF
1688    
1689    This is a constant that is lexically greater than any useful string.
1690    
1691    =cut
1692    
1693    sub EOF {
1694        return "\xFF\xFF\xFF\xFF\xFF";
1695    }
1696    
1697    =head3 TICK
1698    
1699    C<< my @results = TICK($commandString); >>
1700    
1701    Perform a back-tick operation on a command. If this is a Windows environment, any leading
1702    dot-slash (C<./> will be removed. So, for example, if you were doing
1703    
1704        `./protein.cgi`
1705    
1706    from inside a CGI script, it would work fine in Unix, but would issue an error message
1707    in Windows complaining that C<'.'> is not a valid command. If instead you code
1708    
1709        TICK("./protein.cgi")
1710    
1711    it will work correctly in both environments.
1712    
1713    =over 4
1714    
1715    =item commandString
1716    
1717    The command string to pass to the system.
1718    
1719    =item RETURN
1720    
1721    Returns the standard output from the specified command, as a list.
1722    
1723    =back
1724    
1725    =cut
1726    #: Return Type @;
1727    sub TICK {
1728        # Get the parameters.
1729        my ($commandString) = @_;
1730        # Chop off the dot-slash if this is Windows.
1731        if ($FIG_Config::win_mode) {
1732            $commandString =~ s!^\./!!;
1733        }
1734        # Activate the command and return the result.
1735        return `$commandString`;
1736    }
1737    
1738    =head3 ScriptSetup
1739    
1740    C<< my ($query, $varHash) = ScriptSetup(); >>
1741    
1742    Perform standard tracing and debugging setup for scripts. The value returned is
1743    the CGI object followed by a pre-built variable hash.
1744    
1745    The C<Trace> query parameter is used to determine whether or not tracing is active and
1746    which trace modules (other than C<Tracer> and C<FIG>) should be turned on. Specifying
1747    the C<CGI> trace module will trace parameter and environment information. Parameters are
1748    traced at level 3 and environment variables at level 4. At the end of the script, the
1749    client should call L</ScriptFinish> to output the web page.
1750    
1751    =cut
1752    
1753    sub ScriptSetup {
1754        # Get the CGI query object.
1755        my $query = CGI->new();
1756        # Check for tracing. Set it up if the user asked for it.
1757        if ($query->param('Trace')) {
1758            # Set up tracing to be queued for display at the bottom of the web page.
1759            TSetup($query->param('Trace') . " FIG Tracer", "QUEUE");
1760            # Trace the parameter and environment data.
1761            if (T(CGI => 3)) {
1762                # Here we want to trace the parameter data.
1763                my @names = $query->param;
1764                for my $parmName (sort @names) {
1765                    # Note we skip "Trace", which is for our use only.
1766                    if ($parmName ne 'Trace') {
1767                        my @values = $query->param($parmName);
1768                        Trace("CGI: $parmName = " . join(", ", @values));
1769                    }
1770                }
1771            }
1772            if (T(CGI => 4)) {
1773                # Here we want the environment data too.
1774                for my $envName (sort keys %ENV) {
1775                    Trace("ENV: $envName = $ENV{$envName}");
1776                }
1777            }
1778        } else {
1779            # Here tracing is to be turned off. All we allow is errors traced into the
1780            # error log.
1781            TSetup("0", "WARN");
1782        }
1783        # Create the variable hash.
1784        my $varHash = { DebugData => '' };
1785        # If we're in DEBUG mode, set up the debug mode data for forms.
1786        if (Tracer::DebugMode) {
1787            $varHash->{DebugData} = GetFile("Html/DebugFragment.html");
1788        }
1789        # Return the query object and variable hash.
1790        return ($query, $varHash);
1791    }
1792    
1793    =head3 ScriptFinish
1794    
1795    C<< ScriptFinish($webData, $varHash); >>
1796    
1797    Output a web page at the end of a script. Either the string to be output or the
1798    name of a template file can be specified. If the second parameter is omitted,
1799    it is assumed we have a string to be output; otherwise, it is assumed we have the
1800    name of a template file. The template should have the variable C<DebugData>
1801    specified in any form that invokes a standard script. If debugging mode is turned
1802    on, a form field will be put in that allows the user to enter tracing data.
1803    Trace messages will be placed immediately before the terminal C<BODY> tag in
1804    the output, formatted as a list.
1805    
1806    A typical standard script would loook like the following.
1807    
1808        BEGIN {
1809            # Print the HTML header.
1810            print "CONTENT-TYPE: text/html\n\n";
1811        }
1812        use Tracer;
1813        use CGI;
1814        use FIG;
1815        # ... more uses ...
1816    
1817        my ($query, $varHash) = ScriptSetup();
1818        eval {
1819            # ... get data from $query, put it in $varHash ...
1820        };
1821        if ($@) {
1822            Trace("Script Error: $@") if T(0);
1823        }
1824        ScriptFinish("Html/MyTemplate.html", $varHash);
1825    
1826    The idea here is that even if the script fails, you'll see trace messages and
1827    useful output.
1828    
1829    =over 4
1830    
1831    =item webData
1832    
1833    A string containing either the full web page to be written to the output or the
1834    name of a template file from which the page is to be constructed. If the name
1835    of a template file is specified, then the second parameter must be present;
1836    otherwise, it must be absent.
1837    
1838    =item varHash (optional)
1839    
1840    If specified, then a reference to a hash mapping variable names for a template
1841    to their values. The template file will be read into memory, and variable markers
1842    will be replaced by data in this hash reference.
1843    
1844    =back
1845    
1846    =cut
1847    
1848    sub ScriptFinish {
1849        # Get the parameters.
1850        my ($webData, $varHash) = @_;
1851        # Check for a template file situation.
1852        my $outputString;
1853        if (defined $varHash) {
1854            # Here we have a template file. We need to apply the variables to the template.
1855            $outputString = PageBuilder::Build("<$webData", $varHash, "Html");
1856        } else {
1857            # Here the user gave us a raw string.
1858            $outputString = $webData;
1859        }
1860        # Check for trace messages.
1861        if ($Destination eq "QUEUE") {
1862            # We have trace messages, so we want to put them at the end of the body. This
1863            # is either at the end of the whole string or at the beginning of the BODY
1864            # end-tag.
1865            my $pos = length $outputString;
1866            if ($outputString =~ m#</body>#gi) {
1867                $pos = (pos $outputString) - 7;
1868            }
1869            substr $outputString, $pos, 0, QTrace('Html');
1870        }
1871        # Write the output string.
1872        print $outputString;
1873    }
1874    
1875    =head3 Insure
1876    
1877    C<< Insure($dirName); >>
1878    
1879    Insure a directory is present.
1880    
1881    =over 4
1882    
1883    =item dirName
1884    
1885    Name of the directory to check. If it does not exist, it will be created.
1886    
1887    =back
1888    
1889    =cut
1890    
1891    sub Insure {
1892        my ($dirName) = @_;
1893        if (! -d $dirName) {
1894            Trace("Creating $dirName directory.") if T(2);
1895            mkpath $dirName;
1896        }
1897    }
1898    
1899  1;  1;

Legend:
Removed from v.1.9  
changed lines
  Added in v.1.37

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3