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

Diff of /FigKernelPackages/Tracer.pm

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

revision 1.67, Fri Sep 29 15:00:17 2006 UTC revision 1.102, Thu May 8 22:52:30 2008 UTC
# Line 1  Line 1 
1  #  # -*- perl -*-
2    ########################################################################
3  # Copyright (c) 2003-2006 University of Chicago and Fellowship  # Copyright (c) 2003-2006 University of Chicago and Fellowship
4  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
5  #  #
# Line 13  Line 14 
14  # at info@ci.uchicago.edu or the Fellowship for Interpretation of  # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15  # Genomes at veronika@thefig.info or download a copy from  # Genomes at veronika@thefig.info or download a copy from
16  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
17  #  ########################################################################
18    
19  package Tracer;  package Tracer;
20    
21      require Exporter;      require Exporter;
22      @ISA = ('Exporter');      @ISA = ('Exporter');
23      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup ScriptSetup ScriptFinish Insure ChDir);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn);
24      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
25      use strict;      use strict;
26      use Carp qw(longmess croak);      use Carp qw(longmess croak carp);
27      use CGI;      use CGI;
28      use Cwd;      use Cwd;
29      use FIG_Config;      use FIG_Config;
# Line 34  Line 35 
35      use LWP::UserAgent;      use LWP::UserAgent;
36      use Time::HiRes 'gettimeofday';      use Time::HiRes 'gettimeofday';
37      use URI::Escape;      use URI::Escape;
38        use Time::Local;
39        use POSIX qw(strftime);
40        use Time::Zone;
41    
42    
43  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
44    
45  =head2 Introduction  =head2 Tracing
46    
47  This package provides simple tracing for debugging and reporting purposes. To use it simply call the  This package provides simple tracing for debugging and reporting purposes. To use it simply call the
48  L</TSetup> method to set the options and call L</Trace> to write out trace messages. Each trace  L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
49  message has a I<trace level> and I<category> associated with it. In addition, the tracing package itself  L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
50  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace  each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
51  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 the setup trace level and whose category is activated will
52  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
53  is less likely to be seen. A higher trace level passed to B<TSetup> means more trace messages will  is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
54  appear. To generate a trace message, use the following syntax.  appear.
55    
56    =head3 Putting Trace Messages in Your Code
57    
58  C<< Trace($message) if T(errors => 4); >>  To generate a trace message, use the following syntax.
59    
60        Trace($message) if T(errors => 4);
61    
62  This statement will produce a trace message if the trace level is 4 or more and the C<errors>  This statement will produce a trace message if the trace level is 4 or more and the C<errors>
63  category is active. Note that the special category C<main> is always active, so  category is active. There is a special category C<main> that is always active, so
64    
65  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
66    
67  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
68    
# Line 61  Line 70 
70  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
71  active and the trace level is 2 or more.  active and the trace level is 2 or more.
72    
73  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
74    
75    In scripts, where no package name is available, the category defaults to C<main>.
76    
77    =head3 Custom Tracing
78    
79    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
80    the preferred method, but a knowledge of how custom tracing works can make the more modern
81    L</Emergency Tracing> easier to understand.
82    
83  To set up tracing, you call the L</TSetup> method. The method takes as input a trace level, a list  To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
84  of category names, and a set of options. The trace level and list of category names are  a list of category names, and a destination. The trace level and list of category names are
85  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
86    
87  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
88    
89  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
90  specifies that messages should be output as HTML paragraphs.  specifies that messages should be sent to the standard output.
91    
92  To turn on tracing for ALL categories, use an asterisk. The call below sets every category to  To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
93  level 3 and writes the output to the standard error output. This sort of thing might be  level 3 and writes the output to the standard error output. This sort of thing might be
94  useful in a CGI environment.  useful in a CGI environment.
95    
96  C<< TSetup('3 *', 'WARN'); >>      TSetup('3 *', 'WARN');
97    
98  In addition to HTML and file output for trace messages, you can specify that the trace messages  In addition standard error and file output for trace messages, you can specify that the trace messages
99  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
100  is useful if you are building a web page. Instead of having the trace messages interspersed with  is useful if you are building a web page. Instead of having the trace messages interspersed with
101  the page output, they can be gathered together and displayed at the end of the page. This makes  the page output, they can be gathered together and displayed at the end of the page. This makes
102  it easier to debug page formatting problems.  it easier to debug page formatting problems.
103    
104  Finally, you can specify that all trace messages be emitted as warnings.  Finally, you can specify that all trace messages be emitted to a file, or the standard output and
105    a file at the same time. To trace to a file, specify the filename with an output character in front
106    of it.
107    
108        TSetup('4 SQL', ">$fileName");
109    
110    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
111    bracket.
112    
113        TSetup('3 *', "+>$fileName");
114    
115  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
116  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
117  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
118  being used out in the field.  being used out in the field.
119    
120    =head3 Trace Levels
121    
122  There is no hard and fast rule on how to use trace levels. The following is therefore only  There is no hard and fast rule on how to use trace levels. The following is therefore only
123  a suggestion.  a suggestion.
124    
# Line 121  Line 149 
149    
150  =back  =back
151    
152    The format of trace messages is important because some utilities analyze trace files.
153    There are three fields-- the time stamp, the category name, and the text.
154    The time stamp is between square brackets and the category name between angle brackets.
155    After the category name there is a colon (C<:>) followed by the message text.
156    If the square brackets or angle brackets are missing, then the trace management
157    utilities assume that they are encountering a set of pre-formatted lines.
158    
159    Note, however, that this formatting is done automatically by the tracing functions. You
160    only need to know about it if you want to parse a trace file.
161    
162    =head3 Emergency Tracing
163    
164    Sometimes, you need a way for tracing to happen automatically without putting parameters
165    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
166    from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
167    that you specify a tracing key. For command-line tools, the key is
168    taken from the C<TRACING> environment variable. For web services, the key is taken from
169    a cookie. Either way, the key tells the tracing facility who you are, so that you control
170    the tracing in your environment without stepping on other users.
171    
172    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
173    generate one for you.
174    
175    You can activate and de-activate emergency tracing from the debugging control panel, as
176    well as display the trace file itself.
177    
178    To enable emergency tracing in your code, call
179    
180        ETracing($cgi)
181    
182    from a web script and
183    
184        ETracing()
185    
186    from a command-line script.
187    
188    The web script will look for the tracing key in the cookies, and the command-line
189    script will look for it in the C<TRACING> environment variable. If you are
190    using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
191    will be configured automatically.
192    
193  =cut  =cut
194    
195  # Declare the configuration variables.  # Declare the configuration variables.
196    
197  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
198  my $TeeFlag = 0;            # TRUE if output is going to a file and to the  my $TeeFlag = 0;            # TRUE if output is going to a file and to the
199                              # standard output                              # standard output
200  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
201                              # hash of active category names                              # hash of active category names
202    my @LevelNames = qw(error warn notice info detail);
203  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
204                              # messages                              # messages
205  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
206  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
207    my $LastLevel = 0;          # level of the last test call
208  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
209  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
210    my $SavedCGI;               # CGI object passed to ETracing
211    umask 2;                    # Fix the damn umask so everything is group-writable.
212    
213    =head2 Tracing Methods
214    
215    =head3 Setups
216    
217        my $count = Tracer::Setups();
218    
219    Return the number of times L</TSetup> has been called.
220    
221    This method allows for the creation of conditional tracing setups where, for example, we
222    may want to set up tracing if nobody else has done it before us.
223    
224    =cut
225    
226  =head2 Public Methods  sub Setups {
227        return $SetupCount;
228    }
229    
230  =head3 TSetup  =head3 TSetup
231    
232  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
233    
234  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
235  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 191  Line 279 
279          }          }
280      }      }
281      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
282      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
283      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
284        # the standard output (tee mode).
285      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
286          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
287              $TeeFlag = 1;              $TeeFlag = 1;
288              $target = substr($target, 1);              $target = substr($target, 1);
289          }          }
290          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
291                # We need to initialize the file (which clears it).
292              open TRACEFILE, $target;              open TRACEFILE, $target;
293              print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
294              close TRACEFILE;              close TRACEFILE;
295                # Set to append mode now that the file has been cleared.
296              $Destination = ">$target";              $Destination = ">$target";
297          } else {          } else {
298              $Destination = $target;              $Destination = $target;
# Line 213  Line 304 
304      $SetupCount++;      $SetupCount++;
305  }  }
306    
307  =head3 StandardSetup  =head3 SetLevel
308    
309  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
310    
311  This method performs standard command-line parsing and tracing setup. The return  Modify the trace level. A higher trace level will cause more messages to appear.
 values are a hash of the command-line options and a list of the positional  
 parameters. Tracing is automatically set up and the command-line options are  
 validated.  
312    
313  This is a complex method that does a lot of grunt work. The parameters can  =over 4
 be more easily understood, however, once they are examined individually.  
314    
315  The I<categories> parameter is the most obtuse. It is a reference to a list of  =item newLevel
 special-purpose tracing categories. Most tracing categories are PERL package  
 names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,  
 B<ERDB>, and B<SproutLoad> packages, you would specify the categories  
316    
317      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
318    
319  This would cause trace messages in the specified three packages to appear in  =back
 the output. There are threer special tracing categories that are automatically  
 handled by this method. In other words, if you used L</TSetup> you would need  
 to include these categories manually, but if you use this method they are turned  
 on automatically.  
320    
321  =over 4  =cut
322    
323  =item FIG  sub SetLevel {
324        $TraceLevel = $_[0];
325    }
326    
327  Turns on trace messages inside the B<FIG> package.  =head3 ParseDate
328    
329  =item SQL      my $time = Tracer::ParseDate($dateString);
330    
331  Traces SQL commands and activity.  Convert a date into a PERL time number. This method expects a date-like string
332    and parses it into a number. The string must be vaguely date-like or it will
333    return an undefined value. Our requirement is that a month and day be
334    present and that three pieces of the date string (time of day, month and day,
335    year) be separated by likely delimiters, such as spaces, commas, and such-like.
336    
337  =item Tracer  If a time of day is present, it must be in military time with two digits for
338    everything but the hour.
339    
340  Traces error messages and call stacks.  The year must be exactly four digits.
341    
342  =back  Additional stuff can be in the string. We presume it's time zones or weekdays or something
343    equally innocuous. This means, however, that a sufficiently long sentence with date-like
344    parts in it may be interpreted as a date. Hopefully this will not be a problem.
345    
346  C<SQL> is only turned on if the C<-sql> option is specified in the command line.  It should be guaranteed that this method will parse the output of the L</Now> function.
 The trace level is specified using the C<-trace> command-line option. For example,  
 the following command line for C<TransactFeatures> turns on SQL tracing and runs  
 all tracing at level 3.  
347    
348      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  The parameters are as follows.
349    
350  Standard tracing is output to the standard output and echoed to the file  =over 4
 C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the  
 process ID. You can also specify the C<user> parameter to put a user ID  
 instead of a process ID in the trace file name. So, for example  
351    
352  The default trace level is 2. To get all messages, specify a trace level of 4.  =item dateString
 For a genome-by-genome update, use 3.  
353    
354      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  The date string to convert.
355    
356  would send the trace output to C<traceBruce.log> in the temporary directory.  =item RETURN
357    
358  The I<options> parameter is a reference to a hash containing the command-line  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
359  options, their default values, and an explanation of what they mean. Command-line  the date string is invalid. A valid date string must contain a month and day.
 options may be in the form of switches or keywords. In the case of a switch, the  
 option value is 1 if it is specified and 0 if it is not specified. In the case  
 of a keyword, the value is separated from the option name by an equal sign. You  
 can see this last in the command-line example above.  
360    
361  You can specify a different default trace level by setting C<$options->{trace}>  =back
 prior to calling this method.  
362    
363  An example at this point would help. Consider, for example, the command-line utility  =cut
 C<TransactFeatures>. It accepts a list of positional parameters plus the options  
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
364    
365      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  # Universal month conversion table.
366                          { safe => [0, "use database transactions"],  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
367                            noAlias => [0, "do not expect aliases in CHANGE transactions"],                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
368                            start => [' ', "start with this genome"],                              Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
369                            tblFiles => [0, "output TBL files containing the corrected IDs"] },                              Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
370                          "command transactionDirectory IDfile",                              May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
371                        @ARGV);                              Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
372                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
373                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
374                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
375                                Oct =>  9, October  =>   9, '10' =>  9,
376                                Nov => 10, November =>  10, '11' => 10,
377                                Dec => 11, December =>  11, '12' => 11
378                            };
379    
380    sub ParseDate {
381        # Get the parameters.
382        my ($dateString) = @_;
383        # Declare the return variable.
384        my $retVal;
385        # Find the month and day of month. There are two ways that can happen. We check for the
386        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
387        # won't be fooled into thinking the month is Sunday.
388        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
389            my ($mon, $mday) = (MONTHS->{$1}, $2);
390            # Insist that the month and day are valid.
391            if (defined($mon) && $2 >= 1 && $2 <= 31) {
392                # Find the time.
393                my ($hour, $min, $sec) = (0, 0, 0);
394                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
395                    ($hour, $min, $sec) = ($1, $2, $3);
396                }
397                # Find the year.
398                my $year;
399                if ($dateString =~ /\b(\d{4})\b/) {
400                    $year = $1;
401                } else {
402                    # Get the default year, which is this one. Note we must convert it to
403                    # the four-digit value expected by "timelocal".
404                    (undef, undef, undef, undef, undef, $year) = localtime();
405                    $year += 1900;
406                }
407                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
408            }
409        }
410        # Return the result.
411        return $retVal;
412    }
413    
414  The call to C<ParseCommand> specifies the default values for the options and  =head3 LogErrors
 stores the actual options in a hash that is returned as C<$options>. The  
 positional parameters are returned in C<@parameters>.  
415    
416  The following is a sample command line for C<TransactFeatures>.      Tracer::LogErrors($fileName);
417    
418      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  Route the standard error output to a log file.
419    
420  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  =over 4
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<FIG>, C<Tracer>, and <DocUtils>. C<FIG> and C<Tracer> are standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
421    
422      { trace => 2, sql => 0, safe => 0,  =item fileName
       noAlias => 1, start => ' ', tblFiles => 0 }  
423    
424  Use of C<StandardSetup> in this way provides a simple way of performing  Name of the file to receive the error output.
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
425    
426  If the C<background> option is specified on the command line, then the  =back
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
427    
428      -user=Bruce -background  =cut
429    
430  then the trace output would go to C<traceBruce.log>, the standard output to  sub LogErrors {
431  C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to      # Get the file name.
432  simplify starting a command in the background.      my ($fileName) = @_;
433        # Open the file as the standard error output.
434        open STDERR, '>', $fileName;
435    }
436    
437  Finally, if the special option C<-h> is specified, the option names will  =head3 Trace
 be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
438    
439      TransactFeatures -h      Trace($message);
440    
441  he would see the following output.  Write a trace message to the target location specified in L</TSetup>. If there has not been
442    any prior call to B<TSetup>.
443    
444      TransactFeatures [options] command transactionDirectory IDfile  =over 4
         -trace    tracing level (default 2)  
         -sql      trace SQL commands  
         -safe     use database transactions  
         -noAlias  do not expect aliases in CHANGE transactions  
         -start    start with this genome  
         -tblFiles output TBL files containing the corrected IDs  
445    
446  The caller has the option of modifying the tracing scheme by placing a value  =item message
 for C<trace> in the incoming options hash. The default value can be overridden,  
 or the tracing to the standard output can be turned off by suffixing a minus  
 sign to the trace level. So, for example,  
447    
448      { trace => [0, "tracing level (default 0)"],  Message to write.
        ...  
449    
450  would set the default trace level to 0 instead of 2, while  =back
451    
452      { trace => ["2-", "tracing level (default 2)"],  =cut
        ...  
453    
454  would leave the default at 2, but trace only to the log file, not to the  sub Trace {
455  standard output.      # Get the parameters.
456        my ($message) = @_;
457        # Strip off any line terminators at the end of the message. We will add
458        # new-line stuff ourselves.
459        my $stripped = Strip($message);
460        # Compute the caller information.
461        my ($callPackage, $callFile, $callLine) = caller();
462        my $callFileTitle = basename($callFile);
463        # Check the caller.
464        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
465        # Get the timestamp.
466        my $timeStamp = Now();
467        # Build the prefix.
468        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
469        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
470        # Format the message.
471        my $formatted = "$prefix $stripped";
472        # Process according to the destination.
473        if ($Destination eq "TEXT") {
474            # Write the message to the standard output.
475            print "$formatted\n";
476        } elsif ($Destination eq "ERROR") {
477            # Write the message to the error output. Here, we want our prefix fields.
478            print STDERR "$formatted\n";
479        } elsif ($Destination eq "WARN") {
480            # Emit the message to the standard error output. It is presumed that the
481            # error logger will add its own prefix fields, the notable exception being
482            # the caller info.
483            print STDERR "$callerInfo$stripped\n";
484        } elsif ($Destination eq "QUEUE") {
485            # Push the message into the queue.
486            push @Queue, "$formatted";
487        } elsif ($Destination eq "HTML") {
488            # Convert the message to HTML and write it to the standard output.
489            my $escapedMessage = CGI::escapeHTML($stripped);
490            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
491        } elsif ($Destination =~ m/^>>/) {
492            # Write the trace message to an output file.
493            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
494            print TRACING "$formatted\n";
495            close TRACING;
496            # If the Tee flag is on, echo it to the standard output.
497            if ($TeeFlag) {
498                print "$formatted\n";
499            }
500        }
501    }
502    
503  The parameters to this method are as follows.  =head3 T
504    
505  =over 4      my $switch = T($category, $traceLevel);
506    
507  =item categories      or
508    
509  Reference to a list of tracing category names. These should be names of      my $switch = T($traceLevel);
 packages whose internal workings will need to be debugged to get the  
 command working.  
510    
511  =item options  Return TRUE if the trace level is at or above a specified value and the specified category
512    is active, else FALSE. If no category is specified, the caller's package name is used.
513    
514  Reference to a hash containing the legal options for the current command mapped  =over 4
 to their default values and descriptions. The user can override the defaults  
 by specifying the options as command-line switches prefixed by a hyphen.  
 Tracing-related options may be added to this hash. If the C<-h> option is  
 specified on the command line, the option descriptions will be used to  
 explain the options. To turn off tracing to the standard output, add a  
 minus sign to the value for C<trace> (see above).  
515    
516  =item parmHelp  =item category
517    
518  A string that vaguely describes the positional parameters. This is used  Category to which the message belongs. If not specified, the caller's package name is
519  if the user specifies the C<-h> option.  used.
520    
521  =item argv  =item traceLevel
522    
523  List of command line parameters, including the option switches, which must  Relevant tracing level.
 precede the positional parameters and be prefixed by a hyphen.  
524    
525  =item RETURN  =item RETURN
526    
527  Returns a list. The first element of the list is the reference to a hash that  TRUE if a message at the specified trace level would appear in the trace, else FALSE.
 maps the command-line option switches to their values. These will either be the  
 default values or overrides specified on the command line. The remaining  
 elements of the list are the position parameters, in order.  
528    
529  =back  =back
530    
531  =cut  =cut
532    
533  sub StandardSetup {  sub T {
534        # Declare the return variable.
535        my $retVal = 0;
536        # Only proceed if tracing is turned on.
537        if ($Destination ne "NONE") {
538      # Get the parameters.      # Get the parameters.
539      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
540      # Add the tracing options.          if (!defined $traceLevel) {
541      if (! exists $options->{trace}) {              # Here we have no category, so we need to get the calling package.
542          $options->{trace} = [2, "tracing level"];              # The calling package is normally the first parameter. If it is
543      }              # omitted, the first parameter will be the tracelevel. So, the
544      $options->{sql} = [0, "turn on SQL tracing"];              # first thing we do is shift the so-called category into the
545      $options->{h} = [0, "display command-line options"];              # $traceLevel variable where it belongs.
546      $options->{user} = [$$, "trace log file name suffix"];              $traceLevel = $category;
547      $options->{background} = [0, "spool standard and error output"];              my ($package, $fileName, $line) = caller;
548      # Create a parsing hash from the options hash. The parsing hash              # If there is no calling package, we default to "main".
549      # contains the default values rather than the default value              if (!$package) {
550      # and the description. While we're at it, we'll memorize the                  $category = "main";
551      # length of the longest option name.              } else {
552                    my @cats = split /::/, $package;
553                    $category = $cats[$#cats];
554                }
555            }
556            # Save the category name and level.
557            $LastCategory = $category;
558            $LastLevel = $traceLevel;
559            # Convert it to lower case before we hash it.
560            $category = lc $category;
561            # Validate the trace level.
562            if (ref $traceLevel) {
563                Confess("Bad trace level.");
564            } elsif (ref $TraceLevel) {
565                Confess("Bad trace config.");
566            }
567            # Make the check. Note that level 0 shows even if the category is turned off.
568            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
569        }
570        # Return the computed result.
571        return $retVal;
572    }
573    
574    =head3 QTrace
575    
576        my $data = QTrace($format);
577    
578    Return the queued trace data in the specified format.
579    
580    =over 4
581    
582    =item format
583    
584    C<html> to format the data as an HTML list, C<text> to format it as straight text.
585    
586    =back
587    
588    =cut
589    
590    sub QTrace {
591        # Get the parameter.
592        my ($format) = @_;
593        # Create the return variable.
594        my $retVal = "";
595        # Only proceed if there is an actual queue.
596        if (@Queue) {
597            # Process according to the format.
598            if ($format =~ m/^HTML$/i) {
599                # Convert the queue into an HTML list.
600                $retVal = "<ul>\n";
601                for my $line (@Queue) {
602                    my $escapedLine = CGI::escapeHTML($line);
603                    $retVal .= "<li>$escapedLine</li>\n";
604                }
605                $retVal .= "</ul>\n";
606            } elsif ($format =~ m/^TEXT$/i) {
607                # Convert the queue into a list of text lines.
608                $retVal = join("\n", @Queue) . "\n";
609            }
610            # Clear the queue.
611            @Queue = ();
612        }
613        # Return the formatted list.
614        return $retVal;
615    }
616    
617    =head3 Confess
618    
619        Confess($message);
620    
621    Trace the call stack and abort the program with the specified message. When used with
622    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
623    So, for example
624    
625        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
626    
627    Will abort the program with a stack trace if the value of C<$recNum> is negative.
628    
629    =over 4
630    
631    =item message
632    
633    Message to include in the trace.
634    
635    =back
636    
637    =cut
638    
639    sub Confess {
640        # Get the parameters.
641        my ($message) = @_;
642        # Set up the category and level.
643        $LastCategory = "(confess)";
644        $LastLevel = 0;
645        if (! defined($FIG_Config::no_tool_hdr)) {
646            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
647            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
648            # Only proceed if the tool header file is actually present.
649            if (-f $toolHeaderFile) {
650                my $fh;
651                if (open $fh, "<$toolHeaderFile") {
652                    my @lines = <$fh>;
653                    Trace("Tool header has " . scalar(@lines) . " lines.");
654                }
655            }
656        }
657        # Trace the call stack.
658        Cluck($message);
659        # Abort the program.
660        croak(">>> $message");
661    }
662    
663    =head3 Warn
664    
665        Warn($message);
666    
667    This method traces an important message. If an RSS feed is configured
668    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
669    then the message will be echoed to the feed. In general, a tracing
670    destination of C<WARN> indicates that the caller is running as a web
671    service in a production environment; however, this is not a requirement.
672    
673    The L</Cluck> method calls this one for its final message. Since
674    L</Confess> calls L</Cluck>, this means that any error which is caught
675    and confessed will put something in the feed. This insures that someone
676    will be alerted relatively quickly when a failure occurs.
677    
678    =over 4
679    
680    =item message
681    
682    Message to be traced.
683    
684    =back
685    
686    =cut
687    
688    sub Warn {
689        # Get the parameters.
690        my ($message) = @_;
691        # Trace the message.
692        Trace($message);
693        # Check for debug mode.
694        my $debugMode = (exists $Categories{feed} && $TraceLevel > 0);
695        # An error here would be disastrous. Note, however, that we aren't too worried
696        # about losing events. The error log is always available for the occasions where
697        # we mess up. Note that if debug mode is specified, we do this stuff even in a
698        # test environment.
699        eval {
700            # Do we need to put this in the RSS feed?
701            if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $debugMode)) {
702                # Yes. We now need to compute the date, the link, and the title.
703                # First, the date, in a very specific format.
704                my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
705                    (tz_local_offset() / 30);
706                Trace("Generating RSS feed. Date = $date.") if $debugMode;
707                # Environment data goes in here. We start with the date.
708                my $environment = "$date.  ";
709                # If we need to recap the message (because it's too long to be a title), we'll
710                # put it in here.
711                my $recap;
712                # Copy the message and remove excess space.
713                my $title = $message;
714                $title =~ s/\s+/ /gs;
715                # If it's too long, we have to split it up.
716                if (length $title > 60) {
717                    # Put the full message in the environment string.
718                    $recap = $title;
719                    # Excerpt it as the title.
720                    $title = substr($title, 0, 50) . "...";
721                }
722                # If we have a CGI object, then this is a web error. Otherwise, it's
723                # command-line.
724                if (defined $SavedCGI) {
725                    # We're in a web service. The environment is the user's IP, and the link
726                    # is the URL that got us here.
727                    my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
728                    $environment .= "Event Reported at IP address $key.";
729                    my $url = $SavedCGI->url(-full => 1, -query => 1);
730                    # We need the user agent string and (if available) the referrer.
731                    # The referrer will be the link.
732                    $environment .= "User Agent $ENV{HTTP_USER_AGENT}";
733                    if ($ENV{HTTP_REFERER}) {
734                        my $link = $ENV{HTTP_REFERER};
735                        $environment .= " referred from <a href=\"$link\">$link</a>.";
736                    } else {
737                        $environment .= " referrer unknown.";
738                    }
739                    # Close off the sentence with the original link.
740                    $environment .= " URL of error is <a href=\"$url\">$url</a>.";
741                } else {
742                    # No CGI object, so we're a command-line tool. Use the tracing
743                    # key and the PID as the user identifier, and add the command.
744                    my $key = EmergencyKey();
745                    $environment .= "Event Reported by $key Process $$. Command $ENV{_}.";
746                }
747                # Build a GUID. We use the current time, the title, and the process ID,
748                # then digest the result.
749                my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
750                # Finally, the description. This is a stack trace plus various environmental stuff.
751                my $stackTrace = "";
752                my @trace = LongMess();
753                # Only proceed if we got something back.
754                if (scalar(@trace) > 0) {
755                    $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
756                    $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
757                }
758                # We got the stack trace. Now it's time to put it all together.
759                # We have a goofy thing here in that we need to HTML-escape some sections of the description
760                # twice. They will be escaped once here, and then once when written by XML::Simple. They are
761                # unescaped once when processed by the RSS reader, and stuff in the description is treated as
762                # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
763                # our <br>s and <pre>s are used to format the description.
764                $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
765                my $description = "$recap$environment  $stackTrace";
766                Trace("Unescaped description is:\n$description") if $debugMode;
767                # Okay, we have all the pieces. Create a hash of the new event.
768                my $newItem = { title => $title,
769                                description => $description,
770                                category => $LastCategory,
771                                pubDate => $date,
772                                guid => $guid,
773                               };
774                # We need XML capability for this.
775                require XML::Simple;
776                # The RSS document goes in here.
777                my $rss;
778                # Get the name of the RSS file. It's in the FIG temporary directory.
779                my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
780                # Does it exist?
781                if (-s $fileName) {
782                    # Slurp it in.
783                    $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
784                } else {
785                    my $size = -s $fileName;
786                    # Create an empty channel.
787                    $rss = {
788                        channel => {
789                            title => 'NMPDR Warning Feed',
790                            link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
791                            description => "Important messages regarding the status of the NMPDR.",
792                            generator => "NMPDR Trace Facility",
793                            docs => "http://blogs.law.harvard.edu/tech/rss",
794                            item => []
795                        },
796                    };
797                }
798                # Get the channel object.
799                my $channel = $rss->{channel};
800                # Update the last-build date.
801                $channel->{lastBuildDate} = $date;
802                # Get the item array.
803                my $items = $channel->{item};
804                # Insure it has only 100 entries.
805                while (scalar @{$items} > 100) {
806                    pop @{$items};
807                }
808                # Add our new item at the front.
809                unshift @{$items}, $newItem;
810                # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
811                # the requirements for those.
812                my $xml = XML::Simple::XMLout($rss, NoAttr => 1, RootName => undef, XmlDecl => '');
813                # Here we put in the root and declaration. The problem is that the root has to have the version attribute
814                # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
815                $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
816                # We don't use Open here because we can't afford an error.
817                if (open XMLOUT, ">$fileName") {
818                    print XMLOUT $xml;
819                    close XMLOUT;
820                }
821            }
822        };
823        # We only worry about problems in debug mode. The loss of an error message is an annoyance, not a
824        # crisis.
825        if ($@ && $debugMode) {
826            my $error = $@;
827            Trace("Feed Error: $error");
828        }
829    }
830    
831    =head3 Assert
832    
833        Assert($condition1, $condition2, ... $conditionN);
834    
835    Return TRUE if all the conditions are true. This method can be used in conjunction with
836    the OR operator and the L</Confess> method as a debugging assert.
837    So, for example
838    
839        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
840    
841    Will abort the program with a stack trace if the value of C<$recNum> is negative.
842    
843    =cut
844    sub Assert {
845        my $retVal = 1;
846        LOOP: for my $condition (@_) {
847            if (! $condition) {
848                $retVal = 0;
849                last LOOP;
850            }
851        }
852        return $retVal;
853    }
854    
855    =head3 Cluck
856    
857        Cluck($message);
858    
859    Trace the call stack. Note that for best results, you should qualify the call with a
860    trace condition. For example,
861    
862        Cluck("Starting record parse.") if T(3);
863    
864    will only trace the stack if the trace level for the package is 3 or more.
865    
866    =over 4
867    
868    =item message
869    
870    Message to include in the trace.
871    
872    =back
873    
874    =cut
875    
876    sub Cluck {
877        # Get the parameters.
878        my ($message) = @_;
879        # Trace what's happening.
880        Trace("Stack trace for event: $message");
881        # Get the stack trace.
882        my @trace = LongMess();
883        # Convert the trace to a series of messages.
884        for my $line (@trace) {
885            # Replace the tab at the beginning with spaces.
886            $line =~ s/^\t/    /;
887            # Trace the line.
888            Trace($line);
889        }
890        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
891        Warn($message);
892    }
893    
894    =head3 LongMess
895    
896        my @lines = Tracer::LongMess();
897    
898    Return a stack trace with all tracing methods removed. The return will be in the form of a list
899    of message strings.
900    
901    =cut
902    
903    sub LongMess {
904        # Declare the return variable.
905        my @retVal = ();
906        my $confession = longmess("");
907        for my $line (split /\s*\n/, $confession) {
908            unless ($line =~ /Tracer\.pm/) {
909                # Here we have a line worth keeping. Push it onto the result list.
910                push @retVal, $line;
911            }
912        }
913        # Return the result.
914        return @retVal;
915    }
916    
917    =head3 ScriptSetup (deprecated)
918    
919        my ($cgi, $varHash) = ScriptSetup($noTrace);
920    
921    Perform standard tracing and debugging setup for scripts. The value returned is
922    the CGI object followed by a pre-built variable hash. At the end of the script,
923    the client should call L</ScriptFinish> to output the web page.
924    
925    This method calls L</ETracing> to configure tracing, which allows the tracing
926    to be configured via the emergency tracing form on the debugging control panel.
927    Tracing will then be turned on automatically for all programs that use the L</ETracing>
928    method, which includes every program that uses this method or L</StandardSetup>.
929    
930    =over 4
931    
932    =item noTrace (optional)
933    
934    If specified, tracing will be suppressed. This is useful if the script wants to set up
935    tracing manually.
936    
937    =item RETURN
938    
939    Returns a two-element list consisting of a CGI query object and a variable hash for
940    the output page.
941    
942    =back
943    
944    =cut
945    
946    sub ScriptSetup {
947        # Get the parameters.
948        my ($noTrace) = @_;
949        # Get the CGI query object.
950        my $cgi = CGI->new();
951        # Set up tracing if it's not suppressed.
952        ETracing($cgi) unless $noTrace;
953        # Create the variable hash.
954        my $varHash = { results => '' };
955        # Return the query object and variable hash.
956        return ($cgi, $varHash);
957    }
958    
959    =head3 ETracing
960    
961        ETracing($parameter);
962    
963    Set up emergency tracing. Emergency tracing is tracing that is turned
964    on automatically for any program that calls this method. The emergency
965    tracing parameters are stored in a a file identified by a tracing key.
966    If this method is called with a CGI object, then the tracing key is
967    taken from a cookie. If it is called with no parameters, then the tracing
968    key is taken from an environment variable. If it is called with a string,
969    the tracing key is that string.
970    
971    =over 4
972    
973    =item parameter
974    
975    A parameter from which the tracing key is computed. If it is a scalar,
976    that scalar is used as the tracing key. If it is a CGI object, the
977    tracing key is taken from the C<IP> cookie. If it is omitted, the
978    tracing key is taken from the C<TRACING> environment variable. If it
979    is a CGI object and emergency tracing is not on, the C<Trace> and
980    C<TF> parameters will be used to determine the type of tracing.
981    
982    =back
983    
984    =cut
985    
986    sub ETracing {
987        # Get the parameter.
988        my ($parameter) = @_;
989        # Check for CGI mode.
990        if (defined $parameter && ref $parameter eq 'CGI') {
991            $SavedCGI = $parameter;
992        } else {
993            $SavedCGI = undef;
994        }
995        # Default to no tracing except errors.
996        my ($tracing, $dest) = ("0", "WARN");
997        # Check for emergency tracing.
998        my $tkey = EmergencyKey($parameter);
999        my $emergencyFile = EmergencyFileName($tkey);
1000        if (-e $emergencyFile) {
1001            # We have the file. Read in the data.
1002            my @tracing = GetFile($emergencyFile);
1003            # Pull off the time limit.
1004            my $expire = shift @tracing;
1005            # Convert it to seconds.
1006            $expire *= 3600;
1007            # Check the file data.
1008            my $stat = stat($emergencyFile);
1009            my ($now) = gettimeofday;
1010            if ($now - $stat->mtime > $expire) {
1011                # Delete the expired file.
1012                unlink $emergencyFile;
1013            } else {
1014                # Emergency tracing is on. Pull off the destination and
1015                # the trace level;
1016                $dest = shift @tracing;
1017                my $level = shift @tracing;
1018                # Convert the destination to a real tracing destination.
1019                # temp directory.
1020                $dest = EmergencyTracingDest($tkey, $dest);
1021                # Insure Tracer is specified.
1022                my %moduleHash = map { $_ => 1 } @tracing;
1023                $moduleHash{Tracer} = 1;
1024                # Set the trace parameter.
1025                $tracing = join(" ", $level, sort keys %moduleHash);
1026            }
1027        } elsif (defined $SavedCGI) {
1028            # There's no emergency tracing, but we have a CGI object, so check
1029            # for tracing from the form parameters.
1030            if ($SavedCGI->param('Trace')) {
1031                # Here the user has requested tracing via a form.
1032                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1033                $tracing = $SavedCGI->param('Trace') . " Tracer";
1034            }
1035        }
1036        # Setup the tracing we've determined from all the stuff above.
1037        TSetup($tracing, $dest);
1038        # Check to see if we're a web script.
1039        if (defined $SavedCGI) {
1040            # Yes we are. Trace the form and environment data.
1041            TraceParms($SavedCGI);
1042            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1043            # emitted by the script in its raw form.
1044            if (T(Raw => 3)) {
1045                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1046            }
1047        }
1048    }
1049    
1050    =head3 EmergencyFileName
1051    
1052        my $fileName = Tracer::EmergencyFileName($tkey);
1053    
1054    Return the emergency tracing file name. This is the file that specifies
1055    the tracing information.
1056    
1057    =over 4
1058    
1059    =item tkey
1060    
1061    Tracing key for the current program.
1062    
1063    =item RETURN
1064    
1065    Returns the name of the file to contain the emergency tracing information.
1066    
1067    =back
1068    
1069    =cut
1070    
1071    sub EmergencyFileName {
1072        # Get the parameters.
1073        my ($tkey) = @_;
1074        # Compute the emergency tracing file name.
1075        return "$FIG_Config::temp/Emergency$tkey.txt";
1076    }
1077    
1078    =head3 EmergencyFileTarget
1079    
1080        my $fileName = Tracer::EmergencyFileTarget($tkey);
1081    
1082    Return the emergency tracing target file name. This is the file that receives
1083    the tracing output for file-based tracing.
1084    
1085    =over 4
1086    
1087    =item tkey
1088    
1089    Tracing key for the current program.
1090    
1091    =item RETURN
1092    
1093    Returns the name of the file to contain the trace output.
1094    
1095    =back
1096    
1097    =cut
1098    
1099    sub EmergencyFileTarget {
1100        # Get the parameters.
1101        my ($tkey) = @_;
1102        # Compute the emergency tracing file name.
1103        return "$FIG_Config::temp/trace$tkey.log";
1104    }
1105    
1106    =head3 EmergencyTracingDest
1107    
1108        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1109    
1110    This method converts an emergency tracing destination to a real
1111    tracing destination. The main difference is that if the
1112    destination is C<FILE> or C<APPEND>, we convert it to file
1113    output. If the destination is C<DUAL>, we convert it to file
1114    and standard output.
1115    
1116    =over 4
1117    
1118    =item tkey
1119    
1120    Tracing key for this environment.
1121    
1122    =item myDest
1123    
1124    Destination from the emergency tracing file.
1125    
1126    =item RETURN
1127    
1128    Returns a destination that can be passed into L</TSetup>.
1129    
1130    =back
1131    
1132    =cut
1133    
1134    sub EmergencyTracingDest {
1135        # Get the parameters.
1136        my ($tkey, $myDest) = @_;
1137        # Declare the return variable.
1138        my $retVal = $myDest;
1139        # Process according to the destination value.
1140        if ($myDest eq 'FILE') {
1141            $retVal = ">" . EmergencyFileTarget($tkey);
1142        } elsif ($myDest eq 'APPEND') {
1143            $retVal = ">>" . EmergencyFileTarget($tkey);
1144        } elsif ($myDest eq 'DUAL') {
1145            $retVal = "+>" . EmergencyFileTarget($tkey);
1146        } elsif ($myDest eq 'WARN') {
1147            $retVal = "WARN";
1148        }
1149        # Return the result.
1150        return $retVal;
1151    }
1152    
1153    =head3 Emergency
1154    
1155        Emergency($key, $hours, $dest, $level, @modules);
1156    
1157    Turn on emergency tracing. This method is normally invoked over the web from
1158    a debugging console, but it can also be called by the C<trace.pl> script.
1159    The caller specifies the duration of the emergency in hours, the desired tracing
1160    destination, the trace level, and a list of the trace modules to activate.
1161    For the length of the duration, when a program in an environment with the
1162    specified tracing key active invokes a Sprout CGI script, tracing will be
1163    turned on automatically. See L</TSetup> for more about tracing setup and
1164    L</ETracing> for more about emergency tracing.
1165    
1166    =over 4
1167    
1168    =item tkey
1169    
1170    The tracing key. This is used to identify the control file and the trace file.
1171    
1172    =item hours
1173    
1174    Number of hours to keep emergency tracing alive.
1175    
1176    =item dest
1177    
1178    Tracing destination. If no path information is specified for a file
1179    destination, it is put in the FIG temporary directory.
1180    
1181    =item level
1182    
1183    Tracing level. A higher level means more trace messages.
1184    
1185    =item modules
1186    
1187    A list of the tracing modules to activate.
1188    
1189    =back
1190    
1191    =cut
1192    
1193    sub Emergency {
1194        # Get the parameters.
1195        my ($tkey, $hours, $dest, $level, @modules) = @_;
1196        # Create the emergency file.
1197        my $specFile = EmergencyFileName($tkey);
1198        my $outHandle = Open(undef, ">$specFile");
1199        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1200    }
1201    
1202    =head3 EmergencyKey
1203    
1204        my $tkey = EmergencyKey($parameter);
1205    
1206    Return the Key to be used for emergency tracing. This could be an IP address,
1207     a session ID, or a user name, depending on the environment.
1208    
1209    =over 4
1210    
1211    =item parameter
1212    
1213    Parameter defining the method for finding the tracing key. If it is a scalar,
1214    then it is presumed to be the tracing key itself. If it is a CGI object, then
1215    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1216    taken from the C<TRACING> environment variable.
1217    
1218    =item RETURN
1219    
1220    Returns the key to be used for labels in emergency tracing.
1221    
1222    =back
1223    
1224    =cut
1225    
1226    sub EmergencyKey {
1227        # Get the parameters.
1228        my ($parameter) = @_;
1229        # Declare the return variable.
1230        my $retVal;
1231        # Determine the parameter type.
1232        if (! defined $parameter) {
1233            # Here we're supposed to check the environment. If that fails, we
1234            # get the effective login ID.
1235            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1236        } else {
1237            my $ptype = ref $parameter;
1238            if ($ptype eq 'CGI') {
1239                # Here we were invoked from a web page. Look for a cookie.
1240                $retVal = $parameter->cookie('IP');
1241            } elsif (! $ptype) {
1242                # Here the key was passed in.
1243                $retVal = $parameter;
1244            }
1245        }
1246        # If no luck finding a key, use the PID.
1247        if (! defined $retVal) {
1248            $retVal = $$;
1249        }
1250        # Return the result.
1251        return $retVal;
1252    }
1253    
1254    
1255    =head3 TraceParms
1256    
1257        Tracer::TraceParms($cgi);
1258    
1259    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1260    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1261    
1262    =over 4
1263    
1264    =item cgi
1265    
1266    CGI query object containing the parameters to trace.
1267    
1268    =back
1269    
1270    =cut
1271    
1272    sub TraceParms {
1273        # Get the parameters.
1274        my ($cgi) = @_;
1275        if (T(CGI => 2)) {
1276            # Here we trace the GET-style URL for the script.
1277            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1278        }
1279        if (T(CGI => 3)) {
1280            # Here we want to trace the parameter data.
1281            my @names = $cgi->param;
1282            for my $parmName (sort @names) {
1283                # Note we skip the Trace parameters, which are for our use only.
1284                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1285                    my @values = $cgi->param($parmName);
1286                    Trace("[CGI] $parmName = " . join(", ", @values));
1287                }
1288            }
1289            # Display the request method.
1290            my $method = $cgi->request_method();
1291            Trace("Method: $method");
1292        }
1293        if (T(CGI => 4)) {
1294            # Here we want the environment data too.
1295            for my $envName (sort keys %ENV) {
1296                Trace("[ENV] $envName = $ENV{$envName}");
1297            }
1298        }
1299    }
1300    
1301    =head3 TraceImages
1302    
1303        Tracer::TraceImages($htmlString);
1304    
1305    Trace information about all of an html document's images. The tracing
1306    will be for type "IMG" at level 3. The image's source string
1307    will be displayed. This is generally either the URL of the image or
1308    raw data for the image itself. If the source is too long, only the first 300
1309    characters will be shown at trace level 3. The entire source will be shown,
1310    however, at trace level 4. This method is not very smart, and might catch
1311    Javascript code, but it is still useful when debugging the arcane
1312    behavior of images in multiple browser environments.
1313    
1314    =over 4
1315    
1316    =item htmlString
1317    
1318    HTML text for an outgoing web page.
1319    
1320    =back
1321    
1322    =cut
1323    
1324    sub TraceImages {
1325        # Only proceed if we're at the proper trace level.
1326        if (T(IMG => 3)) {
1327            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1328            # into a variable called "$htmlString". This is because we expect html strings to be
1329            # long, and don't want to copy them any more than we have to.
1330            Trace(length($_[0]) . " characters in web page.");
1331            # Loop through the HTML, culling image tags.
1332            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1333                # Extract the source string and determine whether or not it's too long.
1334                my $srcString = $1;
1335                my $pos = pos($_[0]) - length($srcString);
1336                my $excess = length($srcString) - 300;
1337                # We'll put the display string in here.
1338                my $srcDisplay = $srcString;
1339                # If it's a data string, split it at the comma.
1340                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1341                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1342                # a long string, however, we only show the first 300 characters.
1343                if ($excess > 0 && ! T(IMG => 4)) {
1344                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1345                }
1346                # Output the trace message.
1347                Trace("Image tag at position $pos:\n$srcDisplay");
1348            }
1349        }
1350    }
1351    
1352    
1353    =head3 ScriptFinish (deprecated)
1354    
1355        ScriptFinish($webData, $varHash);
1356    
1357    Output a web page at the end of a script. Either the string to be output or the
1358    name of a template file can be specified. If the second parameter is omitted,
1359    it is assumed we have a string to be output; otherwise, it is assumed we have the
1360    name of a template file. The template should have the variable C<DebugData>
1361    specified in any form that invokes a standard script. If debugging mode is turned
1362    on, a form field will be put in that allows the user to enter tracing data.
1363    Trace messages will be placed immediately before the terminal C<BODY> tag in
1364    the output, formatted as a list.
1365    
1366    A typical standard script would loook like the following.
1367    
1368        BEGIN {
1369            # Print the HTML header.
1370            print "CONTENT-TYPE: text/html\n\n";
1371        }
1372        use Tracer;
1373        use CGI;
1374        use FIG;
1375        # ... more uses ...
1376    
1377        my ($cgi, $varHash) = ScriptSetup();
1378        eval {
1379            # ... get data from $cgi, put it in $varHash ...
1380        };
1381        if ($@) {
1382            Trace("Script Error: $@") if T(0);
1383        }
1384        ScriptFinish("Html/MyTemplate.html", $varHash);
1385    
1386    The idea here is that even if the script fails, you'll see trace messages and
1387    useful output.
1388    
1389    =over 4
1390    
1391    =item webData
1392    
1393    A string containing either the full web page to be written to the output or the
1394    name of a template file from which the page is to be constructed. If the name
1395    of a template file is specified, then the second parameter must be present;
1396    otherwise, it must be absent.
1397    
1398    =item varHash (optional)
1399    
1400    If specified, then a reference to a hash mapping variable names for a template
1401    to their values. The template file will be read into memory, and variable markers
1402    will be replaced by data in this hash reference.
1403    
1404    =back
1405    
1406    =cut
1407    
1408    sub ScriptFinish {
1409        # Get the parameters.
1410        my ($webData, $varHash) = @_;
1411        # Check for a template file situation.
1412        my $outputString;
1413        if (defined $varHash) {
1414            # Here we have a template file. We need to determine the template type.
1415            my $template;
1416            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1417                $template = "$FIG_Config::template_url/$webData";
1418            } else {
1419                $template = "<<$webData";
1420            }
1421            $outputString = PageBuilder::Build($template, $varHash, "Html");
1422        } else {
1423            # Here the user gave us a raw string.
1424            $outputString = $webData;
1425        }
1426        # Check for trace messages.
1427        if ($Destination ne "NONE" && $TraceLevel > 0) {
1428            # We have trace messages, so we want to put them at the end of the body. This
1429            # is either at the end of the whole string or at the beginning of the BODY
1430            # end-tag.
1431            my $pos = length $outputString;
1432            if ($outputString =~ m#</body>#gi) {
1433                $pos = (pos $outputString) - 7;
1434            }
1435            # If the trace messages were queued, we unroll them. Otherwise, we display the
1436            # destination.
1437            my $traceHtml;
1438            if ($Destination eq "QUEUE") {
1439                $traceHtml = QTrace('Html');
1440            } elsif ($Destination =~ /^>>(.+)$/) {
1441                # Here the tracing output it to a file. We code it as a hyperlink so the user
1442                # can copy the file name into the clipboard easily.
1443                my $actualDest = $1;
1444                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1445            } else {
1446                # Here we have one of the special destinations.
1447                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1448            }
1449            substr $outputString, $pos, 0, $traceHtml;
1450        }
1451        # Write the output string.
1452        print $outputString;
1453    }
1454    
1455    =head2 Command-Line Utility Methods
1456    
1457    =head3 SendSMS
1458    
1459        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1460    
1461    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1462    user name, password, and API ID for the relevant account in the hash reference variable
1463    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1464    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1465    is C<2561022>, then the FIG_Config file must contain
1466    
1467        $phone =  { user => 'BruceTheHumanPet',
1468                    password => 'silly',
1469                    api_id => '2561022' };
1470    
1471    The original purpose of this method was to insure Bruce would be notified immediately when the
1472    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1473    when you call this method.
1474    
1475    The message ID will be returned if successful, and C<undef> if an error occurs.
1476    
1477    =over 4
1478    
1479    =item phoneNumber
1480    
1481    Phone number to receive the message, in international format. A United States phone number
1482    would be prefixed by "1". A British phone number would be prefixed by "44".
1483    
1484    =item msg
1485    
1486    Message to send to the specified phone.
1487    
1488    =item RETURN
1489    
1490    Returns the message ID if successful, and C<undef> if the message could not be sent.
1491    
1492    =back
1493    
1494    =cut
1495    
1496    sub SendSMS {
1497        # Get the parameters.
1498        my ($phoneNumber, $msg) = @_;
1499        # Declare the return variable. If we do not change it, C<undef> will be returned.
1500        my $retVal;
1501        # Only proceed if we have phone support.
1502        if (! defined $FIG_Config::phone) {
1503            Trace("Phone support not present in FIG_Config.") if T(1);
1504        } else {
1505            # Get the phone data.
1506            my $parms = $FIG_Config::phone;
1507            # Get the Clickatell URL.
1508            my $url = "http://api.clickatell.com/http/";
1509            # Create the user agent.
1510            my $ua = LWP::UserAgent->new;
1511            # Request a Clickatell session.
1512            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1513                                         password => $parms->{password},
1514                                         api_id => $parms->{api_id},
1515                                         to => $phoneNumber,
1516                                         text => $msg});
1517            # Check for an error.
1518            if (! $resp->is_success) {
1519                Trace("Alert failed.") if T(1);
1520            } else {
1521                # Get the message ID.
1522                my $rstring = $resp->content;
1523                if ($rstring =~ /^ID:\s+(.*)$/) {
1524                    $retVal = $1;
1525                } else {
1526                    Trace("Phone attempt failed with $rstring") if T(1);
1527                }
1528            }
1529        }
1530        # Return the result.
1531        return $retVal;
1532    }
1533    
1534    =head3 StandardSetup
1535    
1536        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1537    
1538    This method performs standard command-line parsing and tracing setup. The return
1539    values are a hash of the command-line options and a list of the positional
1540    parameters. Tracing is automatically set up and the command-line options are
1541    validated.
1542    
1543    This is a complex method that does a lot of grunt work. The parameters can
1544    be more easily understood, however, once they are examined individually.
1545    
1546    The I<categories> parameter is the most obtuse. It is a reference to a list of
1547    special-purpose tracing categories. Most tracing categories are PERL package
1548    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1549    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1550    
1551        ["Sprout", "SproutLoad", "ERDB"]
1552    
1553    This would cause trace messages in the specified three packages to appear in
1554    the output. There are two special tracing categories that are automatically
1555    handled by this method. In other words, if you used L</TSetup> you would need
1556    to include these categories manually, but if you use this method they are turned
1557    on automatically.
1558    
1559    =over 4
1560    
1561    =item SQL
1562    
1563    Traces SQL commands and activity.
1564    
1565    =item Tracer
1566    
1567    Traces error messages and call stacks.
1568    
1569    =back
1570    
1571    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1572    The trace level is specified using the C<-trace> command-line option. For example,
1573    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1574    all tracing at level 3.
1575    
1576        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1577    
1578    Standard tracing is output to the standard output and echoed to the file
1579    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1580    process ID. You can also specify the C<user> parameter to put a user ID
1581    instead of a process ID in the trace file name. So, for example
1582    
1583    The default trace level is 2. To get all messages, specify a trace level of 4.
1584    For a genome-by-genome update, use 3.
1585    
1586        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1587    
1588    would send the trace output to C<traceBruce.log> in the temporary directory.
1589    
1590    The I<options> parameter is a reference to a hash containing the command-line
1591    options, their default values, and an explanation of what they mean. Command-line
1592    options may be in the form of switches or keywords. In the case of a switch, the
1593    option value is 1 if it is specified and 0 if it is not specified. In the case
1594    of a keyword, the value is separated from the option name by an equal sign. You
1595    can see this last in the command-line example above.
1596    
1597    You can specify a different default trace level by setting C<$options->{trace}>
1598    prior to calling this method.
1599    
1600    An example at this point would help. Consider, for example, the command-line utility
1601    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1602    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1603    the following code.
1604    
1605        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1606                            { safe => [0, "use database transactions"],
1607                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1608                              start => [' ', "start with this genome"],
1609                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1610                            "<command> <transactionDirectory> <IDfile>",
1611                          @ARGV);
1612    
1613    
1614    The call to C<ParseCommand> specifies the default values for the options and
1615    stores the actual options in a hash that is returned as C<$options>. The
1616    positional parameters are returned in C<@parameters>.
1617    
1618    The following is a sample command line for C<TransactFeatures>.
1619    
1620        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1621    
1622    Single and double hyphens are equivalent. So, you could also code the
1623    above command as
1624    
1625        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1626    
1627    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1628    parameters, and would find themselves in I<@parameters> after executing the
1629    above code fragment. The tracing would be set to level 2, and the categories
1630    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1631    and C<DocUtils> was included because it came in within the first parameter
1632    to this method. The I<$options> hash would be
1633    
1634        { trace => 2, sql => 0, safe => 0,
1635          noAlias => 1, start => ' ', tblFiles => 0 }
1636    
1637    Use of C<StandardSetup> in this way provides a simple way of performing
1638    standard tracing setup and command-line parsing. Note that the caller is
1639    not even aware of the command-line switches C<-trace> and C<-sql>, which
1640    are used by this method to control the tracing. If additional tracing features
1641    need to be added in the future, they can be processed by this method without
1642    upsetting the command-line utilities.
1643    
1644    If the C<background> option is specified on the command line, then the
1645    standard and error outputs will be directed to files in the temporary
1646    directory, using the same suffix as the trace file. So, if the command
1647    line specified
1648    
1649        -user=Bruce -background
1650    
1651    then the trace output would go to C<traceBruce.log>, the standard output to
1652    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1653    simplify starting a command in the background.
1654    
1655    The user name is also used as the tracing key for L</Emergency Tracing>.
1656    Specifying a value of C<E> for the trace level causes emergency tracing to
1657    be used instead of custom tracing. If the user name is not specified,
1658    the tracing key is taken from the C<Tracing> environment variable. If there
1659    is no value for that variable, the tracing key will be computed from the PID.
1660    
1661    Finally, if the special option C<-help> is specified, the option
1662    names will be traced at level 0 and the program will exit without processing.
1663    This provides a limited help capability. For example, if the user enters
1664    
1665        TransactFeatures -help
1666    
1667    he would see the following output.
1668    
1669        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1670            -trace    tracing level (default E)
1671            -sql      trace SQL commands
1672            -safe     use database transactions
1673            -noAlias  do not expect aliases in CHANGE transactions
1674            -start    start with this genome
1675            -tblFiles output TBL files containing the corrected IDs
1676    
1677    The caller has the option of modifying the tracing scheme by placing a value
1678    for C<trace> in the incoming options hash. The default value can be overridden,
1679    or the tracing to the standard output can be turned off by suffixing a minus
1680    sign to the trace level. So, for example,
1681    
1682        { trace => [0, "tracing level (default 0)"],
1683           ...
1684    
1685    would set the default trace level to 0 instead of E, while
1686    
1687        { trace => ["2-", "tracing level (default 2)"],
1688           ...
1689    
1690    would set the default to 2, but trace only to the log file, not to the
1691    standard output.
1692    
1693    The parameters to this method are as follows.
1694    
1695    =over 4
1696    
1697    =item categories
1698    
1699    Reference to a list of tracing category names. These should be names of
1700    packages whose internal workings will need to be debugged to get the
1701    command working.
1702    
1703    =item options
1704    
1705    Reference to a hash containing the legal options for the current command mapped
1706    to their default values and descriptions. The user can override the defaults
1707    by specifying the options as command-line switches prefixed by a hyphen.
1708    Tracing-related options may be added to this hash. If the C<-h> option is
1709    specified on the command line, the option descriptions will be used to
1710    explain the options. To turn off tracing to the standard output, add a
1711    minus sign to the value for C<trace> (see above).
1712    
1713    =item parmHelp
1714    
1715    A string that vaguely describes the positional parameters. This is used
1716    if the user specifies the C<-h> option.
1717    
1718    =item argv
1719    
1720    List of command line parameters, including the option switches, which must
1721    precede the positional parameters and be prefixed by a hyphen.
1722    
1723    =item RETURN
1724    
1725    Returns a list. The first element of the list is the reference to a hash that
1726    maps the command-line option switches to their values. These will either be the
1727    default values or overrides specified on the command line. The remaining
1728    elements of the list are the position parameters, in order.
1729    
1730    =back
1731    
1732    =cut
1733    
1734    sub StandardSetup {
1735        # Get the parameters.
1736        my ($categories, $options, $parmHelp, @argv) = @_;
1737        # Get the default tracing key.
1738        my $tkey = EmergencyKey();
1739        # Add the tracing options.
1740        if (! exists $options->{trace}) {
1741            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1742        }
1743        $options->{sql} = [0, "turn on SQL tracing"];
1744        $options->{help} = [0, "display command-line options"];
1745        $options->{user} = [$tkey, "tracing key"];
1746        $options->{background} = [0, "spool standard and error output"];
1747        # Create a parsing hash from the options hash. The parsing hash
1748        # contains the default values rather than the default value
1749        # and the description. While we're at it, we'll memorize the
1750        # length of the longest option name.
1751      my $longestName = 0;      my $longestName = 0;
1752      my %parseOptions = ();      my %parseOptions = ();
1753      for my $key (keys %{$options}) {      for my $key (keys %{$options}) {
# Line 439  Line 1766 
1766          my $errFileName = "$FIG_Config::temp/err$suffix.log";          my $errFileName = "$FIG_Config::temp/err$suffix.log";
1767          open STDOUT, ">$outFileName";          open STDOUT, ">$outFileName";
1768          open STDERR, ">$errFileName";          open STDERR, ">$errFileName";
1769            # Check for phone support. If we have phone support and a phone number,
1770            # we want to turn it on.
1771            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1772                $retOptions->{phone} = $ENV{PHONE};
1773      }      }
1774      # Now we want to set up tracing. First, we need to know if SQL is to      }
1775      # be traced.      # Now we want to set up tracing. First, we need to know if the user
1776        # wants emergency tracing.
1777        if ($retOptions->{trace} eq 'E') {
1778            ETracing($retOptions->{user});
1779        } else {
1780            # Here the tracing is controlled from the command line.
1781      my @cats = @{$categories};      my @cats = @{$categories};
1782      if ($retOptions->{sql}) {      if ($retOptions->{sql}) {
1783          push @cats, "SQL";          push @cats, "SQL";
1784      }      }
1785      # Add the default categories.      # Add the default categories.
1786      push @cats, "Tracer", "FIG";          push @cats, "Tracer";
1787      # Next, we create the category string by joining the categories.      # Next, we create the category string by joining the categories.
1788      my $cats = join(" ", @cats);      my $cats = join(" ", @cats);
1789      # Check to determine whether or not the caller wants to turn off tracing      # Check to determine whether or not the caller wants to turn off tracing
# Line 472  Line 1808 
1808          # Close the test file.          # Close the test file.
1809          close TESTTRACE;          close TESTTRACE;
1810      } else {      } else {
1811          # Here we can't trace to a file. We trace to the standard output if it's              # Here we can't trace to a file. Complain about this.
1812                warn "Could not open trace file $traceFileName: $!\n";
1813                # We trace to the standard output if it's
1814          # okay, and the error log otherwise.          # okay, and the error log otherwise.
1815          if ($textOKFlag) {          if ($textOKFlag) {
1816              $traceMode = "TEXT";              $traceMode = "TEXT";
# Line 482  Line 1820 
1820      }      }
1821      # Now set up the tracing.      # Now set up the tracing.
1822      TSetup("$traceLevel $cats", $traceMode);      TSetup("$traceLevel $cats", $traceMode);
1823      # Check for the "h" option. If it is specified, dump the command-line      }
1824        # Check for the "help" option. If it is specified, dump the command-line
1825      # options and exit the program.      # options and exit the program.
1826      if ($retOptions->{h}) {      if ($retOptions->{help}) {
1827          $0 =~ m#[/\\](\w+)(\.pl)?$#i;          $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1828          Trace("$1 [options] $parmHelp") if T(0);          print "$1 [options] $parmHelp\n";
1829          for my $key (sort keys %{$options}) {          for my $key (sort keys %{$options}) {
1830              my $name = Pad($key, $longestName, 0, ' ');              my $name = Pad($key, $longestName, 0, ' ');
1831              my $desc = $options->{$key}->[1];              my $desc = $options->{$key}->[1];
1832              if ($options->{$key}->[0]) {              if ($options->{$key}->[0]) {
1833                  $desc .= " (default " . $options->{$key}->[0] . ")";                  $desc .= " (default " . $options->{$key}->[0] . ")";
1834              }              }
1835              Trace("  $name $desc") if T(0);              print "  $name $desc\n";
1836          }          }
1837          exit(0);          exit(0);
1838      }      }
1839      # Return the parsed parameters.      # Trace the options, if applicable.
1840      return ($retOptions, @retParameters);      if (T(3)) {
1841  }          my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1842            Trace("Selected options: " . join(", ", sort @parms) . ".");
 =head3 Setups  
   
 C<< my $count = Tracer::Setups(); >>  
   
 Return the number of times L</TSetup> has been called.  
   
 This method allows for the creation of conditional tracing setups where, for example, we  
 may want to set up tracing if nobody else has done it before us.  
   
 =cut  
   
 sub Setups {  
     return $SetupCount;  
 }  
   
 =head3 Open  
   
 C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  
   
 Open a file.  
   
 The I<$fileSpec> is essentially the second argument of the PERL C<open>  
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
   
     Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  
   
 would open for output appended to the specified file, and  
   
     Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  
   
 would open a pipe that sorts the records written and removes duplicates. Note  
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
   
     my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  
   
 The I<$message> parameter is used if the open fails. If it is set to C<0>, then  
 the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a  
 failed open will throw an exception and the third parameter will be used to construct  
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
   
     Could not open "/usr/spool/news/twitlog"  
   
 Note that the mode characters are automatically cleaned from the file name.  
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
   
     Could not open "/usr/spool/news/twitlog": file not found.  
   
 In some versions of PERL the only error message we get is a number, which  
 corresponds to the C++ C<errno> value.  
   
     Could not open "/usr/spool/news/twitlog": 6.  
   
 =over 4  
   
 =item fileHandle  
   
 File handle. If this parameter is C<undef>, a file handle will be generated  
 and returned as the value of this method.  
   
 =item fileSpec  
   
 File name and mode, as per the PERL C<open> function.  
   
 =item message (optional)  
   
 Error message to use if the open fails. If omitted, a standard error message  
 will be generated. In either case, the error information from the file system  
 is appended to the message. To specify a conditional open that does not throw  
 an error if it fails, use C<0>.  
   
 =item RETURN  
   
 Returns the name of the file handle assigned to the file, or C<undef> if the  
 open failed.  
   
 =back  
   
 =cut  
   
 sub Open {  
     # Get the parameters.  
     my ($fileHandle, $fileSpec, $message) = @_;  
     # Attempt to open the file.  
     my $rv = open $fileHandle, $fileSpec;  
     # If the open failed, generate an error message.  
     if (! $rv) {  
         # Save the system error message.  
         my $sysMessage = $!;  
         # See if we need a default message.  
         if (!$message) {  
             # Clean any obvious mode characters and leading spaces from the  
             # filename.  
             my ($fileName) = FindNamePart($fileSpec);  
             $message = "Could not open \"$fileName\"";  
         }  
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
     }  
     # Return the file handle.  
     return $fileHandle;  
 }  
   
 =head3 FindNamePart  
   
 C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>  
   
 Extract the portion of a file specification that contains the file name.  
   
 A file specification is the string passed to an C<open> call. It specifies the file  
 mode and name. In a truly complex situation, it can specify a pipe sequence. This  
 method assumes that the file name is whatever follows the first angle bracket  
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
   
     >>/usr/fig/myfile.txt  
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
   
 If the method cannot find a file name using its normal methods, it will return the  
 whole incoming string.  
   
 =over 4  
   
 =item fileSpec  
   
 File specification string from which the file name is to be extracted.  
   
 =item RETURN  
   
 Returns a three-element list. The first element contains the file name portion of  
 the specified string, or the whole string if a file name cannot be found via normal  
 methods. The second element contains the start position of the file name portion and  
 the third element contains the length.  
   
 =back  
   
 =cut  
 #: Return Type $;  
 sub FindNamePart {  
     # Get the parameters.  
     my ($fileSpec) = @_;  
     # Default to the whole input string.  
     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);  
     # Parse out the file name if we can.  
     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {  
         $retVal = $2;  
         $len = length $retVal;  
         $pos = (length $fileSpec) - (length $3) - $len;  
     }  
     # Return the result.  
     return ($retVal, $pos, $len);  
 }  
   
 =head3 OpenDir  
   
 C<< my @files = OpenDir($dirName, $filtered, $flag); >>  
   
 Open a directory and return all the file names. This function essentially performs  
 the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  
 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  
 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be  
 filtered out of the return list. If the directory does not open and I<$flag> is not  
 set, an exception is thrown. So, for example,  
   
     my @files = OpenDir("/Volumes/fig/contigs", 1);  
   
 is effectively the same as  
   
     opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
   
 Similarly, the following code  
   
     my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  
   
 Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  
 automatically returns an empty list if the directory fails to open.  
   
 =over 4  
   
 =item dirName  
   
 Name of the directory to open.  
   
 =item filtered  
   
 TRUE if files whose names begin with a period (C<.>) should be automatically removed  
 from the list, else FALSE.  
   
 =item flag  
   
 TRUE if a failure to open is okay, else FALSE  
   
 =back  
   
 =cut  
 #: Return Type @;  
 sub OpenDir {  
     # Get the parameters.  
     my ($dirName, $filtered, $flag) = @_;  
     # Declare the return variable.  
     my @retVal = ();  
     # Open the directory.  
     if (opendir(my $dirHandle, $dirName)) {  
         # The directory opened successfully. Get the appropriate list according to the  
         # strictures of the filter parameter.  
         if ($filtered) {  
             @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;  
         } else {  
             @retVal = readdir $dirHandle;  
         }  
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
     }  
     # Return the result.  
     return @retVal;  
 }  
   
 =head3 SetLevel  
   
 C<< Tracer::SetLevel($newLevel); >>  
   
 Modify the trace level. A higher trace level will cause more messages to appear.  
   
 =over 4  
   
 =item newLevel  
   
 Proposed new trace level.  
   
 =back  
   
 =cut  
   
 sub SetLevel {  
     $TraceLevel = $_[0];  
 }  
   
 =head3 Now  
   
 C<< my $string = Tracer::Now(); >>  
   
 Return a displayable time stamp containing the local time.  
   
 =cut  
   
 sub Now {  
     my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);  
     my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .  
                  _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);  
     return $retVal;  
 }  
   
 # Pad a number to 2 digits.  
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
1843  }  }
1844        # Return the parsed parameters.
1845  =head3 LogErrors      return ($retOptions, @retParameters);
   
 C<< Tracer::LogErrors($fileName); >>  
   
 Route the standard error output to a log file.  
   
 =over 4  
   
 =item fileName  
   
 Name of the file to receive the error output.  
   
 =back  
   
 =cut  
   
 sub LogErrors {  
     # Get the file name.  
     my ($fileName) = @_;  
     # Open the file as the standard error output.  
     open STDERR, '>', $fileName;  
1846  }  }
1847    
1848  =head3 ReadOptions  =head3 ReadOptions
1849    
1850  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1851    
1852  Read a set of options from a file. Each option is encoded in a line of text that has the  Read a set of options from a file. Each option is encoded in a line of text that has the
1853  format  format
# Line 853  Line 1908 
1908    
1909  =head3 GetOptions  =head3 GetOptions
1910    
1911  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1912    
1913  Merge a specified set of options into a table of defaults. This method takes two hash references  Merge a specified set of options into a table of defaults. This method takes two hash references
1914  as input and uses the data from the second to update the first. If the second does not exist,  as input and uses the data from the second to update the first. If the second does not exist,
# Line 862  Line 1917 
1917    
1918  Consider the following example.  Consider the following example.
1919    
1920  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1921    
1922  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1923  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 870  Line 1925 
1925  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1926  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1927    
1928  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1929    
1930  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1931    
# Line 914  Line 1969 
1969    
1970  =head3 MergeOptions  =head3 MergeOptions
1971    
1972  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
1973    
1974  Merge default values into a hash table. This method looks at the key-value pairs in the  Merge default values into a hash table. This method looks at the key-value pairs in the
1975  second (default) hash, and if a matching key is not found in the first hash, the default  second (default) hash, and if a matching key is not found in the first hash, the default
# Line 946  Line 2001 
2001      }      }
2002  }  }
2003    
2004  =head3 Trace  =head3 ParseCommand
2005    
2006        my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2007    
2008    Parse a command line consisting of a list of parameters. The initial parameters may be option
2009    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2010    off and merged into a table of default options. The remainder of the command line is
2011    returned as a list of positional arguments. For example, consider the following invocation.
2012    
2013        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2014    
2015    In this case, the list @words will be treated as a command line and there are two options available,
2016    B<errors> and B<logFile>. If @words has the following format
2017    
2018        -logFile=error.log apple orange rutabaga
2019    
2020    then at the end of the invocation, C<$options> will be
2021    
2022        { errors => 0, logFile => 'error.log' }
2023    
2024    and C<@arguments> will contain
2025    
2026        apple orange rutabaga
2027    
2028    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2029    support for quote characters. Options can be specified with single or double hyphens.
2030    
2031    =over 4
2032    
2033    =item optionTable
2034    
2035    Table of default options.
2036    
2037    =item inputList
2038    
2039    List of words on the command line.
2040    
2041    =item RETURN
2042    
2043    Returns a reference to the option table and a list of the positional arguments.
2044    
2045    =back
2046    
2047    =cut
2048    
2049    sub ParseCommand {
2050        # Get the parameters.
2051        my ($optionTable, @inputList) = @_;
2052        # Process any options in the input list.
2053        my %overrides = ();
2054        while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2055            # Get the current option.
2056            my $arg = shift @inputList;
2057            # Pull out the option name.
2058            $arg =~ /^--?([^=]*)/g;
2059            my $name = $1;
2060            # Check for an option value.
2061            if ($arg =~ /\G=(.*)$/g) {
2062                # Here we have a value for the option.
2063                $overrides{$name} = UnEscape($1);
2064            } else {
2065                # Here there is no value, so we use 1.
2066                $overrides{$name} = 1;
2067            }
2068        }
2069        # Merge the options into the defaults.
2070        GetOptions($optionTable, \%overrides);
2071        # Translate the remaining parameters.
2072        my @retVal = ();
2073        for my $inputParm (@inputList) {
2074            push @retVal, UnEscape($inputParm);
2075        }
2076        # Return the results.
2077        return ($optionTable, @retVal);
2078    }
2079    
2080    
2081    =head2 File Utility Methods
2082    
2083    =head3 GetFile
2084    
2085        my @fileContents = Tracer::GetFile($fileName);
2086    
2087        or
2088    
2089        my $fileContents = Tracer::GetFile($fileName);
2090    
2091    Return the entire contents of a file. In list context, line-ends are removed and
2092    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2093    
2094    =over 4
2095    
2096    =item fileName
2097    
2098    Name of the file to read.
2099    
2100    =item RETURN
2101    
2102    In a list context, returns the entire file as a list with the line terminators removed.
2103    In a scalar context, returns the entire file as a string. If an error occurs opening
2104    the file, an empty list will be returned.
2105    
2106    =back
2107    
2108    =cut
2109    
2110    sub GetFile {
2111        # Get the parameters.
2112        my ($fileName) = @_;
2113        # Declare the return variable.
2114        my @retVal = ();
2115        # Open the file for input.
2116        my $handle = Open(undef, "<$fileName");
2117        # Read the whole file into the return variable, stripping off any terminator
2118        # characters.
2119        my $lineCount = 0;
2120        while (my $line = <$handle>) {
2121            $lineCount++;
2122            $line = Strip($line);
2123            push @retVal, $line;
2124        }
2125        # Close it.
2126        close $handle;
2127        my $actualLines = @retVal;
2128        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2129        # Return the file's contents in the desired format.
2130        if (wantarray) {
2131            return @retVal;
2132        } else {
2133            return join "\n", @retVal;
2134        }
2135    }
2136    
2137    =head3 PutFile
2138    
2139        Tracer::PutFile($fileName, \@lines);
2140    
2141    Write out a file from a list of lines of text.
2142    
2143    =over 4
2144    
2145    =item fileName
2146    
2147    Name of the output file.
2148    
2149    =item lines
2150    
2151    Reference to a list of text lines. The lines will be written to the file in order, with trailing
2152    new-line characters. Alternatively, may be a string, in which case the string will be written without
2153    modification.
2154    
2155    =back
2156    
2157    =cut
2158    
2159    sub PutFile {
2160        # Get the parameters.
2161        my ($fileName, $lines) = @_;
2162        # Open the output file.
2163        my $handle = Open(undef, ">$fileName");
2164        # Count the lines written.
2165        if (ref $lines ne 'ARRAY') {
2166            # Here we have a scalar, so we write it raw.
2167            print $handle $lines;
2168            Trace("Scalar put to file $fileName.") if T(File => 3);
2169        } else {
2170            # Write the lines one at a time.
2171            my $count = 0;
2172            for my $line (@{$lines}) {
2173                print $handle "$line\n";
2174                $count++;
2175            }
2176            Trace("$count lines put to file $fileName.") if T(File => 3);
2177        }
2178        # Close the output file.
2179        close $handle;
2180    }
2181    
2182    =head3 ParseRecord
2183    
2184        my @fields = Tracer::ParseRecord($line);
2185    
2186    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2187    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2188    These will automatically be converted.
2189    
2190    =over 4
2191    
2192    =item line
2193    
2194    Line of data containing the tab-delimited fields.
2195    
2196    =item RETURN
2197    
2198    Returns a list of the fields found in the data line.
2199    
2200    =back
2201    
2202    =cut
2203    
2204    sub ParseRecord {
2205        # Get the parameter.
2206        my ($line) = @_;
2207        # Remove the trailing new-line, if any.
2208        chomp $line;
2209        # Split the line read into pieces using the tab character.
2210        my @retVal = split /\t/, $line;
2211        # Trim and fix the escapes in each piece.
2212        for my $value (@retVal) {
2213            # Trim leading whitespace.
2214            $value =~ s/^\s+//;
2215            # Trim trailing whitespace.
2216            $value =~ s/\s+$//;
2217            # Delete the carriage returns.
2218            $value =~ s/\r//g;
2219            # Convert the escapes into their real values.
2220            $value =~ s/\\t/"\t"/ge;
2221            $value =~ s/\\n/"\n"/ge;
2222        }
2223        # Return the result.
2224        return @retVal;
2225    }
2226    
2227    =head3 Merge
2228    
2229        my @mergedList = Tracer::Merge(@inputList);
2230    
2231    Sort a list of strings and remove duplicates.
2232    
2233    =over 4
2234    
2235    =item inputList
2236    
2237    List of scalars to sort and merge.
2238    
2239    =item RETURN
2240    
2241    Returns a list containing the same elements sorted in ascending order with duplicates
2242    removed.
2243    
2244    =back
2245    
2246    =cut
2247    
2248    sub Merge {
2249        # Get the input list in sort order.
2250        my @inputList = sort @_;
2251        # Only proceed if the list has at least two elements.
2252        if (@inputList > 1) {
2253            # Now we want to move through the list splicing out duplicates.
2254            my $i = 0;
2255            while ($i < @inputList) {
2256                # Get the current entry.
2257                my $thisEntry = $inputList[$i];
2258                # Find out how many elements duplicate the current entry.
2259                my $j = $i + 1;
2260                my $dup1 = $i + 1;
2261                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2262                # If the number is nonzero, splice out the duplicates found.
2263                if ($j > $dup1) {
2264                    splice @inputList, $dup1, $j - $dup1;
2265                }
2266                # Now the element at position $dup1 is different from the element before it
2267                # at position $i. We push $i forward one position and start again.
2268                $i++;
2269            }
2270        }
2271        # Return the merged list.
2272        return @inputList;
2273    }
2274    
2275    =head3 Open
2276    
2277  C<< Trace($message); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2278    
2279  Write a trace message to the target location specified in L</TSetup>. If there has not been  Open a file.
 any prior call to B<TSetup>.  
2280    
2281  =over 4  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2282    function. The mode is specified using Unix-like shell information. So, for
2283    example,
2284    
2285  =item message      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2286    
2287  Message to write.  would open for output appended to the specified file, and
2288    
2289  =back      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2290    
2291  =cut  would open a pipe that sorts the records written and removes duplicates. Note
2292    the use of file handle syntax in the Open call. To use anonymous file handles,
2293    code as follows.
2294    
2295  sub Trace {      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
     # Get the parameters.  
     my ($message) = @_;  
     # Get the timestamp.  
     my $timeStamp = Now();  
     # Format the message. Note we strip off any line terminators at the end.  
     my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);  
     # Process according to the destination.  
     if ($Destination eq "TEXT") {  
         # Write the message to the standard output.  
         print "$formatted\n";  
     } elsif ($Destination eq "ERROR") {  
         # Write the message to the error output.  
         print STDERR "$formatted\n";  
     } elsif ($Destination eq "QUEUE") {  
         # Push the message into the queue.  
         push @Queue, "$formatted";  
     } elsif ($Destination eq "HTML") {  
         # Convert the message to HTML and write it to the standard output.  
         my $escapedMessage = CGI::escapeHTML($message);  
         print "<p>$formatted</p>\n";  
     } elsif ($Destination eq "WARN") {  
        # Emit the message as a warning.  
        warn $message;  
     } elsif ($Destination =~ m/^>>/) {  
         # Write the trace message to an output file.  
         (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";  
         print TRACING "$formatted\n";  
         close TRACING;  
         # If the Tee flag is on, echo it to the standard output.  
         if ($TeeFlag) {  
             print "$formatted\n";  
         }  
     }  
 }  
2296    
2297  =head3 T  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2298    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2299    failed open will throw an exception and the third parameter will be used to construct
2300    an error message. If the parameter is omitted, a standard message is constructed
2301    using the file spec.
2302    
2303  C<< my $switch = T($category, $traceLevel); >>      Could not open "/usr/spool/news/twitlog"
2304    
2305      or  Note that the mode characters are automatically cleaned from the file name.
2306    The actual error message from the file system will be captured and appended to the
2307    message in any case.
2308    
2309  C<< my $switch = T($traceLevel); >>      Could not open "/usr/spool/news/twitlog": file not found.
2310    
2311  Return TRUE if the trace level is at or above a specified value and the specified category  In some versions of PERL the only error message we get is a number, which
2312  is active, else FALSE. If no category is specified, the caller's package name is used.  corresponds to the C++ C<errno> value.
2313    
2314        Could not open "/usr/spool/news/twitlog": 6.
2315    
2316  =over 4  =over 4
2317    
2318  =item category  =item fileHandle
2319    
2320  Category to which the message belongs. If not specified, the caller's package name is  File handle. If this parameter is C<undef>, a file handle will be generated
2321  used.  and returned as the value of this method.
2322    
2323  =item traceLevel  =item fileSpec
2324    
2325  Relevant tracing level.  File name and mode, as per the PERL C<open> function.
2326    
2327    =item message (optional)
2328    
2329    Error message to use if the open fails. If omitted, a standard error message
2330    will be generated. In either case, the error information from the file system
2331    is appended to the message. To specify a conditional open that does not throw
2332    an error if it fails, use C<0>.
2333    
2334  =item RETURN  =item RETURN
2335    
2336  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  Returns the name of the file handle assigned to the file, or C<undef> if the
2337    open failed.
2338    
2339  =back  =back
2340    
2341  =cut  =cut
2342    
2343  sub T {  sub Open {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
2344          # Get the parameters.          # Get the parameters.
2345          my ($category, $traceLevel) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2346          if (!defined $traceLevel) {      # Attempt to open the file.
2347              # Here we have no category, so we need to get the calling package.      my $rv = open $fileHandle, $fileSpec;
2348              # The calling package is normally the first parameter. If it is      # If the open failed, generate an error message.
2349              # omitted, the first parameter will be the tracelevel. So, the      if (! $rv) {
2350              # first thing we do is shift the so-called category into the          # Save the system error message.
2351              # $traceLevel variable where it belongs.          my $sysMessage = $!;
2352              $traceLevel = $category;          # See if we need a default message.
2353              my ($package, $fileName, $line) = caller;          if (!$message) {
2354              # If there is no calling package, we default to "main".              # Clean any obvious mode characters and leading spaces from the
2355              if (!$package) {              # filename.
2356                  $category = "main";              my ($fileName) = FindNamePart($fileSpec);
2357              } else {              $message = "Could not open \"$fileName\"";
                 $category = $package;  
             }  
         }  
         # Save the category name.  
         $LastCategory = $category;  
         # Convert it to lower case before we hash it.  
         $category = lc $category;  
         # Use the category and tracelevel to compute the result.  
         if (ref $traceLevel) {  
             Confess("Bad trace level.");  
         } elsif (ref $TraceLevel) {  
             Confess("Bad trace config.");  
2358          }          }
2359          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));          # Terminate with an error using the supplied message and the
2360            # error message from the file system.
2361            Confess("$message: $!");
2362      }      }
2363      # Return the computed result.      # Return the file handle.
2364      return $retVal;      return $fileHandle;
2365  }  }
2366    
2367  =head3 ParseCommand  =head3 FindNamePart
   
 C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  
   
 Parse a command line consisting of a list of parameters. The initial parameters may be option  
 specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  
 off and merged into a table of default options. The remainder of the command line is  
 returned as a list of positional arguments. For example, consider the following invocation.  
   
 C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  
   
 In this case, the list @words will be treated as a command line. There are two options available,  
 B<errors> and B<logFile>. If @words has the following format  
   
 C<< -logFile=error.log apple orange rutabaga >>  
2368    
2369  then at the end of the invocation, C<$options> will be      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2370    
2371  C<< { errors => 0, logFile => 'error.log' } >>  Extract the portion of a file specification that contains the file name.
2372    
2373  and C<@arguments> will contain  A file specification is the string passed to an C<open> call. It specifies the file
2374    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2375    method assumes that the file name is whatever follows the first angle bracket
2376    sequence.  So, for example, in the following strings the file name is
2377    C</usr/fig/myfile.txt>.
2378    
2379  C<< apple orange rutabaga >>      >>/usr/fig/myfile.txt
2380        </usr/fig/myfile.txt
2381        | sort -u > /usr/fig/myfile.txt
2382    
2383  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  If the method cannot find a file name using its normal methods, it will return the
2384  support for quote characters.  whole incoming string.
2385    
2386  =over 4  =over 4
2387    
2388  =item optionTable  =item fileSpec
   
 Table of default options.  
   
 =item inputList  
2389    
2390  List of words on the command line.  File specification string from which the file name is to be extracted.
2391    
2392  =item RETURN  =item RETURN
2393    
2394  Returns a reference to the option table and a list of the positional arguments.  Returns a three-element list. The first element contains the file name portion of
2395    the specified string, or the whole string if a file name cannot be found via normal
2396    methods. The second element contains the start position of the file name portion and
2397    the third element contains the length.
2398    
2399  =back  =back
2400    
2401  =cut  =cut
2402    #: Return Type $;
2403  sub ParseCommand {  sub FindNamePart {
2404      # Get the parameters.      # Get the parameters.
2405      my ($optionTable, @inputList) = @_;      my ($fileSpec) = @_;
2406      # Process any options in the input list.      # Default to the whole input string.
2407      my %overrides = ();      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2408      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      # Parse out the file name if we can.
2409          # Get the current option.      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2410          my $arg = shift @inputList;          $retVal = $2;
2411          # Pull out the option name.          $len = length $retVal;
2412          $arg =~ /^-([^=]*)/g;          $pos = (length $fileSpec) - (length $3) - $len;
         my $name = $1;  
         # Check for an option value.  
         if ($arg =~ /\G=(.*)$/g) {  
             # Here we have a value for the option.  
             $overrides{$name} = UnEscape($1);  
         } else {  
             # Here there is no value, so we use 1.  
             $overrides{$name} = 1;  
         }  
     }  
     # Merge the options into the defaults.  
     GetOptions($optionTable, \%overrides);  
     # Translate the remaining parameters.  
     my @retVal = ();  
     for my $inputParm (@inputList) {  
         push @retVal, UnEscape($inputParm);  
2413      }      }
2414      # Return the results.      # Return the result.
2415      return ($optionTable, @retVal);      return ($retVal, $pos, $len);
2416  }  }
2417    
2418  =head3 Escape  =head3 OpenDir
2419    
2420  C<< my $codedString = Tracer::Escape($realString); >>      my @files = OpenDir($dirName, $filtered, $flag);
2421    
2422  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  Open a directory and return all the file names. This function essentially performs
2423  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2424  result is to reverse the effect of L</UnEscape>.  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2425    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2426    filtered out of the return list. If the directory does not open and I<$flag> is not
2427    set, an exception is thrown. So, for example,
2428    
2429        my @files = OpenDir("/Volumes/fig/contigs", 1);
2430    
2431    is effectively the same as
2432    
2433        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2434        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2435    
2436    Similarly, the following code
2437    
2438        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2439    
2440    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2441    automatically returns an empty list if the directory fails to open.
2442    
2443  =over 4  =over 4
2444    
2445  =item realString  =item dirName
2446    
2447  String to escape.  Name of the directory to open.
2448    
2449  =item RETURN  =item filtered
2450    
2451  Escaped equivalent of the real string.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2452    from the list, else FALSE.
2453    
2454    =item flag
2455    
2456    TRUE if a failure to open is okay, else FALSE
2457    
2458  =back  =back
2459    
2460  =cut  =cut
2461    #: Return Type @;
2462  sub Escape {  sub OpenDir {
2463      # Get the parameter.      # Get the parameters.
2464      my ($realString) = @_;      my ($dirName, $filtered, $flag) = @_;
2465      # Initialize the return variable.      # Declare the return variable.
2466      my $retVal = "";      my @retVal = ();
2467      # Loop through the parameter string, looking for sequences to escape.      # Open the directory.
2468      while (length $realString > 0) {      if (opendir(my $dirHandle, $dirName)) {
2469          # Look for the first sequence to escape.          # The directory opened successfully. Get the appropriate list according to the
2470          if ($realString =~ /^(.*?)([\n\t\r\\])/) {          # strictures of the filter parameter.
2471              # Here we found it. The text preceding the sequence is in $1. The sequence          if ($filtered) {
2472              # itself is in $2. First, move the clear text to the return variable.              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
             $retVal .= $1;  
             # Strip the processed section off the real string.  
             $realString = substr $realString, (length $2) + (length $1);  
             # Get the matched character.  
             my $char = $2;  
             # If we have a CR, we are done.  
             if ($char ne "\r") {  
                 # It's not a CR, so encode the escape sequence.  
                 $char =~ tr/\t\n/tn/;  
                 $retVal .= "\\" . $char;  
             }  
2473          } else {          } else {
2474              # Here there are no more escape sequences. The rest of the string is              @retVal = readdir $dirHandle;
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
2475          }          }
2476        } elsif (! $flag) {
2477            # Here the directory would not open and it's considered an error.
2478            Confess("Could not open directory $dirName.");
2479      }      }
2480      # Return the result.      # Return the result.
2481      return $retVal;      return @retVal;
2482  }  }
2483    
 =head3 UnEscape  
2484    
2485  C<< my $realString = Tracer::UnEscape($codedString); >>  =head3 Insure
2486    
2487  Replace escape sequences with their actual equivalents. C<\t> will be replaced by      Insure($dirName, $chmod);
2488  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
2489  be deleted.  Insure a directory is present.
2490    
2491  =over 4  =over 4
2492    
2493  =item codedString  =item dirName
2494    
2495  String to un-escape.  Name of the directory to check. If it does not exist, it will be created.
2496    
2497  =item RETURN  =item chmod (optional)
2498    
2499  Returns a copy of the original string with the escape sequences converted to their actual  Security privileges to be given to the directory if it is created.
 values.  
2500    
2501  =back  =back
2502    
2503  =cut  =cut
2504    
2505  sub UnEscape {  sub Insure {
2506      # Get the parameter.      my ($dirName, $chmod) = @_;
2507      my ($codedString) = @_;      if (! -d $dirName) {
2508      # Initialize the return variable.          Trace("Creating $dirName directory.") if T(2);
2509      my $retVal = "";          eval {
2510      # Only proceed if the incoming string is nonempty.              mkpath $dirName;
2511      if (defined $codedString) {              # If we have permissions specified, set them here.
2512          # Loop through the parameter string, looking for escape sequences. We can't do              if (defined($chmod)) {
2513          # translating because it causes problems with the escaped slash. ("\\t" becomes                  chmod $chmod, $dirName;
         # "\<tab>" no matter what we do.)  
         while (length $codedString > 0) {  
             # Look for the first escape sequence.  
             if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {  
                 # Here we found it. The text preceding the sequence is in $1. The sequence  
                 # itself is in $2. First, move the clear text to the return variable.  
                 $retVal .= $1;  
                 $codedString = substr $codedString, (2 + length $1);  
                 # Get the escape value.  
                 my $char = $2;  
                 # If we have a "\r", we are done.  
                 if ($char ne 'r') {  
                     # Here it's not an 'r', so we convert it.  
                     $char =~ tr/\\tn/\\\t\n/;  
                     $retVal .= $char;  
                 }  
             } else {  
                 # Here there are no more escape sequences. The rest of the string is  
                 # transferred unmodified.  
                 $retVal .= $codedString;  
                 $codedString = "";  
2514              }              }
2515            };
2516            if ($@) {
2517                Confess("Error creating $dirName: $@");
2518          }          }
2519      }      }
     # Return the result.  
     return $retVal;  
2520  }  }
2521    
2522  =head3 ParseRecord  =head3 ChDir
2523    
2524  C<< my @fields = Tracer::ParseRecord($line); >>      ChDir($dirName);
2525    
2526  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Change to the specified directory.
 and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
 These will automatically be converted.  
2527    
2528  =over 4  =over 4
2529    
2530  =item line  =item dirName
   
 Line of data containing the tab-delimited fields.  
   
 =item RETURN  
2531    
2532  Returns a list of the fields found in the data line.  Name of the directory to which we want to change.
2533    
2534  =back  =back
2535    
2536  =cut  =cut
2537    
2538  sub ParseRecord {  sub ChDir {
2539      # Get the parameter.      my ($dirName) = @_;
2540      my ($line) = @_;      if (! -d $dirName) {
2541      # Remove the trailing new-line, if any.          Confess("Cannot change to directory $dirName: no such directory.");
2542      chomp $line;      } else {
2543      # Split the line read into pieces using the tab character.          Trace("Changing to directory $dirName.") if T(File => 4);
2544      my @retVal = split /\t/, $line;          my $okFlag = chdir $dirName;
2545      # Trim and fix the escapes in each piece.          if (! $okFlag) {
2546      for my $value (@retVal) {              Confess("Error switching to directory $dirName.");
2547          # Trim leading whitespace.          }
         $value =~ s/^\s+//;  
         # Trim trailing whitespace.  
         $value =~ s/\s+$//;  
         # Delete the carriage returns.  
         $value =~ s/\r//g;  
         # Convert the escapes into their real values.  
         $value =~ s/\\t/"\t"/ge;  
         $value =~ s/\\n/"\n"/ge;  
2548      }      }
     # Return the result.  
     return @retVal;  
2549  }  }
2550    
2551  =head3 Merge  =head3 SetPermissions
2552    
2553  C<< my @mergedList = Tracer::Merge(@inputList); >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2554    
2555  Sort a list of strings and remove duplicates.  Set the permissions for a directory and all the files and folders inside it.
2556    In addition, the group ownership will be changed to the specified value.
2557    
2558    This method is more vulnerable than most to permission and compatability
2559    problems, so it does internal error recovery.
2560    
2561  =over 4  =over 4
2562    
2563  =item inputList  =item dirName
2564    
2565  List of scalars to sort and merge.  Name of the directory to process.
2566    
2567  =item RETURN  =item group
2568    
2569  Returns a list containing the same elements sorted in ascending order with duplicates  Name of the group to be assigned.
2570  removed.  
2571    =item mask
2572    
2573    Permission mask. Bits that are C<1> in this mask will be ORed into the
2574    permission bits of any file or directory that does not already have them
2575    set to 1.
2576    
2577    =item otherMasks
2578    
2579    Map of search patterns to permission masks. If a directory name matches
2580    one of the patterns, that directory and all its members and subdirectories
2581    will be assigned the new pattern. For example, the following would
2582    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2583    
2584        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2585    
2586    The list is ordered, so the following would use 0777 for C<tmp1> and
2587    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2588    
2589        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2590                                                       '^tmp' => 0666);
2591    
2592    Note that the pattern matches are all case-insensitive, and only directory
2593    names are matched, not file names.
2594    
2595  =back  =back
2596    
2597  =cut  =cut
2598    
2599  sub Merge {  sub SetPermissions {
2600      # Get the input list in sort order.      # Get the parameters.
2601      my @inputList = sort @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2602      # Only proceed if the list has at least two elements.      # Set up for error recovery.
2603      if (@inputList > 1) {      eval {
2604          # Now we want to move through the list splicing out duplicates.          # Switch to the specified directory.
2605          my $i = 0;          ChDir($dirName);
2606          while ($i < @inputList) {          # Get the group ID.
2607              # Get the current entry.          my $gid = getgrnam($group);
2608              my $thisEntry = $inputList[$i];          # Get the mask for tracing.
2609              # Find out how many elements duplicate the current entry.          my $traceMask = sprintf("%04o", $mask) . "($mask)";
2610              my $j = $i + 1;          Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2611              my $dup1 = $i + 1;          my $fixCount = 0;
2612              while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };          my $lookCount = 0;
2613              # If the number is nonzero, splice out the duplicates found.          # @dirs will be a stack of directories to be processed.
2614              if ($j > $dup1) {          my @dirs = (getcwd());
2615                  splice @inputList, $dup1, $j - $dup1;          while (scalar(@dirs) > 0) {
2616                # Get the current directory.
2617                my $dir = pop @dirs;
2618                # Check for a match to one of the specified directory names. To do
2619                # that, we need to pull the individual part of the name off of the
2620                # whole path.
2621                my $simpleName = $dir;
2622                if ($dir =~ m!/([^/]+)$!) {
2623                    $simpleName = $1;
2624                }
2625                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2626                # Search for a match.
2627                my $match = 0;
2628                my $i;
2629                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2630                    my $pattern = $otherMasks[$i];
2631                    if ($simpleName =~ /$pattern/i) {
2632                        $match = 1;
2633                    }
2634                }
2635                # Check for a match. Note we use $i-1 because the loop added 2
2636                # before terminating due to the match.
2637                if ($match && $otherMasks[$i-1] != $mask) {
2638                    # This directory matches one of the incoming patterns, and it's
2639                    # a different mask, so we process it recursively with that mask.
2640                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2641                } else {
2642                    # Here we can process normally. Get all of the non-hidden members.
2643                    my @submems = OpenDir($dir, 1);
2644                    for my $submem (@submems) {
2645                        # Get the full name.
2646                        my $thisMem = "$dir/$submem";
2647                        Trace("Checking member $thisMem.") if T(4);
2648                        $lookCount++;
2649                        if ($lookCount % 1000 == 0) {
2650                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2651              }              }
2652              # Now the element at position $dup1 is different from the element before it                      # Fix the group.
2653              # at position $i. We push $i forward one position and start again.                      chown -1, $gid, $thisMem;
2654              $i++;                      # Insure this member is not a symlink.
2655                        if (! -l $thisMem) {
2656                            # Get its info.
2657                            my $fileInfo = stat $thisMem;
2658                            # Only proceed if we got the info. Otherwise, it's a hard link
2659                            # and we want to skip it anyway.
2660                            if ($fileInfo) {
2661                                my $fileMode = $fileInfo->mode;
2662                                if (($fileMode & $mask) != $mask) {
2663                                    # Fix this member.
2664                                    $fileMode |= $mask;
2665                                    chmod $fileMode, $thisMem;
2666                                    $fixCount++;
2667          }          }
2668                                # If it's a subdirectory, stack it.
2669                                if (-d $thisMem) {
2670                                    push @dirs, $thisMem;
2671      }      }
     # Return the merged list.  
     return @inputList;  
2672  }  }
   
 =head3 Percent  
   
 C<< my $percent = Tracer::Percent($number, $base); >>  
   
 Returns the percent of the base represented by the given number. If the base  
 is zero, returns zero.  
   
 =over 4  
   
 =item number  
   
 Percent numerator.  
   
 =item base  
   
 Percent base.  
   
 =item RETURN  
   
 Returns the percentage of the base represented by the numerator.  
   
 =back  
   
 =cut  
   
 sub Percent {  
     # Get the parameters.  
     my ($number, $base) = @_;  
     # Declare the return variable.  
     my $retVal = 0;  
     # Compute the percent.  
     if ($base != 0) {  
         $retVal = $number * 100 / $base;  
2673      }      }
2674      # Return the result.                  }
2675      return $retVal;              }
2676            }
2677            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2678        };
2679        # Check for an error.
2680        if ($@) {
2681            Confess("SetPermissions error: $@");
2682        }
2683  }  }
2684    
2685  =head3 GetFile  =head3 GetLine
   
 C<< my @fileContents = Tracer::GetFile($fileName); >>  
   
     or  
2686    
2687  C<< my $fileContents = Tracer::GetFile($fileName); >>      my @data = Tracer::GetLine($handle);
2688    
2689  Return the entire contents of a file. In list context, line-ends are removed and  Read a line of data from a tab-delimited file.
 each line is a list element. In scalar context, line-ends are replaced by C<\n>.  
2690    
2691  =over 4  =over 4
2692    
2693  =item fileName  =item handle
2694    
2695  Name of the file to read.  Open file handle from which to read.
2696    
2697  =item RETURN  =item RETURN
2698    
2699  In a list context, returns the entire file as a list with the line terminators removed.  Returns a list of the fields in the record read. The fields are presumed to be
2700  In a scalar context, returns the entire file as a string. If an error occurs opening  tab-delimited. If we are at the end of the file, then an empty list will be
2701  the file, an empty list will be returned.  returned. If an empty line is read, a single list item consisting of a null
2702    string will be returned.
2703    
2704  =back  =back
2705    
2706  =cut  =cut
2707    
2708  sub GetFile {  sub GetLine {
2709      # Get the parameters.      # Get the parameters.
2710      my ($fileName) = @_;      my ($handle) = @_;
2711      # Declare the return variable.      # Declare the return variable.
2712      my @retVal = ();      my @retVal = ();
2713      # Open the file for input.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2714      my $handle = Open(undef, "<$fileName");      # Read from the file.
2715      # Read the whole file into the return variable, stripping off any terminator      my $line = <$handle>;
2716      # characters.      # Only proceed if we found something.
2717      my $lineCount = 0;      if (defined $line) {
2718      while (my $line = <$handle>) {          # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2719          $lineCount++;          # upload control and have a nonstandard EOL combination.
2720          $line = Strip($line);          $line =~ s/(\r|\n)+$//;
2721          push @retVal, $line;          # Here we do some fancy tracing to help in debugging complicated EOL marks.
2722            if (T(File => 4)) {
2723                my $escapedLine = $line;
2724                $escapedLine =~ s/\n/\\n/g;
2725                $escapedLine =~ s/\r/\\r/g;
2726                $escapedLine =~ s/\t/\\t/g;
2727                Trace("Line read: -->$escapedLine<--");
2728      }      }
2729      # Close it.          # If the line is empty, return a single empty string; otherwise, parse
2730      close $handle;          # it into fields.
2731      my $actualLines = @retVal;          if ($line eq "") {
2732      # Return the file's contents in the desired format.              push @retVal, "";
     if (wantarray) {  
         return @retVal;  
2733      } else {      } else {
2734          return join "\n", @retVal;              push @retVal, split /\t/,$line;
2735            }
2736        } else {
2737            # Trace the reason the read failed.
2738            Trace("End of file: $!") if T(File => 3);
2739      }      }
2740        # Return the result.
2741        return @retVal;
2742  }  }
2743    
2744  =head3 PutFile  =head3 PutLine
2745    
2746  C<< Tracer::PutFile($fileName, \@lines); >>      Tracer::PutLine($handle, \@fields, $eol);
2747    
2748  Write out a file from a list of lines of text.  Write a line of data to a tab-delimited file. The specified field values will be
2749    output in tab-separated form, with a trailing new-line.
2750    
2751  =over 4  =over 4
2752    
2753  =item fileName  =item handle
2754    
2755  Name of the output file.  Output file handle.
2756    
2757  =item lines  =item fields
2758    
2759  Reference to a list of text lines. The lines will be written to the file in order, with trailing  List of field values.
2760  new-line characters. Alternatively, may be a string, in which case the string will be written without  
2761  modification.  =item eol (optional)
2762    
2763    End-of-line character (default is "\n").
2764    
2765  =back  =back
2766    
2767  =cut  =cut
2768    
2769  sub PutFile {  sub PutLine {
2770      # Get the parameters.      # Get the parameters.
2771      my ($fileName, $lines) = @_;      my ($handle, $fields, $eol) = @_;
2772      # Open the output file.      # Write the data.
2773      my $handle = Open(undef, ">$fileName");      print $handle join("\t", @{$fields}) . ($eol || "\n");
     if (ref $lines ne 'ARRAY') {  
         # Here we have a scalar, so we write it raw.  
         print $handle $lines;  
     } else {  
         # Write the lines one at a time.  
         for my $line (@{$lines}) {  
             print $handle "$line\n";  
         }  
     }  
     # Close the output file.  
     close $handle;  
2774  }  }
2775    
 =head3 QTrace  
2776    
2777  C<< my $data = QTrace($format); >>  =head3 PrintLine
2778    
2779  Return the queued trace data in the specified format.      Tracer::PrintLine($line);
2780    
2781    Print a line of text with a trailing new-line.
2782    
2783  =over 4  =over 4
2784    
2785  =item format  =item line
2786    
2787  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Line of text to print.
2788    
2789  =back  =back
2790    
2791  =cut  =cut
2792    
2793  sub QTrace {  sub PrintLine {
2794      # Get the parameter.      # Get the parameters.
2795      my ($format) = @_;      my ($line) = @_;
2796      # Create the return variable.      # Print the line.
2797      my $retVal = "";      print "$line\n";
     # Only proceed if there is an actual queue.  
     if (@Queue) {  
         # Process according to the format.  
         if ($format =~ m/^HTML$/i) {  
             # Convert the queue into an HTML list.  
             $retVal = "<ul>\n";  
             for my $line (@Queue) {  
                 my $escapedLine = CGI::escapeHTML($line);  
                 $retVal .= "<li>$escapedLine</li>\n";  
             }  
             $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
             # Convert the queue into a list of text lines.  
             $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
     }  
     # Return the formatted list.  
     return $retVal;  
2798  }  }
2799    
 =head3 Confess  
2800    
2801  C<< Confess($message); >>  =head2 Other Useful Methods
2802    
2803  Trace the call stack and abort the program with the specified message. When used with  =head3 ParseParm
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
2804    
2805  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my $listValue = Tracer::ParseParm($string);
2806    
2807  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Convert a parameter into a list reference. If the parameter is undefined,
2808    an undefined value will be returned. Otherwise, it will be parsed as a
2809    comma-separated list of values.
2810    
2811  =over 4  =over 4
2812    
2813  =item message  =item string
2814    
2815  Message to include in the trace.  Incoming string.
2816    
2817    =item RETURN
2818    
2819    Returns a reference to a list of values, or C<undef> if the incoming value
2820    was undefined.
2821    
2822  =back  =back
2823    
2824  =cut  =cut
2825    
2826  sub Confess {  sub ParseParm {
2827      # Get the parameters.      # Get the parameters.
2828      my ($message) = @_;      my ($string) = @_;
2829      # Trace the call stack.      # Declare the return variable.
2830      Cluck($message);      my $retVal;
2831      # Abort the program.      # Check for data.
2832      croak(">>> $message");      if (defined $string) {
2833  }          # We have some, so split it into a list.
2834            $retVal = [ split /\s*,\s*/, $string];
 =head3 Assert  
   
 C<< Assert($condition1, $condition2, ... $conditionN); >>  
   
 Return TRUE if all the conditions are true. This method can be used in conjunction with  
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
   
 C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  
   
 Will abort the program with a stack trace if the value of C<$recNum> is negative.  
   
 =cut  
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
2835      }      }
2836        # Return the result.
2837      return $retVal;      return $retVal;
2838  }  }
2839    
2840  =head3 Cluck  =head3 Now
   
 C<< Cluck($message); >>  
   
 Trace the call stack. Note that for best results, you should qualify the call with a  
 trace condition. For example,  
   
 C<< Cluck("Starting record parse.") if T(3); >>  
   
 will only trace the stack if the trace level for the package is 3 or more.  
   
 =over 4  
   
 =item message  
2841    
2842  Message to include in the trace.      my $string = Tracer::Now();
2843    
2844  =back  Return a displayable time stamp containing the local time. Whatever format this
2845    method produces must be parseable by L</ParseDate>.
2846    
2847  =cut  =cut
2848    
2849  sub Cluck {  sub Now {
2850      # Get the parameters.      return DisplayTime(time);
     my ($message) = @_;  
     # Trace what's happening.  
     Trace("Stack trace for event: $message");  
     my $confession = longmess($message);  
     # Convert the confession to a series of trace messages. Note we skip any  
     # messages relating to calls into Tracer.  
     for my $line (split /\s*\n/, $confession) {  
         Trace($line) if ($line !~ /Tracer\.pm/);  
     }  
2851  }  }
2852    
2853  =head3 Min  =head3 DisplayTime
2854    
2855  C<< my $min = Min($value1, $value2, ... $valueN); >>      my $string = Tracer::DisplayTime($time);
2856    
2857  Return the minimum argument. The arguments are treated as numbers.  Convert a time value to a displayable time stamp. Whatever format this
2858    method produces must be parseable by L</ParseDate>.
2859    
2860  =over 4  =over 4
2861    
2862  =item $value1, $value2, ... $valueN  =item time
2863    
2864  List of numbers to compare.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2865    
2866  =item RETURN  =item RETURN
2867    
2868  Returns the lowest number in the list.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2869    
2870  =back  =back
2871    
2872  =cut  =cut
2873    
2874  sub Min {  sub DisplayTime {
2875      # Get the parameters. Note that we prime the return value with the first parameter.      my ($time) = @_;
2876      my ($retVal, @values) = @_;      my $retVal = "(n/a)";
2877      # Loop through the remaining parameters, looking for the lowest.      if (defined $time) {
2878      for my $value (@values) {          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2879          if ($value < $retVal) {          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2880              $retVal = $value;                    _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
         }  
2881      }      }
     # Return the minimum found.  
2882      return $retVal;      return $retVal;
2883  }  }
2884    
2885  =head3 Max  # Pad a number to 2 digits.
2886    sub _p2 {
2887        my ($value) = @_;
2888        $value = "0$value" if ($value < 10);
2889        return $value;
2890    }
2891    
2892  C<< my $max = Max($value1, $value2, ... $valueN); >>  =head3 Escape
2893    
2894  Return the maximum argument. The arguments are treated as numbers.      my $codedString = Tracer::Escape($realString);
2895    
2896    Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2897    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2898    result is to reverse the effect of L</UnEscape>.
2899    
2900  =over 4  =over 4
2901    
2902  =item $value1, $value2, ... $valueN  =item realString
2903    
2904  List of numbers to compare.  String to escape.
2905    
2906  =item RETURN  =item RETURN
2907    
2908  Returns the highest number in the list.  Escaped equivalent of the real string.
2909    
2910  =back  =back
2911    
2912  =cut  =cut
2913    
2914  sub Max {  sub Escape {
2915      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameter.
2916      my ($retVal, @values) = @_;      my ($realString) = @_;
2917      # Loop through the remaining parameters, looking for the highest.      # Initialize the return variable.
2918      for my $value (@values) {      my $retVal = "";
2919          if ($value > $retVal) {      # Loop through the parameter string, looking for sequences to escape.
2920              $retVal = $value;      while (length $realString > 0) {
2921            # Look for the first sequence to escape.
2922            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2923                # Here we found it. The text preceding the sequence is in $1. The sequence
2924                # itself is in $2. First, move the clear text to the return variable.
2925                $retVal .= $1;
2926                # Strip the processed section off the real string.
2927                $realString = substr $realString, (length $2) + (length $1);
2928                # Get the matched character.
2929                my $char = $2;
2930                # If we have a CR, we are done.
2931                if ($char ne "\r") {
2932                    # It's not a CR, so encode the escape sequence.
2933                    $char =~ tr/\t\n/tn/;
2934                    $retVal .= "\\" . $char;
2935                }
2936            } else {
2937                # Here there are no more escape sequences. The rest of the string is
2938                # transferred unmodified.
2939                $retVal .= $realString;
2940                $realString = "";
2941          }          }
2942      }      }
2943      # Return the maximum found.      # Return the result.
2944      return $retVal;      return $retVal;
2945  }  }
2946    
2947  =head3 AddToListMap  =head3 UnEscape
2948    
2949  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>      my $realString = Tracer::UnEscape($codedString);
2950    
2951  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2952  is created for the key. Otherwise, the new value is pushed onto the list.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2953    be deleted.
2954    
2955  =over 4  =over 4
2956    
2957  =item hash  =item codedString
   
 Reference to the target hash.  
   
 =item key  
2958    
2959  Key for which the value is to be added.  String to un-escape.
2960    
2961  =item value1, value2, ... valueN  =item RETURN
2962    
2963  List of values to add to the key's value list.  Returns a copy of the original string with the escape sequences converted to their actual
2964    values.
2965    
2966  =back  =back
2967    
2968  =cut  =cut
2969    
2970  sub AddToListMap {  sub UnEscape {
2971      # Get the parameters.      # Get the parameter.
2972      my ($hash, $key, @values) = @_;      my ($codedString) = @_;
2973      # Process according to whether or not the key already has a value.      # Initialize the return variable.
2974      if (! exists $hash->{$key}) {      my $retVal = "";
2975          $hash->{$key} = [@values];      # Only proceed if the incoming string is nonempty.
2976        if (defined $codedString) {
2977            # Loop through the parameter string, looking for escape sequences. We can't do
2978            # translating because it causes problems with the escaped slash. ("\\t" becomes
2979            # "\<tab>" no matter what we do.)
2980            while (length $codedString > 0) {
2981                # Look for the first escape sequence.
2982                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2983                    # Here we found it. The text preceding the sequence is in $1. The sequence
2984                    # itself is in $2. First, move the clear text to the return variable.
2985                    $retVal .= $1;
2986                    $codedString = substr $codedString, (2 + length $1);
2987                    # Get the escape value.
2988                    my $char = $2;
2989                    # If we have a "\r", we are done.
2990                    if ($char ne 'r') {
2991                        # Here it's not an 'r', so we convert it.
2992                        $char =~ tr/\\tn/\\\t\n/;
2993                        $retVal .= $char;
2994                    }
2995      } else {      } else {
2996          push @{$hash->{$key}}, @values;                  # Here there are no more escape sequences. The rest of the string is
2997                    # transferred unmodified.
2998                    $retVal .= $codedString;
2999                    $codedString = "";
3000      }      }
3001  }  }
   
 =head3 DebugMode  
   
 C<< if (Tracer::DebugMode) { ...code... } >>  
   
 Return TRUE if debug mode has been turned on, else output an error  
 page and return FALSE.  
   
 Certain CGI scripts are too dangerous to exist in the production  
 environment. This method provides a simple way to prevent them  
 from working unless they are explicitly turned on by creating a password  
 cookie via the B<SetPassword> script.  If debugging mode  
 is not turned on, an error web page will be output directing the  
 user to enter in the correct password.  
   
 =cut  
   
 sub DebugMode {  
     # Declare the return variable.  
     my $retVal = 0;  
     # Check the debug configuration.  
     my $password = CGI::cookie("DebugMode");  
     my $encrypted = Digest::MD5::md5_hex($password);  
     if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {  
         $retVal = 1;  
     } else {  
         # Here debug mode is off, so we generate an error page.  
         my $pageString = PageBuilder::Build("<<Html/ErrorPage.html", {}, "Html");  
         print $pageString;  
3002      }      }
3003      # Return the determination indicator.      # Return the result.
3004      return $retVal;      return $retVal;
3005  }  }
3006    
3007  =head3 Strip  =head3 Percent
3008    
3009  C<< my $string = Tracer::Strip($line); >>      my $percent = Tracer::Percent($number, $base);
3010    
3011  Strip all line terminators off a string. This is necessary when dealing with files  Returns the percent of the base represented by the given number. If the base
3012  that may have been transferred back and forth several times among different  is zero, returns zero.
 operating environments.  
3013    
3014  =over 4  =over 4
3015    
3016  =item line  =item number
3017    
3018  Line of text to be stripped.  Percent numerator.
3019    
3020    =item base
3021    
3022    Percent base.
3023    
3024  =item RETURN  =item RETURN
3025    
3026  The same line of text with all the line-ending characters chopped from the end.  Returns the percentage of the base represented by the numerator.
3027    
3028  =back  =back
3029    
3030  =cut  =cut
3031    
3032  sub Strip {  sub Percent {
3033      # Get a copy of the parameter string.      # Get the parameters.
3034      my ($string) = @_;      my ($number, $base) = @_;
3035      my $retVal = (defined $string ? $string : "");      # Declare the return variable.
3036      # Strip the line terminator characters.      my $retVal = 0;
3037      $retVal =~ s/(\r|\n)+$//g;      # Compute the percent.
3038        if ($base != 0) {
3039            $retVal = $number * 100 / $base;
3040        }
3041      # Return the result.      # Return the result.
3042      return $retVal;      return $retVal;
3043  }  }
3044    
3045  =head3 Pad  =head3 Constrain
3046    
3047  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      my $constrained = Constrain($value, $min, $max);
3048    
3049  Pad a string to a specified length. The pad character will be a  Modify a numeric value to bring it to a point in between a maximum and a minimum.
 space, and the padding will be on the right side unless specified  
 in the third parameter.  
3050    
3051  =over 4  =over 4
3052    
3053  =item string  =item value
   
 String to be padded.  
   
 =item len  
3054    
3055  Desired length of the padded string.  Value to constrain.
3056    
3057  =item left (optional)  =item min (optional)
3058    
3059  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3060    
3061  =item padChar (optional)  =item max (optional)
3062    
3063  Character to use for padding. The default is a space.  Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3064    
3065  =item RETURN  =item RETURN
3066    
3067  Returns a copy of the original string with the pad character added to the  Returns the incoming value, constrained according to the other parameters.
 specified end so that it achieves the desired length.  
3068    
3069  =back  =back
3070    
3071  =cut  =cut
3072    
3073  sub Pad {  sub Constrain {
3074      # Get the parameters.      # Get the parameters.
3075      my ($string, $len, $left, $padChar) = @_;      my ($value, $min, $max) = @_;
3076      # Compute the padding character.      # Declare the return variable.
3077      if (! defined $padChar) {      my $retVal = $value;
3078          $padChar = " ";      # Apply the minimum constraint.
3079      }      if (defined $min && $retVal < $min) {
3080      # Compute the number of spaces needed.          $retVal = $min;
3081      my $needed = $len - length $string;      }
3082      # Copy the string into the return variable.      # Apply the maximum constraint.
3083      my $retVal = $string;      if (defined $max && $retVal > $max) {
3084      # Only proceed if padding is needed.          $retVal = $max;
     if ($needed > 0) {  
         # Create the pad string.  
         my $pad = $padChar x $needed;  
         # Affix it to the return value.  
         if ($left) {  
             $retVal = $pad . $retVal;  
         } else {  
             $retVal .= $pad;  
         }  
3085      }      }
3086      # Return the result.      # Return the result.
3087      return $retVal;      return $retVal;
3088  }  }
3089    
3090  =head3 EOF  =head3 Min
   
 This is a constant that is lexically greater than any useful string.  
   
 =cut  
   
 sub EOF {  
     return "\xFF\xFF\xFF\xFF\xFF";  
 }  
   
 =head3 TICK  
   
 C<< my @results = TICK($commandString); >>  
   
 Perform a back-tick operation on a command. If this is a Windows environment, any leading  
 dot-slash (C<./> will be removed. So, for example, if you were doing  
   
     `./protein.cgi`  
   
 from inside a CGI script, it would work fine in Unix, but would issue an error message  
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
3091    
3092      TICK("./protein.cgi")      my $min = Min($value1, $value2, ... $valueN);
3093    
3094  it will work correctly in both environments.  Return the minimum argument. The arguments are treated as numbers.
3095    
3096  =over 4  =over 4
3097    
3098  =item commandString  =item $value1, $value2, ... $valueN
3099    
3100  The command string to pass to the system.  List of numbers to compare.
3101    
3102  =item RETURN  =item RETURN
3103    
3104  Returns the standard output from the specified command, as a list.  Returns the lowest number in the list.
3105    
3106  =back  =back
3107    
3108  =cut  =cut
3109  #: Return Type @;  
3110  sub TICK {  sub Min {
3111      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3112      my ($commandString) = @_;      my ($retVal, @values) = @_;
3113      # Chop off the dot-slash if this is Windows.      # Loop through the remaining parameters, looking for the lowest.
3114      if ($FIG_Config::win_mode) {      for my $value (@values) {
3115          $commandString =~ s!^\./!!;          if ($value < $retVal) {
3116                $retVal = $value;
3117      }      }
3118      # Activate the command and return the result.      }
3119      return `$commandString`;      # Return the minimum found.
3120        return $retVal;
3121  }  }
3122    
3123  =head3 ScriptSetup  =head3 Max
   
 C<< my ($query, $varHash) = ScriptSetup(); >>  
   
 Perform standard tracing and debugging setup for scripts. The value returned is  
 the CGI object followed by a pre-built variable hash.  
   
 The C<Trace> query parameter is used to determine whether or not tracing is active and  
 which trace modules (other than C<Tracer> and C<FIG>) should be turned on. Specifying  
 the C<CGI> trace module will trace parameter and environment information. Parameters are  
 traced at level 3 and environment variables at level 4. At the end of the script, the  
 client should call L</ScriptFinish> to output the web page.  
   
 =cut  
3124    
3125  sub ScriptSetup {      my $max = Max($value1, $value2, ... $valueN);
     # Get the CGI query object.  
     my $query = CGI->new();  
     # Check for tracing. Set it up if the user asked for it.  
     if ($query->param('Trace')) {  
         # Set up tracing.  
         my $ttype = ($query->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");  
         TSetup($query->param('Trace') . " FIG Tracer", $ttype);  
         # Trace the parameter and environment data.  
         TraceParms($query);  
     } else {  
         # Here tracing is to be turned off. All we allow is errors traced into the  
         # error log.  
         TSetup("0", "WARN");  
     }  
     # Create the variable hash.  
     my $varHash = { DebugData => '' };  
     # Return the query object and variable hash.  
     return ($query, $varHash);  
 }  
3126    
3127  =head3 TraceParms  Return the maximum argument. The arguments are treated as numbers.
3128    
3129  C<< Tracer::TraceParms($query); >>  =over 4
3130    
3131  Trace the CGI parameters at trace level CGI => 3 and the environment variables  =item $value1, $value2, ... $valueN
 at level CGI => 4.  
3132    
3133  =over 4  List of numbers to compare.
3134    
3135  =item query  =item RETURN
3136    
3137  CGI query object containing the parameters to trace.  Returns the highest number in the list.
3138    
3139  =back  =back
3140    
3141  =cut  =cut
3142    
3143  sub TraceParms {  sub Max {
3144      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3145      my ($query) = @_;      my ($retVal, @values) = @_;
3146      if (T(CGI => 3)) {      # Loop through the remaining parameters, looking for the highest.
3147          # Here we want to trace the parameter data.      for my $value (@values) {
3148          my @names = $query->param;          if ($value > $retVal) {
3149          for my $parmName (sort @names) {              $retVal = $value;
             # Note we skip "Trace", which is for our use only.  
             if ($parmName ne 'Trace') {  
                 my @values = $query->param($parmName);  
                 Trace("CGI: $parmName = " . join(", ", @values));  
             }  
         }  
         # Now output a GET-style URL for this query.  
         my $getURL = $query->url(-relative => 1, -query => 1);  
         # Strip out the Trace parameters.  
         $getURL =~ s/Trace=\d[^;&]+[;&]//;  
         $getURL =~ s/TF=\d[;&]//;  
         # Output the URL.  
         Trace("URL: ../FIG/$getURL");  
         # Display the request method.  
         my $method = $query->request_method();  
         Trace("Method: $method");  
     }  
     if (T(CGI => 4)) {  
         # Here we want the environment data too.  
         for my $envName (sort keys %ENV) {  
             Trace("ENV: $envName = $ENV{$envName}");  
3150          }          }
3151      }      }
3152        # Return the maximum found.
3153        return $retVal;
3154  }  }
3155    
 =head3 ScriptFinish  
   
 C<< ScriptFinish($webData, $varHash); >>  
   
 Output a web page at the end of a script. Either the string to be output or the  
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
3156    
3157  A typical standard script would loook like the following.  =head3 Strip
   
     BEGIN {  
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
3158    
3159      my ($query, $varHash) = ScriptSetup();      my $string = Tracer::Strip($line);
     eval {  
         # ... get data from $query, put it in $varHash ...  
     };  
     if ($@) {  
         Trace("Script Error: $@") if T(0);  
     }  
     ScriptFinish("Html/MyTemplate.html", $varHash);  
3160    
3161  The idea here is that even if the script fails, you'll see trace messages and  Strip all line terminators off a string. This is necessary when dealing with files
3162  useful output.  that may have been transferred back and forth several times among different
3163    operating environments.
3164    
3165  =over 4  =over 4
3166    
3167  =item webData  =item line
3168    
3169  A string containing either the full web page to be written to the output or the  Line of text to be stripped.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3170    
3171  =item varHash (optional)  =item RETURN
3172    
3173  If specified, then a reference to a hash mapping variable names for a template  The same line of text with all the line-ending characters chopped from the end.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3174    
3175  =back  =back
3176    
3177  =cut  =cut
3178    
3179  sub ScriptFinish {  sub Strip {
3180      # Get the parameters.      # Get a copy of the parameter string.
3181      my ($webData, $varHash) = @_;      my ($string) = @_;
3182      # Check for a template file situation.      my $retVal = (defined $string ? $string : "");
3183      my $outputString;      # Strip the line terminator characters.
3184      if (defined $varHash) {      $retVal =~ s/(\r|\n)+$//g;
3185          # Here we have a template file. We need to determine the template type.      # Return the result.
3186          my $template;      return $retVal;
         if ($FIG_Config::template_url && $webData =~ /\.php$/) {  
             $template = "$FIG_Config::template_url/$webData";  
         } else {  
             $template = "<<$webData";  
         }  
         $outputString = PageBuilder::Build($template, $varHash, "Html");  
     } else {  
         # Here the user gave us a raw string.  
         $outputString = $webData;  
     }  
     # Check for trace messages.  
     if ($Destination eq "QUEUE") {  
         # We have trace messages, so we want to put them at the end of the body. This  
         # is either at the end of the whole string or at the beginning of the BODY  
         # end-tag.  
         my $pos = length $outputString;  
         if ($outputString =~ m#</body>#gi) {  
             $pos = (pos $outputString) - 7;  
         }  
         substr $outputString, $pos, 0, QTrace('Html');  
     }  
     # Write the output string.  
     print $outputString;  
3187  }  }
3188    
3189  =head3 Insure  =head3 Pad
3190    
3191  C<< Insure($dirName); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3192    
3193  Insure a directory is present.  Pad a string to a specified length. The pad character will be a
3194    space, and the padding will be on the right side unless specified
3195    in the third parameter.
3196    
3197  =over 4  =over 4
3198    
3199  =item dirName  =item string
   
 Name of the directory to check. If it does not exist, it will be created.  
3200    
3201  =back  String to be padded.
3202    
3203  =cut  =item len
3204    
3205  sub Insure {  Desired length of the padded string.
     my ($dirName) = @_;  
     if (! -d $dirName) {  
         Trace("Creating $dirName directory.") if T(2);  
         eval { mkpath $dirName; };  
         if ($@) {  
             Confess("Error creating $dirName: $@");  
         }  
     }  
 }  
3206    
3207  =head3 ChDir  =item left (optional)
3208    
3209  C<< ChDir($dirName); >>  TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3210    
3211  Change to the specified directory.  =item padChar (optional)
3212    
3213  =over 4  Character to use for padding. The default is a space.
3214    
3215  =item dirName  =item RETURN
3216    
3217  Name of the directory to which we want to change.  Returns a copy of the original string with the pad character added to the
3218    specified end so that it achieves the desired length.
3219    
3220  =back  =back
3221    
3222  =cut  =cut
3223    
3224  sub ChDir {  sub Pad {
3225      my ($dirName) = @_;      # Get the parameters.
3226      if (! -d $dirName) {      my ($string, $len, $left, $padChar) = @_;
3227          Confess("Cannot change to directory $dirName: no such directory.");      # Compute the padding character.
3228        if (! defined $padChar) {
3229            $padChar = " ";
3230        }
3231        # Compute the number of spaces needed.
3232        my $needed = $len - length $string;
3233        # Copy the string into the return variable.
3234        my $retVal = $string;
3235        # Only proceed if padding is needed.
3236        if ($needed > 0) {
3237            # Create the pad string.
3238            my $pad = $padChar x $needed;
3239            # Affix it to the return value.
3240            if ($left) {
3241                $retVal = $pad . $retVal;
3242      } else {      } else {
3243          Trace("Changing to directory $dirName.") if T(4);              $retVal .= $pad;
         my $okFlag = chdir $dirName;  
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
3244          }          }
3245      }      }
3246        # Return the result.
3247        return $retVal;
3248  }  }
3249    
3250  =head3 SendSMS  =head3 EOF
3251    
3252  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>  This is a constant that is lexically greater than any useful string.
3253    
3254  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  =cut
 user name, password, and API ID for the relevant account in the hash reference variable  
 I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For  
 example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID  
 is C<2561022>, then the FIG_Config file must contain  
3255    
3256      $phone =  { user => 'BruceTheHumanPet',  sub EOF {
3257                  password => 'silly',      return "\xFF\xFF\xFF\xFF\xFF";
3258                  api_id => '2561022' };  }
3259    
3260  The original purpose of this method was to insure Bruce would be notified immediately when the  =head3 TICK
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3261    
3262  The message ID will be returned if successful, and C<undef> if an error occurs.      my @results = TICK($commandString);
3263    
3264  =over 4  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3265    dot-slash (C<./> will be removed. So, for example, if you were doing
3266    
3267  =item phoneNumber      `./protein.cgi`
3268    
3269  Phone number to receive the message, in international format. A United States phone number  from inside a CGI script, it would work fine in Unix, but would issue an error message
3270  would be prefixed by "1". A British phone number would be prefixed by "44".  in Windows complaining that C<'.'> is not a valid command. If instead you code
3271    
3272  =item msg      TICK("./protein.cgi")
3273    
3274  Message to send to the specified phone.  it will work correctly in both environments.
3275    
3276    =over 4
3277    
3278    =item commandString
3279    
3280    The command string to pass to the system.
3281    
3282  =item RETURN  =item RETURN
3283    
3284  Returns the message ID if successful, and C<undef> if the message could not be sent.  Returns the standard output from the specified command, as a list.
3285    
3286  =back  =back
3287    
3288  =cut  =cut
3289    #: Return Type @;
3290  sub SendSMS {  sub TICK {
3291      # Get the parameters.      # Get the parameters.
3292      my ($phoneNumber, $msg) = @_;      my ($commandString) = @_;
3293      # Declare the return variable. If we do not change it, C<undef> will be returned.      # Chop off the dot-slash if this is Windows.
3294      my $retVal;      if ($FIG_Config::win_mode) {
3295      # Only proceed if we have phone support.          $commandString =~ s!^\./!!;
     if (! defined $FIG_Config::phone) {  
         Trace("Phone support not present in FIG_Config.") if T(1);  
     } else {  
         # Get the phone data.  
         my $parms = $FIG_Config::phone;  
         # Get the Clickatell URL.  
         my $url = "http://api.clickatell.com/http/";  
         # Create the user agent.  
         my $ua = LWP::UserAgent->new;  
         # Request a Clickatell session.  
         my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},  
                                      password => $parms->{password},  
                                      api_id => $parms->{api_id},  
                                      to => $phoneNumber,  
                                      text => $msg});  
         # Check for an error.  
         if (! $resp->is_success) {  
             Trace("Alert failed.") if T(1);  
         } else {  
             # Get the message ID.  
             my $rstring = $resp->content;  
             if ($rstring =~ /^ID:\s+(.*)$/) {  
                 $retVal = $1;  
             } else {  
                 Trace("Phone attempt failed with $rstring") if T(1);  
             }  
         }  
3296      }      }
3297      # Return the result.      # Activate the command and return the result.
3298      return $retVal;      return `$commandString`;
3299  }  }
3300    
3301    
3302  =head3 CommaFormat  =head3 CommaFormat
3303    
3304  C<< my $formatted = Tracer::CommaFormat($number); >>      my $formatted = Tracer::CommaFormat($number);
3305    
3306  Insert commas into a number.  Insert commas into a number.
3307    
# Line 2234  Line 3334 
3334      # Return the result.      # Return the result.
3335      return $retVal;      return $retVal;
3336  }  }
 =head3 SetPermissions  
   
 C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  
   
 Set the permissions for a directory and all the files and folders inside it.  
 In addition, the group ownership will be changed to the specified value.  
   
 This method is more vulnerable than most to permission and compatability  
 problems, so it does internal error recovery.  
   
 =over 4  
   
 =item dirName  
   
 Name of the directory to process.  
   
 =item group  
   
 Name of the group to be assigned.  
   
 =item mask  
   
 Permission mask. Bits that are C<1> in this mask will be ORed into the  
 permission bits of any file or directory that does not already have them  
 set to 1.  
   
 =item otherMasks  
3337    
 Map of search patterns to permission masks. If a directory name matches  
 one of the patterns, that directory and all its members and subdirectories  
 will be assigned the new pattern. For example, the following would  
 assign 01664 to most files, but would use 01777 for directories named C<tmp>.  
   
     Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  
   
 The list is ordered, so the following would use 0777 for C<tmp1> and  
 0666 for C<tmp>, C<tmp2>, or C<tmp3>.  
   
     Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  
                                                    '^tmp' => 0666);  
   
 Note that the pattern matches are all case-insensitive, and only directory  
 names are matched, not file names.  
   
 =back  
   
 =cut  
   
 sub SetPermissions {  
     # Get the parameters.  
     my ($dirName, $group, $mask, @otherMasks) = @_;  
     # Set up for error recovery.  
     eval {  
         # Switch to the specified directory.  
         ChDir($dirName);  
         # Get the group ID.  
         my $gid = getgrnam($group);  
         # Get the mask for tracing.  
         my $traceMask = sprintf("%04o", $mask) . "($mask)";  
         Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(2);  
         my $fixCount = 0;  
         my $lookCount = 0;  
         # @dirs will be a stack of directories to be processed.  
         my @dirs = (getcwd());  
         while (scalar(@dirs) > 0) {  
             # Get the current directory.