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revision 1.69, Mon Oct 2 02:59:47 2006 UTC revision 1.104, Fri May 9 06:22:49 2008 UTC
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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 EmergencyIP ScriptSetup ScriptFinish Insure ChDir Emergency);      @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 122  Line 150 
150  =back  =back
151    
152  The format of trace messages is important because some utilities analyze trace files.  The format of trace messages is important because some utilities analyze trace files.
153  The time stamp is between square brackets, the module name between angle brackets,  There are three fields-- the time stamp, the category name, and the text.
154  a colon (C<:>), and the message text after that. If the square brackets or angle  The time stamp is between square brackets and the category name between angle brackets.
155  brackets are missing, then the trace management utilities assume that they  After the category name there is a colon (C<:>) followed by the message text.
156  are encountering a set of pre-formatted lines.  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    my $CommandLine;            # Command line passed to StandardSetup
212    umask 2;                    # Fix the damn umask so everything is group-writable.
213    
214    =head2 Tracing Methods
215    
216    =head3 Setups
217    
218        my $count = Tracer::Setups();
219    
220    Return the number of times L</TSetup> has been called.
221    
222    This method allows for the creation of conditional tracing setups where, for example, we
223    may want to set up tracing if nobody else has done it before us.
224    
225  =head2 Public Methods  =cut
226    
227    sub Setups {
228        return $SetupCount;
229    }
230    
231  =head3 TSetup  =head3 TSetup
232    
233  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
234    
235  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
236  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 197  Line 280 
280          }          }
281      }      }
282      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
283      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
284      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
285        # the standard output (tee mode).
286      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
287          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
288              $TeeFlag = 1;              $TeeFlag = 1;
289              $target = substr($target, 1);              $target = substr($target, 1);
290          }          }
291          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
292                # We need to initialize the file (which clears it).
293              open TRACEFILE, $target;              open TRACEFILE, $target;
294              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
295              close TRACEFILE;              close TRACEFILE;
296                # Set to append mode now that the file has been cleared.
297              $Destination = ">$target";              $Destination = ">$target";
298          } else {          } else {
299              $Destination = $target;              $Destination = $target;
# Line 219  Line 305 
305      $SetupCount++;      $SetupCount++;
306  }  }
307    
308  =head3 StandardSetup  =head3 SetLevel
309    
310  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
311    
312  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.  
313    
314  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.  
315    
316  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  
317    
318      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
319    
320  This would cause trace messages in the specified three packages to appear in  =back
 the output. There are two 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.  
321    
322  =over 4  =cut
323    
324  =item SQL  sub SetLevel {
325        $TraceLevel = $_[0];
326    }
327    
328  Traces SQL commands and activity.  =head3 ParseDate
329    
330  =item Tracer      my $time = Tracer::ParseDate($dateString);
331    
332  Traces error messages and call stacks.  Convert a date into a PERL time number. This method expects a date-like string
333    and parses it into a number. The string must be vaguely date-like or it will
334    return an undefined value. Our requirement is that a month and day be
335    present and that three pieces of the date string (time of day, month and day,
336    year) be separated by likely delimiters, such as spaces, commas, and such-like.
337    
338  =back  If a time of day is present, it must be in military time with two digits for
339    everything but the hour.
340    
341  C<SQL> is only turned on if the C<-sql> option is specified in the command line.  The year must be exactly four digits.
 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.  
342    
343      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  Additional stuff can be in the string. We presume it's time zones or weekdays or something
344    equally innocuous. This means, however, that a sufficiently long sentence with date-like
345    parts in it may be interpreted as a date. Hopefully this will not be a problem.
346    
347  Standard tracing is output to the standard output and echoed to the file  It should be guaranteed that this method will parse the output of the L</Now> function.
 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  
348    
349  The default trace level is 2. To get all messages, specify a trace level of 4.  The parameters are as follows.
 For a genome-by-genome update, use 3.  
350    
351      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  =over 4
352    
353  would send the trace output to C<traceBruce.log> in the temporary directory.  =item dateString
354    
355  The I<options> parameter is a reference to a hash containing the command-line  The date string to convert.
 options, their default values, and an explanation of what they mean. Command-line  
 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.  
356    
357  You can specify a different default trace level by setting C<$options->{trace}>  =item RETURN
 prior to calling this method.  
358    
359  An example at this point would help. Consider, for example, the command-line utility  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
360  C<TransactFeatures>. It accepts a list of positional parameters plus the options  the date string is invalid. A valid date string must contain a month and day.
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
361    
362      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  =back
                         { safe => [0, "use database transactions"],  
                           noAlias => [0, "do not expect aliases in CHANGE transactions"],  
                           start => [' ', "start with this genome"],  
                           tblFiles => [0, "output TBL files containing the corrected IDs"] },  
                         "command transactionDirectory IDfile",  
                       @ARGV);  
363    
364    =cut
365    
366  The call to C<ParseCommand> specifies the default values for the options and  # Universal month conversion table.
367  stores the actual options in a hash that is returned as C<$options>. The  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
368  positional parameters are returned in C<@parameters>.                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
369                                Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
370                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
371                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
372                                Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
373                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
374                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
375                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
376                                Oct =>  9, October  =>   9, '10' =>  9,
377                                Nov => 10, November =>  10, '11' => 10,
378                                Dec => 11, December =>  11, '12' => 11
379                            };
380    
381  The following is a sample command line for C<TransactFeatures>.  sub ParseDate {
382        # Get the parameters.
383        my ($dateString) = @_;
384        # Declare the return variable.
385        my $retVal;
386        # Find the month and day of month. There are two ways that can happen. We check for the
387        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
388        # won't be fooled into thinking the month is Sunday.
389        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
390            my ($mon, $mday) = (MONTHS->{$1}, $2);
391            # Insist that the month and day are valid.
392            if (defined($mon) && $2 >= 1 && $2 <= 31) {
393                # Find the time.
394                my ($hour, $min, $sec) = (0, 0, 0);
395                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
396                    ($hour, $min, $sec) = ($1, $2, $3);
397                }
398                # Find the year.
399                my $year;
400                if ($dateString =~ /\b(\d{4})\b/) {
401                    $year = $1;
402                } else {
403                    # Get the default year, which is this one. Note we must convert it to
404                    # the four-digit value expected by "timelocal".
405                    (undef, undef, undef, undef, undef, $year) = localtime();
406                    $year += 1900;
407                }
408                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
409            }
410        }
411        # Return the result.
412        return $retVal;
413    }
414    
415      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  =head3 LogErrors
416    
417  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional      Tracer::LogErrors($fileName);
 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<Tracer>, and <DocUtils>. C<Tracer> is standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
418    
419      { trace => 2, sql => 0, safe => 0,  Route the standard error output to a log file.
       noAlias => 1, start => ' ', tblFiles => 0 }  
420    
421  Use of C<StandardSetup> in this way provides a simple way of performing  =over 4
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
422    
423  If the C<background> option is specified on the command line, then the  =item fileName
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
424    
425      -user=Bruce -background  Name of the file to receive the error output.
426    
427  then the trace output would go to C<traceBruce.log>, the standard output to  =back
 C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to  
 simplify starting a command in the background.  
428    
429  Finally, if the special option C<-h> is specified, the option names will  =cut
 be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
430    
431      TransactFeatures -h  sub LogErrors {
432        # Get the file name.
433        my ($fileName) = @_;
434        # Open the file as the standard error output.
435        open STDERR, '>', $fileName;
436    }
437    
438  he would see the following output.  =head3 Trace
439    
440      TransactFeatures [options] command transactionDirectory IDfile      Trace($message);
         -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  
441    
442  The caller has the option of modifying the tracing scheme by placing a value  Write a trace message to the target location specified in L</TSetup>. If there has not been
443  for C<trace> in the incoming options hash. The default value can be overridden,  any prior call to B<TSetup>.
 or the tracing to the standard output can be turned off by suffixing a minus  
 sign to the trace level. So, for example,  
444    
445      { trace => [0, "tracing level (default 0)"],  =over 4
        ...  
446    
447  would set the default trace level to 0 instead of 2, while  =item message
448    
449      { trace => ["2-", "tracing level (default 2)"],  Message to write.
        ...  
450    
451  would leave the default at 2, but trace only to the log file, not to the  =back
 standard output.  
452    
453  The parameters to this method are as follows.  =cut
454    
455  =over 4  sub Trace {
456        # Get the parameters.
457        my ($message) = @_;
458        # Strip off any line terminators at the end of the message. We will add
459        # new-line stuff ourselves.
460        my $stripped = Strip($message);
461        # Compute the caller information.
462        my ($callPackage, $callFile, $callLine) = caller();
463        my $callFileTitle = basename($callFile);
464        # Check the caller.
465        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
466        # Get the timestamp.
467        my $timeStamp = Now();
468        # Build the prefix.
469        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
470        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
471        # Format the message.
472        my $formatted = "$prefix $stripped";
473        # Process according to the destination.
474        if ($Destination eq "TEXT") {
475            # Write the message to the standard output.
476            print "$formatted\n";
477        } elsif ($Destination eq "ERROR") {
478            # Write the message to the error output. Here, we want our prefix fields.
479            print STDERR "$formatted\n";
480        } elsif ($Destination eq "WARN") {
481            # Emit the message to the standard error output. It is presumed that the
482            # error logger will add its own prefix fields, the notable exception being
483            # the caller info.
484            print STDERR "$callerInfo$stripped\n";
485        } elsif ($Destination eq "QUEUE") {
486            # Push the message into the queue.
487            push @Queue, "$formatted";
488        } elsif ($Destination eq "HTML") {
489            # Convert the message to HTML and write it to the standard output.
490            my $escapedMessage = CGI::escapeHTML($stripped);
491            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
492        } elsif ($Destination =~ m/^>>/) {
493            # Write the trace message to an output file.
494            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
495            print TRACING "$formatted\n";
496            close TRACING;
497            # If the Tee flag is on, echo it to the standard output.
498            if ($TeeFlag) {
499                print "$formatted\n";
500            }
501        }
502    }
503    
504  =item categories  =head3 T
505    
506  Reference to a list of tracing category names. These should be names of      my $switch = T($category, $traceLevel);
 packages whose internal workings will need to be debugged to get the  
 command working.  
507    
508  =item options      or
509    
510  Reference to a hash containing the legal options for the current command mapped      my $switch = T($traceLevel);
 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).  
511    
512  =item parmHelp  Return TRUE if the trace level is at or above a specified value and the specified category
513    is active, else FALSE. If no category is specified, the caller's package name is used.
514    
515  A string that vaguely describes the positional parameters. This is used  =over 4
 if the user specifies the C<-h> option.  
516    
517  =item argv  =item category
518    
519  List of command line parameters, including the option switches, which must  Category to which the message belongs. If not specified, the caller's package name is
520  precede the positional parameters and be prefixed by a hyphen.  used.
521    
522    =item traceLevel
523    
524    Relevant tracing level.
525    
526  =item RETURN  =item RETURN
527    
528  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.  
529    
530  =back  =back
531    
532  =cut  =cut
533    
534  sub StandardSetup {  sub T {
535        # Declare the return variable.
536        my $retVal = 0;
537        # Only proceed if tracing is turned on.
538        if ($Destination ne "NONE") {
539      # Get the parameters.      # Get the parameters.
540      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
541      # Add the tracing options.          if (!defined $traceLevel) {
542      if (! exists $options->{trace}) {              # Here we have no category, so we need to get the calling package.
543          $options->{trace} = [2, "tracing level"];              # The calling package is normally the first parameter. If it is
544      }              # omitted, the first parameter will be the tracelevel. So, the
545      $options->{sql} = [0, "turn on SQL tracing"];              # first thing we do is shift the so-called category into the
546      $options->{h} = [0, "display command-line options"];              # $traceLevel variable where it belongs.
547      $options->{user} = [$$, "trace log file name suffix"];              $traceLevel = $category;
548      $options->{background} = [0, "spool standard and error output"];              my ($package, $fileName, $line) = caller;
549      # Create a parsing hash from the options hash. The parsing hash              # If there is no calling package, we default to "main".
550      # contains the default values rather than the default value              if (!$package) {
551      # and the description. While we're at it, we'll memorize the                  $category = "main";
     # length of the longest option name.  
     my $longestName = 0;  
     my %parseOptions = ();  
     for my $key (keys %{$options}) {  
         if (length $key > $longestName) {  
             $longestName = length $key;  
         }  
         $parseOptions{$key} = $options->{$key}->[0];  
     }  
     # Parse the command line.  
     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);  
     # Get the logfile suffix.  
     my $suffix = $retOptions->{user};  
     # Check for background mode.  
     if ($retOptions->{background}) {  
         my $outFileName = "$FIG_Config::temp/out$suffix.log";  
         my $errFileName = "$FIG_Config::temp/err$suffix.log";  
         open STDOUT, ">$outFileName";  
         open STDERR, ">$errFileName";  
     }  
     # Now we want to set up tracing. First, we need to know if SQL is to  
     # be traced.  
     my @cats = @{$categories};  
     if ($retOptions->{sql}) {  
         push @cats, "SQL";  
     }  
     # Add the default categories.  
     push @cats, "Tracer";  
     # Next, we create the category string by joining the categories.  
     my $cats = join(" ", @cats);  
     # Check to determine whether or not the caller wants to turn off tracing  
     # to the standard output.  
     my $traceLevel = $retOptions->{trace};  
     my $textOKFlag = 1;  
     if ($traceLevel =~ /^(.)-/) {  
         $traceLevel = $1;  
         $textOKFlag = 0;  
     }  
     # Now we set up the trace mode.  
     my $traceMode;  
     # Verify that we can open a file in the FIG temporary directory.  
     my $traceFileName = "$FIG_Config::temp/trace$suffix.log";  
     if (open TESTTRACE, ">$traceFileName") {  
         # Here we can trace to a file.  
         $traceMode = ">$traceFileName";  
         if ($textOKFlag) {  
             # Echo to standard output if the text-OK flag is set.  
             $traceMode = "+$traceMode";  
         }  
         # Close the test file.  
         close TESTTRACE;  
     } else {  
         # Here we can't trace to a file. We trace to the standard output if it's  
         # okay, and the error log otherwise.  
         if ($textOKFlag) {  
             $traceMode = "TEXT";  
552          } else {          } else {
553              $traceMode = "WARN";                  my @cats = split /::/, $package;
554                    $category = $cats[$#cats];
555          }          }
556      }      }
557      # Now set up the tracing.          # Save the category name and level.
558      TSetup("$traceLevel $cats", $traceMode);          $LastCategory = $category;
559      # Check for the "h" option. If it is specified, dump the command-line          $LastLevel = $traceLevel;
560      # options and exit the program.          # Convert it to lower case before we hash it.
561      if ($retOptions->{h}) {          $category = lc $category;
562          $0 =~ m#[/\\](\w+)(\.pl)?$#i;          # Validate the trace level.
563          print "$1 [options] $parmHelp\n";          if (ref $traceLevel) {
564          for my $key (sort keys %{$options}) {              Confess("Bad trace level.");
565              my $name = Pad($key, $longestName, 0, ' ');          } elsif (ref $TraceLevel) {
566              my $desc = $options->{$key}->[1];              Confess("Bad trace config.");
             if ($options->{$key}->[0]) {  
                 $desc .= " (default " . $options->{$key}->[0] . ")";  
             }  
             print "  $name $desc\n";  
567          }          }
568          exit(0);          # Make the check. Note that level 0 shows even if the category is turned off.
569            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
570      }      }
571      # Return the parsed parameters.      # Return the computed result.
572      return ($retOptions, @retParameters);      return $retVal;
573  }  }
574    
575  =head3 Setups  =head3 QTrace
   
 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  
576    
577  sub Setups {      my $data = QTrace($format);
     return $SetupCount;  
 }  
578    
579  =head3 Open  Return the queued trace data in the specified format.
580    
581  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  =over 4
582    
583  Open a file.  =item format
584    
585  The I<$fileSpec> is essentially the second argument of the PERL C<open>  C<html> to format the data as an HTML list, C<text> to format it as straight text.
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
586    
587      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =back
588    
589  would open for output appended to the specified file, and  =cut
590    
591      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  sub QTrace {
592        # Get the parameter.
593        my ($format) = @_;
594        # Create the return variable.
595        my $retVal = "";
596        # Only proceed if there is an actual queue.
597        if (@Queue) {
598            # Process according to the format.
599            if ($format =~ m/^HTML$/i) {
600                # Convert the queue into an HTML list.
601                $retVal = "<ul>\n";
602                for my $line (@Queue) {
603                    my $escapedLine = CGI::escapeHTML($line);
604                    $retVal .= "<li>$escapedLine</li>\n";
605                }
606                $retVal .= "</ul>\n";
607            } elsif ($format =~ m/^TEXT$/i) {
608                # Convert the queue into a list of text lines.
609                $retVal = join("\n", @Queue) . "\n";
610            }
611            # Clear the queue.
612            @Queue = ();
613        }
614        # Return the formatted list.
615        return $retVal;
616    }
617    
618  would open a pipe that sorts the records written and removes duplicates. Note  =head3 Confess
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
619    
620      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");      Confess($message);
621    
622  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  Trace the call stack and abort the program with the specified message. When used with
623  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
624  failed open will throw an exception and the third parameter will be used to construct  So, for example
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
625    
626      Could not open "/usr/spool/news/twitlog"      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
627    
628  Note that the mode characters are automatically cleaned from the file name.  Will abort the program with a stack trace if the value of C<$recNum> is negative.
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
629    
630      Could not open "/usr/spool/news/twitlog": file not found.  =over 4
631    
632  In some versions of PERL the only error message we get is a number, which  =item message
 corresponds to the C++ C<errno> value.  
633    
634      Could not open "/usr/spool/news/twitlog": 6.  Message to include in the trace.
635    
636  =over 4  =back
637    
638  =item fileHandle  =cut
639    
640  File handle. If this parameter is C<undef>, a file handle will be generated  sub Confess {
641  and returned as the value of this method.      # Get the parameters.
642        my ($message) = @_;
643        # Set up the category and level.
644        $LastCategory = "(confess)";
645        $LastLevel = 0;
646        if (! defined($FIG_Config::no_tool_hdr)) {
647            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
648            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
649            # Only proceed if the tool header file is actually present.
650            if (-f $toolHeaderFile) {
651                my $fh;
652                if (open $fh, "<$toolHeaderFile") {
653                    my @lines = <$fh>;
654                    Trace("Tool header has " . scalar(@lines) . " lines.");
655                }
656            }
657        }
658        # Trace the call stack.
659        Cluck($message);
660        # Abort the program.
661        croak(">>> $message");
662    }
663    
664  =item fileSpec  =head3 Warn
665    
666  File name and mode, as per the PERL C<open> function.      Warn($message);
667    
668  =item message (optional)  This method traces an important message. If an RSS feed is configured
669    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
670    then the message will be echoed to the feed. In general, a tracing
671    destination of C<WARN> indicates that the caller is running as a web
672    service in a production environment; however, this is not a requirement.
673    
674    To force warnings into the RSS feed even when the tracing destination
675    is not C<WARN>, simply specify the C<Feed> tracing module. This can be
676    configured automatically when L</StandardSetup> is used.
677    
678    The L</Cluck> method calls this one for its final message. Since
679    L</Confess> calls L</Cluck>, this means that any error which is caught
680    and confessed will put something in the feed. This insures that someone
681    will be alerted relatively quickly when a failure occurs.
682    
683  Error message to use if the open fails. If omitted, a standard error message  =over 4
 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>.  
684    
685  =item RETURN  =item message
686    
687  Returns the name of the file handle assigned to the file, or C<undef> if the  Message to be traced.
 open failed.  
688    
689  =back  =back
690    
691  =cut  =cut
692    
693  sub Open {  sub Warn {
694      # Get the parameters.      # Get the parameters.
695      my ($fileHandle, $fileSpec, $message) = @_;      my ($message) = @_;
696      # Attempt to open the file.      # Trace the message.
697      my $rv = open $fileHandle, $fileSpec;      Trace($message);
698      # If the open failed, generate an error message.      # Check for feed forcing.
699      if (! $rv) {      my $forceFeed = exists $Categories{feed};
700          # Save the system error message.      # An error here would be disastrous. Note, however, that we aren't too worried
701          my $sysMessage = $!;      # about losing events. The error log is always available for the occasions where
702          # See if we need a default message.      # we mess up. Note that if debug mode is specified, we do this stuff even in a
703          if (!$message) {      # test environment.
704              # Clean any obvious mode characters and leading spaces from the      eval {
705              # filename.          # Do we need to put this in the RSS feed?
706              my ($fileName) = FindNamePart($fileSpec);          if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
707              $message = "Could not open \"$fileName\"";              # Yes. We now need to compute the date, the link, and the title.
708                # First, the date, in a very specific format.
709                my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
710                    (tz_local_offset() / 30);
711                # Environment data goes in here. We start with the date.
712                my $environment = "$date.  ";
713                # If we need to recap the message (because it's too long to be a title), we'll
714                # put it in here.
715                my $recap;
716                # Copy the message and remove excess space.
717                my $title = $message;
718                $title =~ s/\s+/ /gs;
719                # If it's too long, we have to split it up.
720                if (length $title > 60) {
721                    # Put the full message in the environment string.
722                    $recap = $title;
723                    # Excerpt it as the title.
724                    $title = substr($title, 0, 50) . "...";
725                }
726                # If we have a CGI object, then this is a web error. Otherwise, it's
727                # command-line.
728                if (defined $SavedCGI) {
729                    # We're in a web service. The environment is the user's IP, and the link
730                    # is the URL that got us here.
731                    my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
732                    $environment .= "Event Reported at IP address $key.";
733                    my $url = $SavedCGI->url(-full => 1, -query => 1);
734                    # We need the user agent string and (if available) the referrer.
735                    # The referrer will be the link.
736                    $environment .= "User Agent $ENV{HTTP_USER_AGENT}";
737                    if ($ENV{HTTP_REFERER}) {
738                        my $link = $ENV{HTTP_REFERER};
739                        $environment .= " referred from <a href=\"$link\">$link</a>.";
740                    } else {
741                        $environment .= " referrer unknown.";
742                    }
743                    # Close off the sentence with the original link.
744                    $environment .= " URL of error is <a href=\"$url\">$url</a>.";
745                } else {
746                    # No CGI object, so we're a command-line tool. Use the tracing
747                    # key and the PID as the user identifier, and add the command.
748                    my $key = EmergencyKey();
749                    $environment .= "Event Reported by $key Process $$.";
750                    if ($CommandLine) {
751                        # We're in a StandardSetup script, so we have the real command line.
752                        $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
753                    } elsif ($ENV{_}) {
754                        # We're in a BASH script, so the command has been stored in the _ variable.
755                        $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
756                    }
757                }
758                # Build a GUID. We use the current time, the title, and the process ID,
759                # then digest the result.
760                my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
761                # Finally, the description. This is a stack trace plus various environmental stuff.
762                my $stackTrace = "";
763                my @trace = LongMess();
764                # Only proceed if we got something back.
765                if (scalar(@trace) > 0) {
766                    $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
767                    $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
768                }
769                # We got the stack trace. Now it's time to put it all together.
770                # We have a goofy thing here in that we need to HTML-escape some sections of the description
771                # twice. They will be escaped once here, and then once when written by XML::Simple. They are
772                # unescaped once when processed by the RSS reader, and stuff in the description is treated as
773                # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
774                # our <br>s and <pre>s are used to format the description.
775                $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
776                my $description = "$recap$environment  $stackTrace";
777                # Okay, we have all the pieces. Create a hash of the new event.
778                my $newItem = { title => $title,
779                                description => $description,
780                                category => $LastCategory,
781                                pubDate => $date,
782                                guid => $guid,
783                               };
784                # We need XML capability for this.
785                require XML::Simple;
786                # The RSS document goes in here.
787                my $rss;
788                # Get the name of the RSS file. It's in the FIG temporary directory.
789                my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
790                # Does it exist?
791                if (-s $fileName) {
792                    # Slurp it in.
793                    $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
794                } else {
795                    my $size = -s $fileName;
796                    # Create an empty channel.
797                    $rss = {
798                        channel => {
799                            title => 'NMPDR Warning Feed',
800                            link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
801                            description => "Important messages regarding the status of the NMPDR.",
802                            generator => "NMPDR Trace Facility",
803                            docs => "http://blogs.law.harvard.edu/tech/rss",
804                            item => []
805                        },
806                    };
807          }          }
808          # Terminate with an error using the supplied message and the              # Get the channel object.
809          # error message from the file system.              my $channel = $rss->{channel};
810          Confess("$message: $!");              # Update the last-build date.
811                $channel->{lastBuildDate} = $date;
812                # Get the item array.
813                my $items = $channel->{item};
814                # Insure it has only 100 entries.
815                while (scalar @{$items} > 100) {
816                    pop @{$items};
817                }
818                # Add our new item at the front.
819                unshift @{$items}, $newItem;
820                # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
821                # the requirements for those.
822                my $xml = XML::Simple::XMLout($rss, NoAttr => 1, RootName => undef, XmlDecl => '');
823                # Here we put in the root and declaration. The problem is that the root has to have the version attribute
824                # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
825                $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
826                # We don't use Open here because we can't afford an error.
827                if (open XMLOUT, ">$fileName") {
828                    print XMLOUT $xml;
829                    close XMLOUT;
830                }
831            }
832        };
833        if ($@) {
834            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
835            # (which is a good thing).
836            my $error = $@;
837            Trace("Feed Error: $error") if T(Feed => 0);
838      }      }
     # Return the file handle.  
     return $fileHandle;  
839  }  }
840    
841  =head3 FindNamePart  =head3 Assert
842    
843  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>      Assert($condition1, $condition2, ... $conditionN);
844    
845  Extract the portion of a file specification that contains the file name.  Return TRUE if all the conditions are true. This method can be used in conjunction with
846    the OR operator and the L</Confess> method as a debugging assert.
847    So, for example
848    
849  A file specification is the string passed to an C<open> call. It specifies the file      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
 mode and name. In a truly complex situation, it can specify a pipe sequence. This  
 method assumes that the file name is whatever follows the first angle bracket  
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
850    
851      >>/usr/fig/myfile.txt  Will abort the program with a stack trace if the value of C<$recNum> is negative.
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
852    
853  If the method cannot find a file name using its normal methods, it will return the  =cut
854  whole incoming string.  sub Assert {
855        my $retVal = 1;
856        LOOP: for my $condition (@_) {
857            if (! $condition) {
858                $retVal = 0;
859                last LOOP;
860            }
861        }
862        return $retVal;
863    }
864    
865  =over 4  =head3 Cluck
866    
867  =item fileSpec      Cluck($message);
868    
869  File specification string from which the file name is to be extracted.  Trace the call stack. Note that for best results, you should qualify the call with a
870    trace condition. For example,
871    
872  =item RETURN      Cluck("Starting record parse.") if T(3);
873    
874  Returns a three-element list. The first element contains the file name portion of  will only trace the stack if the trace level for the package is 3 or more.
875  the specified string, or the whole string if a file name cannot be found via normal  
876  methods. The second element contains the start position of the file name portion and  =over 4
877  the third element contains the length.  
878    =item message
879    
880    Message to include in the trace.
881    
882  =back  =back
883    
884  =cut  =cut
885  #: Return Type $;  
886  sub FindNamePart {  sub Cluck {
887      # Get the parameters.      # Get the parameters.
888      my ($fileSpec) = @_;      my ($message) = @_;
889      # Default to the whole input string.      # Trace what's happening.
890      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);      Trace("Stack trace for event: $message");
891      # Parse out the file name if we can.      # Get the stack trace.
892      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {      my @trace = LongMess();
893          $retVal = $2;      # Convert the trace to a series of messages.
894          $len = length $retVal;      for my $line (@trace) {
895          $pos = (length $fileSpec) - (length $3) - $len;          # Replace the tab at the beginning with spaces.
896            $line =~ s/^\t/    /;
897            # Trace the line.
898            Trace($line);
899      }      }
900      # Return the result.      # Issue a warning. This displays the event message and inserts it into the RSS error feed.
901      return ($retVal, $pos, $len);      Warn($message);
902  }  }
903    
904  =head3 OpenDir  =head3 LongMess
905    
906  C<< my @files = OpenDir($dirName, $filtered, $flag); >>      my @lines = Tracer::LongMess();
907    
908  Open a directory and return all the file names. This function essentially performs  Return a stack trace with all tracing methods removed. The return will be in the form of a list
909  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  of message strings.
 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,  
910    
911      my @files = OpenDir("/Volumes/fig/contigs", 1);  =cut
912    
913  is effectively the same as  sub LongMess {
914        # Declare the return variable.
915        my @retVal = ();
916        my $confession = longmess("");
917        for my $line (split /\s*\n/, $confession) {
918            unless ($line =~ /Tracer\.pm/) {
919                # Here we have a line worth keeping. Push it onto the result list.
920                push @retVal, $line;
921            }
922        }
923        # Return the result.
924        return @retVal;
925    }
926    
927      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  =head3 ScriptSetup (deprecated)
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
928    
929  Similarly, the following code      my ($cgi, $varHash) = ScriptSetup($noTrace);
930    
931      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  Perform standard tracing and debugging setup for scripts. The value returned is
932    the CGI object followed by a pre-built variable hash. At the end of the script,
933    the client should call L</ScriptFinish> to output the web page.
934    
935  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  This method calls L</ETracing> to configure tracing, which allows the tracing
936  automatically returns an empty list if the directory fails to open.  to be configured via the emergency tracing form on the debugging control panel.
937    Tracing will then be turned on automatically for all programs that use the L</ETracing>
938    method, which includes every program that uses this method or L</StandardSetup>.
939    
940  =over 4  =over 4
941    
942  =item dirName  =item noTrace (optional)
   
 Name of the directory to open.  
   
 =item filtered  
943    
944  TRUE if files whose names begin with a period (C<.>) should be automatically removed  If specified, tracing will be suppressed. This is useful if the script wants to set up
945  from the list, else FALSE.  tracing manually.
946    
947  =item flag  =item RETURN
948    
949  TRUE if a failure to open is okay, else FALSE  Returns a two-element list consisting of a CGI query object and a variable hash for
950    the output page.
951    
952  =back  =back
953    
954  =cut  =cut
955  #: Return Type @;  
956  sub OpenDir {  sub ScriptSetup {
957      # Get the parameters.      # Get the parameters.
958      my ($dirName, $filtered, $flag) = @_;      my ($noTrace) = @_;
959      # Declare the return variable.      # Get the CGI query object.
960      my @retVal = ();      my $cgi = CGI->new();
961      # Open the directory.      # Set up tracing if it's not suppressed.
962      if (opendir(my $dirHandle, $dirName)) {      ETracing($cgi) unless $noTrace;
963          # The directory opened successfully. Get the appropriate list according to the      # Create the variable hash.
964          # strictures of the filter parameter.      my $varHash = { results => '' };
965          if ($filtered) {      # Return the query object and variable hash.
966              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;      return ($cgi, $varHash);
         } else {  
             @retVal = readdir $dirHandle;  
         }  
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
     }  
     # Return the result.  
     return @retVal;  
967  }  }
968    
969  =head3 SetLevel  =head3 ETracing
970    
971  C<< Tracer::SetLevel($newLevel); >>      ETracing($parameter);
972    
973  Modify the trace level. A higher trace level will cause more messages to appear.  Set up emergency tracing. Emergency tracing is tracing that is turned
974    on automatically for any program that calls this method. The emergency
975    tracing parameters are stored in a a file identified by a tracing key.
976    If this method is called with a CGI object, then the tracing key is
977    taken from a cookie. If it is called with no parameters, then the tracing
978    key is taken from an environment variable. If it is called with a string,
979    the tracing key is that string.
980    
981  =over 4  =over 4
982    
983  =item newLevel  =item parameter
984    
985  Proposed new trace level.  A parameter from which the tracing key is computed. If it is a scalar,
986    that scalar is used as the tracing key. If it is a CGI object, the
987    tracing key is taken from the C<IP> cookie. If it is omitted, the
988    tracing key is taken from the C<TRACING> environment variable. If it
989    is a CGI object and emergency tracing is not on, the C<Trace> and
990    C<TF> parameters will be used to determine the type of tracing.
991    
992  =back  =back
993    
994  =cut  =cut
995    
996  sub SetLevel {  sub ETracing {
997      $TraceLevel = $_[0];      # Get the parameter.
998        my ($parameter) = @_;
999        # Check for CGI mode.
1000        if (defined $parameter && ref $parameter eq 'CGI') {
1001            $SavedCGI = $parameter;
1002        } else {
1003            $SavedCGI = undef;
1004        }
1005        # Default to no tracing except errors.
1006        my ($tracing, $dest) = ("0", "WARN");
1007        # Check for emergency tracing.
1008        my $tkey = EmergencyKey($parameter);
1009        my $emergencyFile = EmergencyFileName($tkey);
1010        if (-e $emergencyFile) {
1011            # We have the file. Read in the data.
1012            my @tracing = GetFile($emergencyFile);
1013            # Pull off the time limit.
1014            my $expire = shift @tracing;
1015            # Convert it to seconds.
1016            $expire *= 3600;
1017            # Check the file data.
1018            my $stat = stat($emergencyFile);
1019            my ($now) = gettimeofday;
1020            if ($now - $stat->mtime > $expire) {
1021                # Delete the expired file.
1022                unlink $emergencyFile;
1023            } else {
1024                # Emergency tracing is on. Pull off the destination and
1025                # the trace level;
1026                $dest = shift @tracing;
1027                my $level = shift @tracing;
1028                # Convert the destination to a real tracing destination.
1029                # temp directory.
1030                $dest = EmergencyTracingDest($tkey, $dest);
1031                # Insure Tracer is specified.
1032                my %moduleHash = map { $_ => 1 } @tracing;
1033                $moduleHash{Tracer} = 1;
1034                # Set the trace parameter.
1035                $tracing = join(" ", $level, sort keys %moduleHash);
1036            }
1037        } elsif (defined $SavedCGI) {
1038            # There's no emergency tracing, but we have a CGI object, so check
1039            # for tracing from the form parameters.
1040            if ($SavedCGI->param('Trace')) {
1041                # Here the user has requested tracing via a form.
1042                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1043                $tracing = $SavedCGI->param('Trace') . " Tracer";
1044            }
1045        }
1046        # Setup the tracing we've determined from all the stuff above.
1047        TSetup($tracing, $dest);
1048        # Check to see if we're a web script.
1049        if (defined $SavedCGI) {
1050            # Yes we are. Trace the form and environment data.
1051            TraceParms($SavedCGI);
1052            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1053            # emitted by the script in its raw form.
1054            if (T(Raw => 3)) {
1055                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1056  }  }
   
 =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;  
1057  }  }
   
 # Pad a number to 2 digits.  
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
1058  }  }
1059    
1060  =head3 LogErrors  =head3 EmergencyFileName
1061    
1062  C<< Tracer::LogErrors($fileName); >>      my $fileName = Tracer::EmergencyFileName($tkey);
1063    
1064  Route the standard error output to a log file.  Return the emergency tracing file name. This is the file that specifies
1065    the tracing information.
1066    
1067  =over 4  =over 4
1068    
1069  =item fileName  =item tkey
1070    
1071  Name of the file to receive the error output.  Tracing key for the current program.
1072    
1073    =item RETURN
1074    
1075    Returns the name of the file to contain the emergency tracing information.
1076    
1077  =back  =back
1078    
1079  =cut  =cut
1080    
1081  sub LogErrors {  sub EmergencyFileName {
1082      # Get the file name.      # Get the parameters.
1083      my ($fileName) = @_;      my ($tkey) = @_;
1084      # Open the file as the standard error output.      # Compute the emergency tracing file name.
1085      open STDERR, '>', $fileName;      return "$FIG_Config::temp/Emergency$tkey.txt";
1086  }  }
1087    
1088  =head3 ReadOptions  =head3 EmergencyFileTarget
   
 C<< my %options = Tracer::ReadOptions($fileName); >>  
   
 Read a set of options from a file. Each option is encoded in a line of text that has the  
 format  
1089    
1090  I<optionName>C<=>I<optionValue>C<; >I<comment>      my $fileName = Tracer::EmergencyFileTarget($tkey);
1091    
1092  The option name must consist entirely of letters, digits, and the punctuation characters  Return the emergency tracing target file name. This is the file that receives
1093  C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  the tracing output for file-based tracing.
 character is a semi-colon will be ignored. The return hash will map each option name to  
 the corresponding option value.  
1094    
1095  =over 4  =over 4
1096    
1097  =item fileName  =item tkey
1098    
1099  Name of the file containing the option data.  Tracing key for the current program.
1100    
1101  =item RETURN  =item RETURN
1102    
1103  Returns a hash mapping the option names specified in the file to their corresponding option  Returns the name of the file to contain the trace output.
 value.  
1104    
1105  =back  =back
1106    
1107  =cut  =cut
1108    
1109  sub ReadOptions {  sub EmergencyFileTarget {
1110      # Get the parameters.      # Get the parameters.
1111      my ($fileName) = @_;      my ($tkey) = @_;
1112      # Open the file.      # Compute the emergency tracing file name.
1113      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");      return "$FIG_Config::temp/trace$tkey.log";
     # Count the number of records read.  
     my ($records, $comments) = 0;  
     # Create the return hash.  
     my %retVal = ();  
     # Loop through the file, accumulating key-value pairs.  
     while (my $line = <CONFIGFILE>) {  
         # Denote we've read a line.  
         $records++;  
         # Determine the line type.  
         if ($line =~ /^\s*[\n\r]/) {  
             # A blank line is a comment.  
             $comments++;  
         } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {  
             # Here we have an option assignment.  
             retVal{$1} = $2;  
         } elsif ($line =~ /^\s*;/) {  
             # Here we have a text comment.  
             $comments++;  
         } else {  
             # Here we have an invalid line.  
             Trace("Invalid option statement in record $records.") if T(0);  
         }  
     }  
     # Return the hash created.  
     return %retVal;  
1114  }  }
1115    
1116  =head3 GetOptions  =head3 EmergencyTracingDest
1117    
1118  C<< Tracer::GetOptions(\%defaults, \%options); >>      my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1119    
1120  Merge a specified set of options into a table of defaults. This method takes two hash references  This method converts an emergency tracing destination to a real
1121  as input and uses the data from the second to update the first. If the second does not exist,  tracing destination. The main difference is that if the
1122  there will be no effect. An error will be thrown if one of the entries in the second hash does not  destination is C<FILE> or C<APPEND>, we convert it to file
1123  exist in the first.  output. If the destination is C<DUAL>, we convert it to file
1124    and standard output.
1125    
1126  Consider the following example.  =over 4
1127    
1128  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  =item tkey
1129    
1130  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  Tracing key for this environment.
 B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  
 B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and  
 the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  
 will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  
1131    
1132  C<< {databaseType => 'Oracle'} >>  =item myDest
1133    
1134  an error will occur because the B<databaseType> option does not exist.  Destination from the emergency tracing file.
1135    
1136  =over 4  =item RETURN
1137    
1138  =item defaults  Returns a destination that can be passed into L</TSetup>.
1139    
1140  Table of default option values.  =back
1141    
1142  =item options  =cut
1143    
1144  Table of overrides, if any.  sub EmergencyTracingDest {
1145        # Get the parameters.
1146        my ($tkey, $myDest) = @_;
1147        # Declare the return variable.
1148        my $retVal = $myDest;
1149        # Process according to the destination value.
1150        if ($myDest eq 'FILE') {
1151            $retVal = ">" . EmergencyFileTarget($tkey);
1152        } elsif ($myDest eq 'APPEND') {
1153            $retVal = ">>" . EmergencyFileTarget($tkey);
1154        } elsif ($myDest eq 'DUAL') {
1155            $retVal = "+>" . EmergencyFileTarget($tkey);
1156        } elsif ($myDest eq 'WARN') {
1157            $retVal = "WARN";
1158        }
1159        # Return the result.
1160        return $retVal;
1161    }
1162    
1163  =item RETURN  =head3 Emergency
1164    
1165  Returns a reference to the default table passed in as the first parameter.      Emergency($key, $hours, $dest, $level, @modules);
1166    
1167    Turn on emergency tracing. This method is normally invoked over the web from
1168    a debugging console, but it can also be called by the C<trace.pl> script.
1169    The caller specifies the duration of the emergency in hours, the desired tracing
1170    destination, the trace level, and a list of the trace modules to activate.
1171    For the length of the duration, when a program in an environment with the
1172    specified tracing key active invokes a Sprout CGI script, tracing will be
1173    turned on automatically. See L</TSetup> for more about tracing setup and
1174    L</ETracing> for more about emergency tracing.
1175    
1176    =over 4
1177    
1178    =item tkey
1179    
1180    The tracing key. This is used to identify the control file and the trace file.
1181    
1182    =item hours
1183    
1184    Number of hours to keep emergency tracing alive.
1185    
1186    =item dest
1187    
1188    Tracing destination. If no path information is specified for a file
1189    destination, it is put in the FIG temporary directory.
1190    
1191    =item level
1192    
1193    Tracing level. A higher level means more trace messages.
1194    
1195    =item modules
1196    
1197    A list of the tracing modules to activate.
1198    
1199  =back  =back
1200    
1201  =cut  =cut
1202    
1203  sub GetOptions {  sub Emergency {
1204      # Get the parameters.      # Get the parameters.
1205      my ($defaults, $options) = @_;      my ($tkey, $hours, $dest, $level, @modules) = @_;
1206      # Check for overrides.      # Create the emergency file.
1207      if ($options) {      my $specFile = EmergencyFileName($tkey);
1208          # Loop through the overrides.      my $outHandle = Open(undef, ">$specFile");
1209          while (my ($option, $setting) = each %{$options}) {      print $outHandle join("\n", $hours, $dest, $level, @modules, "");
             # Insure this override exists.  
             if (!exists $defaults->{$option}) {  
                 croak "Unrecognized option $option encountered.";  
             } else {  
                 # Apply the override.  
                 $defaults->{$option} = $setting;  
             }  
         }  
     }  
     # Return the merged table.  
     return $defaults;  
1210  }  }
1211    
1212  =head3 MergeOptions  =head3 EmergencyKey
1213    
1214  C<< Tracer::MergeOptions(\%table, \%defaults); >>      my $tkey = EmergencyKey($parameter);
1215    
1216  Merge default values into a hash table. This method looks at the key-value pairs in the  Return the Key to be used for emergency tracing. This could be an IP address,
1217  second (default) hash, and if a matching key is not found in the first hash, the default   a session ID, or a user name, depending on the environment.
 pair is copied in. The process is similar to L</GetOptions>, but there is no error-  
 checking and no return value.  
1218    
1219  =over 4  =over 4
1220    
1221  =item table  =item parameter
1222    
1223  Hash table to be updated with the default values.  Parameter defining the method for finding the tracing key. If it is a scalar,
1224    then it is presumed to be the tracing key itself. If it is a CGI object, then
1225    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1226    taken from the C<TRACING> environment variable.
1227    
1228  =item defaults  =item RETURN
1229    
1230  Default values to be merged into the first hash table if they are not already present.  Returns the key to be used for labels in emergency tracing.
1231    
1232  =back  =back
1233    
1234  =cut  =cut
1235    
1236  sub MergeOptions {  sub EmergencyKey {
1237      # Get the parameters.      # Get the parameters.
1238      my ($table, $defaults) = @_;      my ($parameter) = @_;
1239      # Loop through the defaults.      # Declare the return variable.
1240      while (my ($key, $value) = each %{$defaults}) {      my $retVal;
1241          if (!exists $table->{$key}) {      # Determine the parameter type.
1242              $table->{$key} = $value;      if (! defined $parameter) {
1243          }          # Here we're supposed to check the environment. If that fails, we
1244            # get the effective login ID.
1245            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1246        } else {
1247            my $ptype = ref $parameter;
1248            if ($ptype eq 'CGI') {
1249                # Here we were invoked from a web page. Look for a cookie.
1250                $retVal = $parameter->cookie('IP');
1251            } elsif (! $ptype) {
1252                # Here the key was passed in.
1253                $retVal = $parameter;
1254            }
1255        }
1256        # If no luck finding a key, use the PID.
1257        if (! defined $retVal) {
1258            $retVal = $$;
1259      }      }
1260        # Return the result.
1261        return $retVal;
1262  }  }
1263    
 =head3 Trace  
1264    
1265  C<< Trace($message); >>  =head3 TraceParms
1266    
1267  Write a trace message to the target location specified in L</TSetup>. If there has not been      Tracer::TraceParms($cgi);
1268  any prior call to B<TSetup>.  
1269    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1270    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1271    
1272  =over 4  =over 4
1273    
1274  =item message  =item cgi
1275    
1276  Message to write.  CGI query object containing the parameters to trace.
1277    
1278  =back  =back
1279    
1280  =cut  =cut
1281    
1282  sub Trace {  sub TraceParms {
1283      # Get the parameters.      # Get the parameters.
1284      my ($message) = @_;      my ($cgi) = @_;
1285      # Get the timestamp.      if (T(CGI => 2)) {
1286      my $timeStamp = Now();          # Here we trace the GET-style URL for the script.
1287      # Format the message. Note we strip off any line terminators at the end.          Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1288      my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);      }
1289      # Process according to the destination.      if (T(CGI => 3)) {
1290      if ($Destination eq "TEXT") {          # Here we want to trace the parameter data.
1291          # Write the message to the standard output.          my @names = $cgi->param;
1292          print "$formatted\n";          for my $parmName (sort @names) {
1293      } elsif ($Destination eq "ERROR") {              # Note we skip the Trace parameters, which are for our use only.
1294          # Write the message to the error output.              if ($parmName ne 'Trace' && $parmName ne 'TF') {
1295          print STDERR "$formatted\n";                  my @values = $cgi->param($parmName);
1296      } elsif ($Destination eq "QUEUE") {                  Trace("[CGI] $parmName = " . join(", ", @values));
1297          # Push the message into the queue.              }
1298          push @Queue, "$formatted";          }
1299      } elsif ($Destination eq "HTML") {          # Display the request method.
1300          # Convert the message to HTML and write it to the standard output.          my $method = $cgi->request_method();
1301          my $escapedMessage = CGI::escapeHTML($message);          Trace("Method: $method");
1302          print "<p>$formatted</p>\n";      }
1303      } elsif ($Destination eq "WARN") {      if (T(CGI => 4)) {
1304         # Emit the message as a warning.          # Here we want the environment data too.
1305         warn $message;          for my $envName (sort keys %ENV) {
1306      } elsif ($Destination =~ m/^>>/) {              Trace("[ENV] $envName = $ENV{$envName}");
         # 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";  
1307          }          }
1308      }      }
1309  }  }
1310    
1311  =head3 T  =head3 TraceImages
1312    
1313  C<< my $switch = T($category, $traceLevel); >>      Tracer::TraceImages($htmlString);
1314    
1315      or  Trace information about all of an html document's images. The tracing
1316    will be for type "IMG" at level 3. The image's source string
1317    will be displayed. This is generally either the URL of the image or
1318    raw data for the image itself. If the source is too long, only the first 300
1319    characters will be shown at trace level 3. The entire source will be shown,
1320    however, at trace level 4. This method is not very smart, and might catch
1321    Javascript code, but it is still useful when debugging the arcane
1322    behavior of images in multiple browser environments.
1323    
1324  C<< my $switch = T($traceLevel); >>  =over 4
1325    
1326  Return TRUE if the trace level is at or above a specified value and the specified category  =item htmlString
 is active, else FALSE. If no category is specified, the caller's package name is used.  
1327    
1328  =over 4  HTML text for an outgoing web page.
1329    
1330  =item category  =back
1331    
1332  Category to which the message belongs. If not specified, the caller's package name is  =cut
 used.  
1333    
1334  =item traceLevel  sub TraceImages {
1335        # Only proceed if we're at the proper trace level.
1336        if (T(IMG => 3)) {
1337            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1338            # into a variable called "$htmlString". This is because we expect html strings to be
1339            # long, and don't want to copy them any more than we have to.
1340            Trace(length($_[0]) . " characters in web page.");
1341            # Loop through the HTML, culling image tags.
1342            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1343                # Extract the source string and determine whether or not it's too long.
1344                my $srcString = $1;
1345                my $pos = pos($_[0]) - length($srcString);
1346                my $excess = length($srcString) - 300;
1347                # We'll put the display string in here.
1348                my $srcDisplay = $srcString;
1349                # If it's a data string, split it at the comma.
1350                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1351                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1352                # a long string, however, we only show the first 300 characters.
1353                if ($excess > 0 && ! T(IMG => 4)) {
1354                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1355                }
1356                # Output the trace message.
1357                Trace("Image tag at position $pos:\n$srcDisplay");
1358            }
1359        }
1360    }
1361    
 Relevant tracing level.  
1362    
1363  =item RETURN  =head3 ScriptFinish (deprecated)
1364    
1365  TRUE if a message at the specified trace level would appear in the trace, else FALSE.      ScriptFinish($webData, $varHash);
1366    
1367    Output a web page at the end of a script. Either the string to be output or the
1368    name of a template file can be specified. If the second parameter is omitted,
1369    it is assumed we have a string to be output; otherwise, it is assumed we have the
1370    name of a template file. The template should have the variable C<DebugData>
1371    specified in any form that invokes a standard script. If debugging mode is turned
1372    on, a form field will be put in that allows the user to enter tracing data.
1373    Trace messages will be placed immediately before the terminal C<BODY> tag in
1374    the output, formatted as a list.
1375    
1376    A typical standard script would loook like the following.
1377    
1378        BEGIN {
1379            # Print the HTML header.
1380            print "CONTENT-TYPE: text/html\n\n";
1381        }
1382        use Tracer;
1383        use CGI;
1384        use FIG;
1385        # ... more uses ...
1386    
1387        my ($cgi, $varHash) = ScriptSetup();
1388        eval {
1389            # ... get data from $cgi, put it in $varHash ...
1390        };
1391        if ($@) {
1392            Trace("Script Error: $@") if T(0);
1393        }
1394        ScriptFinish("Html/MyTemplate.html", $varHash);
1395    
1396    The idea here is that even if the script fails, you'll see trace messages and
1397    useful output.
1398    
1399    =over 4
1400    
1401    =item webData
1402    
1403    A string containing either the full web page to be written to the output or the
1404    name of a template file from which the page is to be constructed. If the name
1405    of a template file is specified, then the second parameter must be present;
1406    otherwise, it must be absent.
1407    
1408    =item varHash (optional)
1409    
1410    If specified, then a reference to a hash mapping variable names for a template
1411    to their values. The template file will be read into memory, and variable markers
1412    will be replaced by data in this hash reference.
1413    
1414  =back  =back
1415    
1416  =cut  =cut
1417    
1418  sub T {  sub ScriptFinish {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
1419          # Get the parameters.          # Get the parameters.
1420          my ($category, $traceLevel) = @_;      my ($webData, $varHash) = @_;
1421          if (!defined $traceLevel) {      # Check for a template file situation.
1422              # Here we have no category, so we need to get the calling package.      my $outputString;
1423              # The calling package is normally the first parameter. If it is      if (defined $varHash) {
1424              # omitted, the first parameter will be the tracelevel. So, the          # Here we have a template file. We need to determine the template type.
1425              # first thing we do is shift the so-called category into the          my $template;
1426              # $traceLevel variable where it belongs.          if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1427              $traceLevel = $category;              $template = "$FIG_Config::template_url/$webData";
             my ($package, $fileName, $line) = caller;  
             # If there is no calling package, we default to "main".  
             if (!$package) {  
                 $category = "main";  
1428              } else {              } else {
1429                  $category = $package;              $template = "<<$webData";
1430              }              }
1431            $outputString = PageBuilder::Build($template, $varHash, "Html");
1432        } else {
1433            # Here the user gave us a raw string.
1434            $outputString = $webData;
1435          }          }
1436          # Save the category name.      # Check for trace messages.
1437          $LastCategory = $category;      if ($Destination ne "NONE" && $TraceLevel > 0) {
1438          # Convert it to lower case before we hash it.          # We have trace messages, so we want to put them at the end of the body. This
1439          $category = lc $category;          # is either at the end of the whole string or at the beginning of the BODY
1440          # Use the category and tracelevel to compute the result.          # end-tag.
1441          if (ref $traceLevel) {          my $pos = length $outputString;
1442              Confess("Bad trace level.");          if ($outputString =~ m#</body>#gi) {
1443          } elsif (ref $TraceLevel) {              $pos = (pos $outputString) - 7;
1444              Confess("Bad trace config.");          }
1445            # If the trace messages were queued, we unroll them. Otherwise, we display the
1446            # destination.
1447            my $traceHtml;
1448            if ($Destination eq "QUEUE") {
1449                $traceHtml = QTrace('Html');
1450            } elsif ($Destination =~ /^>>(.+)$/) {
1451                # Here the tracing output it to a file. We code it as a hyperlink so the user
1452                # can copy the file name into the clipboard easily.
1453                my $actualDest = $1;
1454                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1455            } else {
1456                # Here we have one of the special destinations.
1457                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1458            }
1459            substr $outputString, $pos, 0, $traceHtml;
1460        }
1461        # Write the output string.
1462        print $outputString;
1463    }
1464    
1465    =head2 Command-Line Utility Methods
1466    
1467    =head3 SendSMS
1468    
1469        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1470    
1471    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1472    user name, password, and API ID for the relevant account in the hash reference variable
1473    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1474    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1475    is C<2561022>, then the FIG_Config file must contain
1476    
1477        $phone =  { user => 'BruceTheHumanPet',
1478                    password => 'silly',
1479                    api_id => '2561022' };
1480    
1481    The original purpose of this method was to insure Bruce would be notified immediately when the
1482    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1483    when you call this method.
1484    
1485    The message ID will be returned if successful, and C<undef> if an error occurs.
1486    
1487    =over 4
1488    
1489    =item phoneNumber
1490    
1491    Phone number to receive the message, in international format. A United States phone number
1492    would be prefixed by "1". A British phone number would be prefixed by "44".
1493    
1494    =item msg
1495    
1496    Message to send to the specified phone.
1497    
1498    =item RETURN
1499    
1500    Returns the message ID if successful, and C<undef> if the message could not be sent.
1501    
1502    =back
1503    
1504    =cut
1505    
1506    sub SendSMS {
1507        # Get the parameters.
1508        my ($phoneNumber, $msg) = @_;
1509        # Declare the return variable. If we do not change it, C<undef> will be returned.
1510        my $retVal;
1511        # Only proceed if we have phone support.
1512        if (! defined $FIG_Config::phone) {
1513            Trace("Phone support not present in FIG_Config.") if T(1);
1514        } else {
1515            # Get the phone data.
1516            my $parms = $FIG_Config::phone;
1517            # Get the Clickatell URL.
1518            my $url = "http://api.clickatell.com/http/";
1519            # Create the user agent.
1520            my $ua = LWP::UserAgent->new;
1521            # Request a Clickatell session.
1522            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1523                                         password => $parms->{password},
1524                                         api_id => $parms->{api_id},
1525                                         to => $phoneNumber,
1526                                         text => $msg});
1527            # Check for an error.
1528            if (! $resp->is_success) {
1529                Trace("Alert failed.") if T(1);
1530            } else {
1531                # Get the message ID.
1532                my $rstring = $resp->content;
1533                if ($rstring =~ /^ID:\s+(.*)$/) {
1534                    $retVal = $1;
1535                } else {
1536                    Trace("Phone attempt failed with $rstring") if T(1);
1537                }
1538            }
1539        }
1540        # Return the result.
1541        return $retVal;
1542    }
1543    
1544    =head3 StandardSetup
1545    
1546        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1547    
1548    This method performs standard command-line parsing and tracing setup. The return
1549    values are a hash of the command-line options and a list of the positional
1550    parameters. Tracing is automatically set up and the command-line options are
1551    validated.
1552    
1553    This is a complex method that does a lot of grunt work. The parameters can
1554    be more easily understood, however, once they are examined individually.
1555    
1556    The I<categories> parameter is the most obtuse. It is a reference to a list of
1557    special-purpose tracing categories. Most tracing categories are PERL package
1558    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1559    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1560    
1561        ["Sprout", "SproutLoad", "ERDB"]
1562    
1563    This would cause trace messages in the specified three packages to appear in
1564    the output. There are two special tracing categories that are automatically
1565    handled by this method. In other words, if you used L</TSetup> you would need
1566    to include these categories manually, but if you use this method they are turned
1567    on automatically.
1568    
1569    =over 4
1570    
1571    =item SQL
1572    
1573    Traces SQL commands and activity.
1574    
1575    =item Tracer
1576    
1577    Traces error messages and call stacks.
1578    
1579    =back
1580    
1581    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1582    The trace level is specified using the C<-trace> command-line option. For example,
1583    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1584    all tracing at level 3.
1585    
1586        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1587    
1588    Standard tracing is output to the standard output and echoed to the file
1589    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1590    process ID. You can also specify the C<user> parameter to put a user ID
1591    instead of a process ID in the trace file name. So, for example
1592    
1593    The default trace level is 2. To get all messages, specify a trace level of 4.
1594    For a genome-by-genome update, use 3.
1595    
1596        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1597    
1598    would send the trace output to C<traceBruce.log> in the temporary directory.
1599    
1600    The I<options> parameter is a reference to a hash containing the command-line
1601    options, their default values, and an explanation of what they mean. Command-line
1602    options may be in the form of switches or keywords. In the case of a switch, the
1603    option value is 1 if it is specified and 0 if it is not specified. In the case
1604    of a keyword, the value is separated from the option name by an equal sign. You
1605    can see this last in the command-line example above.
1606    
1607    You can specify a different default trace level by setting C<$options->{trace}>
1608    prior to calling this method.
1609    
1610    An example at this point would help. Consider, for example, the command-line utility
1611    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1612    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1613    the following code.
1614    
1615        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1616                            { safe => [0, "use database transactions"],
1617                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1618                              start => [' ', "start with this genome"],
1619                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1620                            "<command> <transactionDirectory> <IDfile>",
1621                          @ARGV);
1622    
1623    
1624    The call to C<ParseCommand> specifies the default values for the options and
1625    stores the actual options in a hash that is returned as C<$options>. The
1626    positional parameters are returned in C<@parameters>.
1627    
1628    The following is a sample command line for C<TransactFeatures>.
1629    
1630        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1631    
1632    Single and double hyphens are equivalent. So, you could also code the
1633    above command as
1634    
1635        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1636    
1637    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1638    parameters, and would find themselves in I<@parameters> after executing the
1639    above code fragment. The tracing would be set to level 2, and the categories
1640    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1641    and C<DocUtils> was included because it came in within the first parameter
1642    to this method. The I<$options> hash would be
1643    
1644        { trace => 2, sql => 0, safe => 0,
1645          noAlias => 1, start => ' ', tblFiles => 0 }
1646    
1647    Use of C<StandardSetup> in this way provides a simple way of performing
1648    standard tracing setup and command-line parsing. Note that the caller is
1649    not even aware of the command-line switches C<-trace> and C<-sql>, which
1650    are used by this method to control the tracing. If additional tracing features
1651    need to be added in the future, they can be processed by this method without
1652    upsetting the command-line utilities.
1653    
1654    If the C<background> option is specified on the command line, then the
1655    standard and error outputs will be directed to files in the temporary
1656    directory, using the same suffix as the trace file. So, if the command
1657    line specified
1658    
1659        -user=Bruce -background
1660    
1661    then the trace output would go to C<traceBruce.log>, the standard output to
1662    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1663    simplify starting a command in the background.
1664    
1665    The user name is also used as the tracing key for L</Emergency Tracing>.
1666    Specifying a value of C<E> for the trace level causes emergency tracing to
1667    be used instead of custom tracing. If the user name is not specified,
1668    the tracing key is taken from the C<Tracing> environment variable. If there
1669    is no value for that variable, the tracing key will be computed from the active
1670    login ID.
1671    
1672    Since the default situation in StandardSetup is to trace to the standard
1673    output, errors that occur in command-line scripts will not generate
1674    RSS events. To force the events, use the C<warn> option.
1675    
1676        TransactFeatures -background -warn register ../xacts IDs.tbl
1677    
1678    Finally, if the special option C<-help> is specified, the option
1679    names will be traced at level 0 and the program will exit without processing.
1680    This provides a limited help capability. For example, if the user enters
1681    
1682        TransactFeatures -help
1683    
1684    he would see the following output.
1685    
1686        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1687            -trace    tracing level (default E)
1688            -sql      trace SQL commands
1689            -safe     use database transactions
1690            -noAlias  do not expect aliases in CHANGE transactions
1691            -start    start with this genome
1692            -tblFiles output TBL files containing the corrected IDs
1693    
1694    The caller has the option of modifying the tracing scheme by placing a value
1695    for C<trace> in the incoming options hash. The default value can be overridden,
1696    or the tracing to the standard output can be turned off by suffixing a minus
1697    sign to the trace level. So, for example,
1698    
1699        { trace => [0, "tracing level (default 0)"],
1700           ...
1701    
1702    would set the default trace level to 0 instead of E, while
1703    
1704        { trace => ["2-", "tracing level (default 2)"],
1705           ...
1706    
1707    would set the default to 2, but trace only to the log file, not to the
1708    standard output.
1709    
1710    The parameters to this method are as follows.
1711    
1712    =over 4
1713    
1714    =item categories
1715    
1716    Reference to a list of tracing category names. These should be names of
1717    packages whose internal workings will need to be debugged to get the
1718    command working.
1719    
1720    =item options
1721    
1722    Reference to a hash containing the legal options for the current command mapped
1723    to their default values and descriptions. The user can override the defaults
1724    by specifying the options as command-line switches prefixed by a hyphen.
1725    Tracing-related options may be added to this hash. If the C<-h> option is
1726    specified on the command line, the option descriptions will be used to
1727    explain the options. To turn off tracing to the standard output, add a
1728    minus sign to the value for C<trace> (see above).
1729    
1730    =item parmHelp
1731    
1732    A string that vaguely describes the positional parameters. This is used
1733    if the user specifies the C<-h> option.
1734    
1735    =item argv
1736    
1737    List of command line parameters, including the option switches, which must
1738    precede the positional parameters and be prefixed by a hyphen.
1739    
1740    =item RETURN
1741    
1742    Returns a list. The first element of the list is the reference to a hash that
1743    maps the command-line option switches to their values. These will either be the
1744    default values or overrides specified on the command line. The remaining
1745    elements of the list are the position parameters, in order.
1746    
1747    =back
1748    
1749    =cut
1750    
1751    sub StandardSetup {
1752        # Get the parameters.
1753        my ($categories, $options, $parmHelp, @argv) = @_;
1754        # Get the default tracing key.
1755        my $tkey = EmergencyKey();
1756        # Save the command line.
1757        $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1758        # Add the tracing options.
1759        if (! exists $options->{trace}) {
1760            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1761        }
1762        $options->{sql} = [0, "turn on SQL tracing"];
1763        $options->{help} = [0, "display command-line options"];
1764        $options->{user} = [$tkey, "tracing key"];
1765        $options->{background} = [0, "spool standard and error output"];
1766        $options->{warn} = [0, "send errors to RSS feed"];
1767        # Create a parsing hash from the options hash. The parsing hash
1768        # contains the default values rather than the default value
1769        # and the description. While we're at it, we'll memorize the
1770        # length of the longest option name.
1771        my $longestName = 0;
1772        my %parseOptions = ();
1773        for my $key (keys %{$options}) {
1774            if (length $key > $longestName) {
1775                $longestName = length $key;
1776            }
1777            $parseOptions{$key} = $options->{$key}->[0];
1778        }
1779        # Parse the command line.
1780        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1781        # Get the logfile suffix.
1782        my $suffix = $retOptions->{user};
1783        # Check for background mode.
1784        if ($retOptions->{background}) {
1785            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1786            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1787            open STDOUT, ">$outFileName";
1788            open STDERR, ">$errFileName";
1789            # Check for phone support. If we have phone support and a phone number,
1790            # we want to turn it on.
1791            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1792                $retOptions->{phone} = $ENV{PHONE};
1793            }
1794        }
1795        # Now we want to set up tracing. First, we need to know if the user
1796        # wants emergency tracing.
1797        if ($retOptions->{trace} eq 'E') {
1798            ETracing($retOptions->{user});
1799        } else {
1800            # Here the tracing is controlled from the command line.
1801            my @cats = @{$categories};
1802            if ($retOptions->{sql}) {
1803                push @cats, "SQL";
1804            }
1805            if ($retOptions->{warn}) {
1806                push @cats, "Feed";
1807            }
1808            # Add the default categories.
1809            push @cats, "Tracer";
1810            # Next, we create the category string by joining the categories.
1811            my $cats = join(" ", @cats);
1812            # Check to determine whether or not the caller wants to turn off tracing
1813            # to the standard output.
1814            my $traceLevel = $retOptions->{trace};
1815            my $textOKFlag = 1;
1816            if ($traceLevel =~ /^(.)-/) {
1817                $traceLevel = $1;
1818                $textOKFlag = 0;
1819            }
1820            # Now we set up the trace mode.
1821            my $traceMode;
1822            # Verify that we can open a file in the FIG temporary directory.
1823            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1824            if (open TESTTRACE, ">$traceFileName") {
1825                # Here we can trace to a file.
1826                $traceMode = ">$traceFileName";
1827                if ($textOKFlag) {
1828                    # Echo to standard output if the text-OK flag is set.
1829                    $traceMode = "+$traceMode";
1830                }
1831                # Close the test file.
1832                close TESTTRACE;
1833            } else {
1834                # Here we can't trace to a file. Complain about this.
1835                warn "Could not open trace file $traceFileName: $!\n";
1836                # We trace to the standard output if it's
1837                # okay, and the error log otherwise.
1838                if ($textOKFlag) {
1839                    $traceMode = "TEXT";
1840                } else {
1841                    $traceMode = "WARN";
1842                }
1843            }
1844            # Now set up the tracing.
1845            TSetup("$traceLevel $cats", $traceMode);
1846        }
1847        # Check for the "help" option. If it is specified, dump the command-line
1848        # options and exit the program.
1849        if ($retOptions->{help}) {
1850            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1851            print "$1 [options] $parmHelp\n";
1852            for my $key (sort keys %{$options}) {
1853                my $name = Pad($key, $longestName, 0, ' ');
1854                my $desc = $options->{$key}->[1];
1855                if ($options->{$key}->[0]) {
1856                    $desc .= " (default " . $options->{$key}->[0] . ")";
1857                }
1858                print "  $name $desc\n";
1859            }
1860            exit(0);
1861          }          }
1862          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));      # Trace the options, if applicable.
1863        if (T(3)) {
1864            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1865            Trace("Selected options: " . join(", ", sort @parms) . ".");
1866      }      }
1867      # Return the computed result.      # Return the parsed parameters.
1868      return $retVal;      return ($retOptions, @retParameters);
1869  }  }
1870    
1871  =head3 ParseCommand  =head3 ReadOptions
   
 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 >>  
   
 then at the end of the invocation, C<$options> will be  
1872    
1873  C<< { errors => 0, logFile => 'error.log' } >>      my %options = Tracer::ReadOptions($fileName);
1874    
1875  and C<@arguments> will contain  Read a set of options from a file. Each option is encoded in a line of text that has the
1876    format
1877    
1878  C<< apple orange rutabaga >>  I<optionName>C<=>I<optionValue>C<; >I<comment>
1879    
1880  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The option name must consist entirely of letters, digits, and the punctuation characters
1881  support for quote characters.  C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1882    character is a semi-colon will be ignored. The return hash will map each option name to
1883    the corresponding option value.
1884    
1885  =over 4  =over 4
1886    
1887  =item optionTable  =item fileName
   
 Table of default options.  
   
 =item inputList  
1888    
1889  List of words on the command line.  Name of the file containing the option data.
1890    
1891  =item RETURN  =item RETURN
1892    
1893  Returns a reference to the option table and a list of the positional arguments.  Returns a hash mapping the option names specified in the file to their corresponding option
1894    value.
1895    
1896  =back  =back
1897    
1898  =cut  =cut
1899    
1900  sub ParseCommand {  sub ReadOptions {
1901      # Get the parameters.      # Get the parameters.
1902      my ($optionTable, @inputList) = @_;      my ($fileName) = @_;
1903      # Process any options in the input list.      # Open the file.
1904      my %overrides = ();      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1905      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      # Count the number of records read.
1906          # Get the current option.      my ($records, $comments) = 0;
1907          my $arg = shift @inputList;      # Create the return hash.
1908          # Pull out the option name.      my %retVal = ();
1909          $arg =~ /^-([^=]*)/g;      # Loop through the file, accumulating key-value pairs.
1910          my $name = $1;      while (my $line = <CONFIGFILE>) {
1911          # Check for an option value.          # Denote we've read a line.
1912          if ($arg =~ /\G=(.*)$/g) {          $records++;
1913              # Here we have a value for the option.          # Determine the line type.
1914              $overrides{$name} = UnEscape($1);          if ($line =~ /^\s*[\n\r]/) {
1915                # A blank line is a comment.
1916                $comments++;
1917            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1918                # Here we have an option assignment.
1919                retVal{$1} = $2;
1920            } elsif ($line =~ /^\s*;/) {
1921                # Here we have a text comment.
1922                $comments++;
1923          } else {          } else {
1924              # Here there is no value, so we use 1.              # Here we have an invalid line.
1925              $overrides{$name} = 1;              Trace("Invalid option statement in record $records.") if T(0);
         }  
1926      }      }
     # Merge the options into the defaults.  
     GetOptions($optionTable, \%overrides);  
     # Translate the remaining parameters.  
     my @retVal = ();  
     for my $inputParm (@inputList) {  
         push @retVal, UnEscape($inputParm);  
1927      }      }
1928      # Return the results.      # Return the hash created.
1929      return ($optionTable, @retVal);      return %retVal;
1930  }  }
1931    
1932  =head3 Escape  =head3 GetOptions
   
 C<< my $codedString = Tracer::Escape($realString); >>  
   
 Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  
 replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
 result is to reverse the effect of L</UnEscape>.  
   
 =over 4  
   
 =item realString  
1933    
1934  String to escape.      Tracer::GetOptions(\%defaults, \%options);
1935    
1936  =item RETURN  Merge a specified set of options into a table of defaults. This method takes two hash references
1937    as input and uses the data from the second to update the first. If the second does not exist,
1938    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1939    exist in the first.
1940    
1941  Escaped equivalent of the real string.  Consider the following example.
1942    
1943  =back      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1944    
1945  =cut  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1946    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1947    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1948    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1949    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1950    
1951  sub Escape {      {databaseType => 'Oracle'}
     # Get the parameter.  
     my ($realString) = @_;  
     # Initialize the return variable.  
     my $retVal = "";  
     # Loop through the parameter string, looking for sequences to escape.  
     while (length $realString > 0) {  
         # Look for the first sequence to escape.  
         if ($realString =~ /^(.*?)([\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;  
             # 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;  
             }  
         } else {  
             # Here there are no more escape sequences. The rest of the string is  
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
         }  
     }  
     # Return the result.  
     return $retVal;  
 }  
1952    
1953  =head3 UnEscape  an error will occur because the B<databaseType> option does not exist.
1954    
1955  C<< my $realString = Tracer::UnEscape($codedString); >>  =over 4
1956    
1957  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  =item defaults
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
1958    
1959  =over 4  Table of default option values.
1960    
1961  =item codedString  =item options
1962    
1963  String to un-escape.  Table of overrides, if any.
1964    
1965  =item RETURN  =item RETURN
1966    
1967  Returns a copy of the original string with the escape sequences converted to their actual  Returns a reference to the default table passed in as the first parameter.
 values.  
1968    
1969  =back  =back
1970    
1971  =cut  =cut
1972    
1973  sub UnEscape {  sub GetOptions {
1974      # Get the parameter.      # Get the parameters.
1975      my ($codedString) = @_;      my ($defaults, $options) = @_;
1976      # Initialize the return variable.      # Check for overrides.
1977      my $retVal = "";      if ($options) {
1978      # Only proceed if the incoming string is nonempty.          # Loop through the overrides.
1979      if (defined $codedString) {          while (my ($option, $setting) = each %{$options}) {
1980          # Loop through the parameter string, looking for escape sequences. We can't do              # Insure this override exists.
1981          # translating because it causes problems with the escaped slash. ("\\t" becomes              if (!exists $defaults->{$option}) {
1982          # "\<tab>" no matter what we do.)                  croak "Unrecognized option $option encountered.";
         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;  
                 }  
1983              } else {              } else {
1984                  # Here there are no more escape sequences. The rest of the string is                  # Apply the override.
1985                  # transferred unmodified.                  $defaults->{$option} = $setting;
                 $retVal .= $codedString;  
                 $codedString = "";  
1986              }              }
1987          }          }
1988      }      }
1989      # Return the result.      # Return the merged table.
1990      return $retVal;      return $defaults;
1991  }  }
1992    
1993  =head3 ParseRecord  =head3 MergeOptions
1994    
1995  C<< my @fields = Tracer::ParseRecord($line); >>      Tracer::MergeOptions(\%table, \%defaults);
1996    
1997  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Merge default values into a hash table. This method looks at the key-value pairs in the
1998  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  second (default) hash, and if a matching key is not found in the first hash, the default
1999  These will automatically be converted.  pair is copied in. The process is similar to L</GetOptions>, but there is no error-
2000    checking and no return value.
2001    
2002  =over 4  =over 4
2003    
2004  =item line  =item table
2005    
2006  Line of data containing the tab-delimited fields.  Hash table to be updated with the default values.
2007    
2008  =item RETURN  =item defaults
2009    
2010  Returns a list of the fields found in the data line.  Default values to be merged into the first hash table if they are not already present.
2011    
2012  =back  =back
2013    
2014  =cut  =cut
2015    
2016  sub ParseRecord {  sub MergeOptions {
2017      # Get the parameter.      # Get the parameters.
2018      my ($line) = @_;      my ($table, $defaults) = @_;
2019      # Remove the trailing new-line, if any.      # Loop through the defaults.
2020      chomp $line;      while (my ($key, $value) = each %{$defaults}) {
2021      # Split the line read into pieces using the tab character.          if (!exists $table->{$key}) {
2022      my @retVal = split /\t/, $line;              $table->{$key} = $value;
2023      # Trim and fix the escapes in each piece.          }
2024      for my $value (@retVal) {      }
         # 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;  
     }  
     # Return the result.  
     return @retVal;  
2025  }  }
2026    
2027  =head3 Merge  =head3 ParseCommand
   
 C<< my @mergedList = Tracer::Merge(@inputList); >>  
   
 Sort a list of strings and remove duplicates.  
   
 =over 4  
2028    
2029  =item inputList      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2030    
2031  List of scalars to sort and merge.  Parse a command line consisting of a list of parameters. The initial parameters may be option
2032    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2033    off and merged into a table of default options. The remainder of the command line is
2034    returned as a list of positional arguments. For example, consider the following invocation.
2035    
2036  =item RETURN      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2037    
2038  Returns a list containing the same elements sorted in ascending order with duplicates  In this case, the list @words will be treated as a command line and there are two options available,
2039  removed.  B<errors> and B<logFile>. If @words has the following format
2040    
2041  =back      -logFile=error.log apple orange rutabaga
2042    
2043  =cut  then at the end of the invocation, C<$options> will be
2044    
2045  sub Merge {      { errors => 0, logFile => 'error.log' }
     # Get the input list in sort order.  
     my @inputList = sort @_;  
     # Only proceed if the list has at least two elements.  
     if (@inputList > 1) {  
         # Now we want to move through the list splicing out duplicates.  
         my $i = 0;  
         while ($i < @inputList) {  
             # Get the current entry.  
             my $thisEntry = $inputList[$i];  
             # Find out how many elements duplicate the current entry.  
             my $j = $i + 1;  
             my $dup1 = $i + 1;  
             while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };  
             # If the number is nonzero, splice out the duplicates found.  
             if ($j > $dup1) {  
                 splice @inputList, $dup1, $j - $dup1;  
             }  
             # Now the element at position $dup1 is different from the element before it  
             # at position $i. We push $i forward one position and start again.  
             $i++;  
         }  
     }  
     # Return the merged list.  
     return @inputList;  
 }  
2046    
2047  =head3 Percent  and C<@arguments> will contain
2048    
2049  C<< my $percent = Tracer::Percent($number, $base); >>      apple orange rutabaga
2050    
2051  Returns the percent of the base represented by the given number. If the base  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2052  is zero, returns zero.  support for quote characters. Options can be specified with single or double hyphens.
2053    
2054  =over 4  =over 4
2055    
2056  =item number  =item optionTable
2057    
2058  Percent numerator.  Table of default options.
2059    
2060  =item base  =item inputList
2061    
2062  Percent base.  List of words on the command line.
2063    
2064  =item RETURN  =item RETURN
2065    
2066  Returns the percentage of the base represented by the numerator.  Returns a reference to the option table and a list of the positional arguments.
2067    
2068  =back  =back
2069    
2070  =cut  =cut
2071    
2072  sub Percent {  sub ParseCommand {
2073      # Get the parameters.      # Get the parameters.
2074      my ($number, $base) = @_;      my ($optionTable, @inputList) = @_;
2075      # Declare the return variable.      # Process any options in the input list.
2076      my $retVal = 0;      my %overrides = ();
2077      # Compute the percent.      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2078      if ($base != 0) {          # Get the current option.
2079          $retVal = $number * 100 / $base;          my $arg = shift @inputList;
2080            # Pull out the option name.
2081            $arg =~ /^--?([^=]*)/g;
2082            my $name = $1;
2083            # Check for an option value.
2084            if ($arg =~ /\G=(.*)$/g) {
2085                # Here we have a value for the option.
2086                $overrides{$name} = UnEscape($1);
2087            } else {
2088                # Here there is no value, so we use 1.
2089                $overrides{$name} = 1;
2090      }      }
2091      # Return the result.      }
2092      return $retVal;      # Merge the options into the defaults.
2093        GetOptions($optionTable, \%overrides);
2094        # Translate the remaining parameters.
2095        my @retVal = ();
2096        for my $inputParm (@inputList) {
2097            push @retVal, UnEscape($inputParm);
2098        }
2099        # Return the results.
2100        return ($optionTable, @retVal);
2101  }  }
2102    
2103    
2104    =head2 File Utility Methods
2105    
2106  =head3 GetFile  =head3 GetFile
2107    
2108  C<< my @fileContents = Tracer::GetFile($fileName); >>      my @fileContents = Tracer::GetFile($fileName);
2109    
2110      or      or
2111    
2112  C<< my $fileContents = Tracer::GetFile($fileName); >>      my $fileContents = Tracer::GetFile($fileName);
2113    
2114  Return the entire contents of a file. In list context, line-ends are removed and  Return the entire contents of a file. In list context, line-ends are removed and
2115  each line is a list element. In scalar context, line-ends are replaced by C<\n>.  each line is a list element. In scalar context, line-ends are replaced by C<\n>.
# Line 1436  Line 2148 
2148      # Close it.      # Close it.
2149      close $handle;      close $handle;
2150      my $actualLines = @retVal;      my $actualLines = @retVal;
2151        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2152      # Return the file's contents in the desired format.      # Return the file's contents in the desired format.
2153      if (wantarray) {      if (wantarray) {
2154          return @retVal;          return @retVal;
# Line 1446  Line 2159 
2159    
2160  =head3 PutFile  =head3 PutFile
2161    
2162  C<< Tracer::PutFile($fileName, \@lines); >>      Tracer::PutFile($fileName, \@lines);
2163    
2164  Write out a file from a list of lines of text.  Write out a file from a list of lines of text.
2165    
# Line 1471  Line 2184 
2184      my ($fileName, $lines) = @_;      my ($fileName, $lines) = @_;
2185      # Open the output file.      # Open the output file.
2186      my $handle = Open(undef, ">$fileName");      my $handle = Open(undef, ">$fileName");
2187        # Count the lines written.
2188      if (ref $lines ne 'ARRAY') {      if (ref $lines ne 'ARRAY') {
2189          # Here we have a scalar, so we write it raw.          # Here we have a scalar, so we write it raw.
2190          print $handle $lines;          print $handle $lines;
2191            Trace("Scalar put to file $fileName.") if T(File => 3);
2192      } else {      } else {
2193          # Write the lines one at a time.          # Write the lines one at a time.
2194            my $count = 0;
2195          for my $line (@{$lines}) {          for my $line (@{$lines}) {
2196              print $handle "$line\n";              print $handle "$line\n";
2197                $count++;
2198          }          }
2199            Trace("$count lines put to file $fileName.") if T(File => 3);
2200      }      }
2201      # Close the output file.      # Close the output file.
2202      close $handle;      close $handle;
2203  }  }
2204    
2205  =head3 QTrace  =head3 ParseRecord
   
 C<< my $data = QTrace($format); >>  
   
 Return the queued trace data in the specified format.  
   
 =over 4  
   
 =item format  
   
 C<html> to format the data as an HTML list, C<text> to format it as straight text.  
   
 =back  
   
 =cut  
   
 sub QTrace {  
     # Get the parameter.  
     my ($format) = @_;  
     # Create the return variable.  
     my $retVal = "";  
     # Only proceed if there is an actual queue.  
     if (@Queue) {  
         # Process according to the format.  
         if ($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;  
 }  
   
 =head3 Confess  
   
 C<< Confess($message); >>  
   
 Trace the call stack and abort the program with the specified message. When used with  
 the OR operator and the L</Assert> method, B<Confess> can function 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.  
   
 =over 4  
   
 =item message  
   
 Message to include in the trace.  
   
 =back  
   
 =cut  
   
 sub Confess {  
     # Get the parameters.  
     my ($message) = @_;  
     # Trace the call stack.  
     Cluck($message);  
     # Abort the program.  
     croak(">>> $message");  
 }  
   
 =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;  
         }  
     }  
     return $retVal;  
 }  
   
 =head3 Cluck  
   
 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  
   
 Message to include in the trace.  
   
 =back  
   
 =cut  
   
 sub Cluck {  
     # Get the parameters.  
     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/);  
     }  
 }  
   
 =head3 Min  
2206    
2207  C<< my $min = Min($value1, $value2, ... $valueN); >>      my @fields = Tracer::ParseRecord($line);
2208    
2209  Return the minimum argument. The arguments are treated as numbers.  Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2210    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2211    These will automatically be converted.
2212    
2213  =over 4  =over 4
2214    
2215  =item $value1, $value2, ... $valueN  =item line
2216    
2217  List of numbers to compare.  Line of data containing the tab-delimited fields.
2218    
2219  =item RETURN  =item RETURN
2220    
2221  Returns the lowest number in the list.  Returns a list of the fields found in the data line.
2222    
2223  =back  =back
2224    
2225  =cut  =cut
2226    
2227  sub Min {  sub ParseRecord {
2228      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameter.
2229      my ($retVal, @values) = @_;      my ($line) = @_;
2230      # Loop through the remaining parameters, looking for the lowest.      # Remove the trailing new-line, if any.
2231      for my $value (@values) {      chomp $line;
2232          if ($value < $retVal) {      # Split the line read into pieces using the tab character.
2233              $retVal = $value;      my @retVal = split /\t/, $line;
2234          }      # Trim and fix the escapes in each piece.
2235        for my $value (@retVal) {
2236            # Trim leading whitespace.
2237            $value =~ s/^\s+//;
2238            # Trim trailing whitespace.
2239            $value =~ s/\s+$//;
2240            # Delete the carriage returns.
2241            $value =~ s/\r//g;
2242            # Convert the escapes into their real values.
2243            $value =~ s/\\t/"\t"/ge;
2244            $value =~ s/\\n/"\n"/ge;
2245      }      }
2246      # Return the minimum found.      # Return the result.
2247      return $retVal;      return @retVal;
2248  }  }
2249    
2250  =head3 Max  =head3 Merge
2251    
2252  C<< my $max = Max($value1, $value2, ... $valueN); >>      my @mergedList = Tracer::Merge(@inputList);
2253    
2254  Return the maximum argument. The arguments are treated as numbers.  Sort a list of strings and remove duplicates.
2255    
2256  =over 4  =over 4
2257    
2258  =item $value1, $value2, ... $valueN  =item inputList
2259    
2260  List of numbers to compare.  List of scalars to sort and merge.
2261    
2262  =item RETURN  =item RETURN
2263    
2264  Returns the highest number in the list.  Returns a list containing the same elements sorted in ascending order with duplicates
2265    removed.
2266    
2267  =back  =back
2268    
2269  =cut  =cut
2270    
2271  sub Max {  sub Merge {
2272      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the input list in sort order.
2273      my ($retVal, @values) = @_;      my @inputList = sort @_;
2274      # Loop through the remaining parameters, looking for the highest.      # Only proceed if the list has at least two elements.
2275      for my $value (@values) {      if (@inputList > 1) {
2276          if ($value > $retVal) {          # Now we want to move through the list splicing out duplicates.
2277              $retVal = $value;          my $i = 0;
2278            while ($i < @inputList) {
2279                # Get the current entry.
2280                my $thisEntry = $inputList[$i];
2281                # Find out how many elements duplicate the current entry.
2282                my $j = $i + 1;
2283                my $dup1 = $i + 1;
2284                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2285                # If the number is nonzero, splice out the duplicates found.
2286                if ($j > $dup1) {
2287                    splice @inputList, $dup1, $j - $dup1;
2288          }          }
2289                # Now the element at position $dup1 is different from the element before it
2290                # at position $i. We push $i forward one position and start again.
2291                $i++;
2292      }      }
2293      # Return the maximum found.      }
2294      return $retVal;      # Return the merged list.
2295        return @inputList;
2296  }  }
2297    
2298  =head3 AddToListMap  =head3 Open
2299    
2300  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2301    
2302  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Open a file.
 is created for the key. Otherwise, the new value is pushed onto the list.  
2303    
2304  =over 4  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2305    function. The mode is specified using Unix-like shell information. So, for
2306    example,
2307    
2308  =item hash      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2309    
2310  Reference to the target hash.  would open for output appended to the specified file, and
2311    
2312  =item key      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2313    
2314  Key for which the value is to be added.  would open a pipe that sorts the records written and removes duplicates. Note
2315    the use of file handle syntax in the Open call. To use anonymous file handles,
2316    code as follows.
2317    
2318  =item value1, value2, ... valueN      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2319    
2320  List of values to add to the key's value list.  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2321    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2322    failed open will throw an exception and the third parameter will be used to construct
2323    an error message. If the parameter is omitted, a standard message is constructed
2324    using the file spec.
2325    
2326  =back      Could not open "/usr/spool/news/twitlog"
2327    
2328  =cut  Note that the mode characters are automatically cleaned from the file name.
2329    The actual error message from the file system will be captured and appended to the
2330    message in any case.
2331    
2332  sub AddToListMap {      Could not open "/usr/spool/news/twitlog": file not found.
2333      # Get the parameters.  
2334      my ($hash, $key, @values) = @_;  In some versions of PERL the only error message we get is a number, which
2335      # Process according to whether or not the key already has a value.  corresponds to the C++ C<errno> value.
2336      if (! exists $hash->{$key}) {  
2337          $hash->{$key} = [@values];      Could not open "/usr/spool/news/twitlog": 6.
2338      } else {  
2339          push @{$hash->{$key}}, @values;  =over 4
     }  
 }  
2340    
2341  =head3 DebugMode  =item fileHandle
2342    
2343    File handle. If this parameter is C<undef>, a file handle will be generated
2344    and returned as the value of this method.
2345    
2346    =item fileSpec
2347    
2348    File name and mode, as per the PERL C<open> function.
2349    
2350  C<< if (Tracer::DebugMode) { ...code... } >>  =item message (optional)
2351    
2352    Error message to use if the open fails. If omitted, a standard error message
2353    will be generated. In either case, the error information from the file system
2354    is appended to the message. To specify a conditional open that does not throw
2355    an error if it fails, use C<0>.
2356    
2357    =item RETURN
2358    
2359  Return TRUE if debug mode has been turned on, else abort.  Returns the name of the file handle assigned to the file, or C<undef> if the
2360    open failed.
2361    
2362  Certain CGI scripts are too dangerous to exist in the production  =back
 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 will occur.  
2363    
2364  =cut  =cut
2365    
2366  sub DebugMode {  sub Open {
2367      # Declare the return variable.      # Get the parameters.
2368      my $retVal = 0;      my ($fileHandle, $fileSpec, $message) = @_;
2369      # Check the debug configuration.      # Attempt to open the file.
2370      my $password = CGI::cookie("DebugMode");      my $rv = open $fileHandle, $fileSpec;
2371      my $encrypted = Digest::MD5::md5_hex($password);      # If the open failed, generate an error message.
2372      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {      if (! $rv) {
2373          $retVal = 1;          # Save the system error message.
2374      } else {          my $sysMessage = $!;
2375          # Here debug mode is off, so we generate an error.          # See if we need a default message.
2376          Confess("Cannot use this facility without logging in.");          if (!$message) {
2377                # Clean any obvious mode characters and leading spaces from the
2378                # filename.
2379                my ($fileName) = FindNamePart($fileSpec);
2380                $message = "Could not open \"$fileName\"";
2381      }      }
2382      # Return the determination indicator.          # Terminate with an error using the supplied message and the
2383      return $retVal;          # error message from the file system.
2384            Confess("$message: $!");
2385        }
2386        # Return the file handle.
2387        return $fileHandle;
2388  }  }
2389    
2390  =head3 Strip  =head3 FindNamePart
2391    
2392  C<< my $string = Tracer::Strip($line); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2393    
2394  Strip all line terminators off a string. This is necessary when dealing with files  Extract the portion of a file specification that contains the file name.
2395  that may have been transferred back and forth several times among different  
2396  operating environments.  A file specification is the string passed to an C<open> call. It specifies the file
2397    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2398    method assumes that the file name is whatever follows the first angle bracket
2399    sequence.  So, for example, in the following strings the file name is
2400    C</usr/fig/myfile.txt>.
2401    
2402        >>/usr/fig/myfile.txt
2403        </usr/fig/myfile.txt
2404        | sort -u > /usr/fig/myfile.txt
2405    
2406    If the method cannot find a file name using its normal methods, it will return the
2407    whole incoming string.
2408    
2409  =over 4  =over 4
2410    
2411  =item line  =item fileSpec
2412    
2413  Line of text to be stripped.  File specification string from which the file name is to be extracted.
2414    
2415  =item RETURN  =item RETURN
2416    
2417  The same line of text with all the line-ending characters chopped from the end.  Returns a three-element list. The first element contains the file name portion of
2418    the specified string, or the whole string if a file name cannot be found via normal
2419    methods. The second element contains the start position of the file name portion and
2420    the third element contains the length.
2421    
2422  =back  =back
2423    
2424  =cut  =cut
2425    #: Return Type $;
2426  sub Strip {  sub FindNamePart {
2427      # Get a copy of the parameter string.      # Get the parameters.
2428      my ($string) = @_;      my ($fileSpec) = @_;
2429      my $retVal = (defined $string ? $string : "");      # Default to the whole input string.
2430      # Strip the line terminator characters.      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2431      $retVal =~ s/(\r|\n)+$//g;      # Parse out the file name if we can.
2432        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2433            $retVal = $2;
2434            $len = length $retVal;
2435            $pos = (length $fileSpec) - (length $3) - $len;
2436        }
2437      # Return the result.      # Return the result.
2438      return $retVal;      return ($retVal, $pos, $len);
2439  }  }
2440    
2441  =head3 Pad  =head3 OpenDir
2442    
2443  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      my @files = OpenDir($dirName, $filtered, $flag);
2444    
2445  Pad a string to a specified length. The pad character will be a  Open a directory and return all the file names. This function essentially performs
2446  space, and the padding will be on the right side unless specified  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2447  in the third parameter.  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2448    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2449    filtered out of the return list. If the directory does not open and I<$flag> is not
2450    set, an exception is thrown. So, for example,
2451    
2452  =over 4      my @files = OpenDir("/Volumes/fig/contigs", 1);
2453    
2454  =item string  is effectively the same as
2455    
2456  String to be padded.      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2457        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2458    
2459  =item len  Similarly, the following code
2460    
2461  Desired length of the padded string.      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2462    
2463  =item left (optional)  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2464    automatically returns an empty list if the directory fails to open.
2465    
2466  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  =over 4
2467    
2468  =item padChar (optional)  =item dirName
2469    
2470  Character to use for padding. The default is a space.  Name of the directory to open.
2471    
2472  =item RETURN  =item filtered
2473    
2474  Returns a copy of the original string with the pad character added to the  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2475  specified end so that it achieves the desired length.  from the list, else FALSE.
2476    
2477    =item flag
2478    
2479    TRUE if a failure to open is okay, else FALSE
2480    
2481  =back  =back
2482    
2483  =cut  =cut
2484    #: Return Type @;
2485  sub Pad {  sub OpenDir {
2486      # Get the parameters.      # Get the parameters.
2487      my ($string, $len, $left, $padChar) = @_;      my ($dirName, $filtered, $flag) = @_;
2488      # Compute the padding character.      # Declare the return variable.
2489      if (! defined $padChar) {      my @retVal = ();
2490          $padChar = " ";      # Open the directory.
2491      }      if (opendir(my $dirHandle, $dirName)) {
2492      # Compute the number of spaces needed.          # The directory opened successfully. Get the appropriate list according to the
2493      my $needed = $len - length $string;          # strictures of the filter parameter.
2494      # Copy the string into the return variable.          if ($filtered) {
2495      my $retVal = $string;              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
     # Only proceed if padding is needed.  
     if ($needed > 0) {  
         # Create the pad string.  
         my $pad = $padChar x $needed;  
         # Affix it to the return value.  
         if ($left) {  
             $retVal = $pad . $retVal;  
2496          } else {          } else {
2497              $retVal .= $pad;              @retVal = readdir $dirHandle;
2498          }          }
2499        } elsif (! $flag) {
2500            # Here the directory would not open and it's considered an error.
2501            Confess("Could not open directory $dirName.");
2502      }      }
2503      # Return the result.      # Return the result.
2504      return $retVal;      return @retVal;
2505  }  }
2506    
 =head3 EOF  
2507    
2508  This is a constant that is lexically greater than any useful string.  =head3 Insure
2509    
2510        Insure($dirName, $chmod);
2511    
2512    Insure a directory is present.
2513    
2514  =cut  =over 4
2515    
2516  sub EOF {  =item dirName
     return "\xFF\xFF\xFF\xFF\xFF";  
 }  
2517    
2518  =head3 TICK  Name of the directory to check. If it does not exist, it will be created.
2519    
2520  C<< my @results = TICK($commandString); >>  =item chmod (optional)
2521    
2522  Perform a back-tick operation on a command. If this is a Windows environment, any leading  Security privileges to be given to the directory if it is created.
 dot-slash (C<./> will be removed. So, for example, if you were doing  
2523    
2524      `./protein.cgi`  =back
2525    
2526  from inside a CGI script, it would work fine in Unix, but would issue an error message  =cut
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
2527    
2528      TICK("./protein.cgi")  sub Insure {
2529        my ($dirName, $chmod) = @_;
2530        if (! -d $dirName) {
2531            Trace("Creating $dirName directory.") if T(2);
2532            eval {
2533                mkpath $dirName;
2534                # If we have permissions specified, set them here.
2535                if (defined($chmod)) {
2536                    chmod $chmod, $dirName;
2537                }
2538            };
2539            if ($@) {
2540                Confess("Error creating $dirName: $@");
2541            }
2542        }
2543    }
2544    
2545  it will work correctly in both environments.  =head3 ChDir
2546    
2547  =over 4      ChDir($dirName);
2548    
2549  =item commandString  Change to the specified directory.
2550    
2551  The command string to pass to the system.  =over 4
2552    
2553  =item RETURN  =item dirName
2554    
2555  Returns the standard output from the specified command, as a list.  Name of the directory to which we want to change.
2556    
2557  =back  =back
2558    
2559  =cut  =cut
2560  #: Return Type @;  
2561  sub TICK {  sub ChDir {
2562      # Get the parameters.      my ($dirName) = @_;
2563      my ($commandString) = @_;      if (! -d $dirName) {
2564      # Chop off the dot-slash if this is Windows.          Confess("Cannot change to directory $dirName: no such directory.");
2565      if ($FIG_Config::win_mode) {      } else {
2566          $commandString =~ s!^\./!!;          Trace("Changing to directory $dirName.") if T(File => 4);
2567            my $okFlag = chdir $dirName;
2568            if (! $okFlag) {
2569                Confess("Error switching to directory $dirName.");
2570            }
2571      }      }
     # Activate the command and return the result.  
     return `$commandString`;  
2572  }  }
2573    
2574  =head3 ScriptSetup  =head3 SetPermissions
2575    
2576  C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2577    
2578  Perform standard tracing and debugging setup for scripts. The value returned is  Set the permissions for a directory and all the files and folders inside it.
2579  the CGI object followed by a pre-built variable hash.  In addition, the group ownership will be changed to the specified value.
2580    
2581  The C<Trace> query parameter is used to determine whether or not tracing is active and  This method is more vulnerable than most to permission and compatability
2582  which trace modules (other than C<Tracer> itself) should be turned on. Specifying  problems, so it does internal error recovery.
 the C<CGI> trace module will trace parameter and environment information. Parameters are  
 traced at level 3 and environment variables at level 4. To trace to a file instead of to  
 the web page, set C<TF> to 1. At the end of the script, the client should call  
 L</ScriptFinish> to output the web page.  
   
 In some situations, it is not practical to invoke tracing via form parameters. For this  
 situation, you can turn on emergency tracing by invoking the L</Emergency> method from  
 a web page. Emergency tracing is detected via a file with the name  
 C<Emergency>I<IPaddr>C<.txt> in the FIG temporary directory, where I<IPaddr> is the  
 IP address of the remote user who wants tracing turned on. The file contains a time  
 limit in hours on the first line, a tracing destination on the second line, a trace  
 level on the third line, and the tracing modules on subsequent lines.  
2583    
2584  =over 4  =over 4
2585    
2586  =item noTrace (optional)  =item dirName
2587    
2588  If specified, tracing will be suppressed. This is useful if the script wants to set up  Name of the directory to process.
 tracing manually.  
2589    
2590  =item RETURN  =item group
2591    
2592  Returns a two-element list consisting of a CGI query object and a variable hash for  Name of the group to be assigned.
2593  the output page.  
2594    =item mask
2595    
2596    Permission mask. Bits that are C<1> in this mask will be ORed into the
2597    permission bits of any file or directory that does not already have them
2598    set to 1.
2599    
2600    =item otherMasks
2601    
2602    Map of search patterns to permission masks. If a directory name matches
2603    one of the patterns, that directory and all its members and subdirectories
2604    will be assigned the new pattern. For example, the following would
2605    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2606    
2607        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2608    
2609    The list is ordered, so the following would use 0777 for C<tmp1> and
2610    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2611    
2612        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2613                                                       '^tmp' => 0666);
2614    
2615    Note that the pattern matches are all case-insensitive, and only directory
2616    names are matched, not file names.
2617    
2618  =back  =back
2619    
2620  =cut  =cut
2621    
2622  sub ScriptSetup {  sub SetPermissions {
2623      # Get the parameters.      # Get the parameters.
2624      my ($noTrace) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2625      # Get the CGI query object.      # Set up for error recovery.
2626      my $cgi = CGI->new();      eval {
2627      # Set up tracing if it's not suppressed.          # Switch to the specified directory.
2628      CGITrace($cgi) unless $noTrace;          ChDir($dirName);
2629      # Create the variable hash.          # Get the group ID.
2630      my $varHash = { results => '' };          my $gid = getgrnam($group);
2631      # Return the query object and variable hash.          # Get the mask for tracing.
2632      return ($cgi, $varHash);          my $traceMask = sprintf("%04o", $mask) . "($mask)";
2633            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2634            my $fixCount = 0;
2635            my $lookCount = 0;
2636            # @dirs will be a stack of directories to be processed.
2637            my @dirs = (getcwd());
2638            while (scalar(@dirs) > 0) {
2639                # Get the current directory.
2640                my $dir = pop @dirs;
2641                # Check for a match to one of the specified directory names. To do
2642                # that, we need to pull the individual part of the name off of the
2643                # whole path.
2644                my $simpleName = $dir;
2645                if ($dir =~ m!/([^/]+)$!) {
2646                    $simpleName = $1;
2647                }
2648                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2649                # Search for a match.
2650                my $match = 0;
2651                my $i;
2652                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2653                    my $pattern = $otherMasks[$i];
2654                    if ($simpleName =~ /$pattern/i) {
2655                        $match = 1;
2656                    }
2657                }
2658                # Check for a match. Note we use $i-1 because the loop added 2
2659                # before terminating due to the match.
2660                if ($match && $otherMasks[$i-1] != $mask) {
2661                    # This directory matches one of the incoming patterns, and it's
2662                    # a different mask, so we process it recursively with that mask.
2663                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2664                } else {
2665                    # Here we can process normally. Get all of the non-hidden members.
2666                    my @submems = OpenDir($dir, 1);
2667                    for my $submem (@submems) {
2668                        # Get the full name.
2669                        my $thisMem = "$dir/$submem";
2670                        Trace("Checking member $thisMem.") if T(4);
2671                        $lookCount++;
2672                        if ($lookCount % 1000 == 0) {
2673                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2674                        }
2675                        # Fix the group.
2676                        chown -1, $gid, $thisMem;
2677                        # Insure this member is not a symlink.
2678                        if (! -l $thisMem) {
2679                            # Get its info.
2680                            my $fileInfo = stat $thisMem;
2681                            # Only proceed if we got the info. Otherwise, it's a hard link
2682                            # and we want to skip it anyway.
2683                            if ($fileInfo) {
2684                                my $fileMode = $fileInfo->mode;
2685                                if (($fileMode & $mask) != $mask) {
2686                                    # Fix this member.
2687                                    $fileMode |= $mask;
2688                                    chmod $fileMode, $thisMem;
2689                                    $fixCount++;
2690                                }
2691                                # If it's a subdirectory, stack it.
2692                                if (-d $thisMem) {
2693                                    push @dirs, $thisMem;
2694                                }
2695                            }
2696                        }
2697                    }
2698                }
2699            }
2700            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2701        };
2702        # Check for an error.
2703        if ($@) {
2704            Confess("SetPermissions error: $@");
2705        }
2706  }  }
2707    
2708  =head3 CGITrace  =head3 GetLine
2709    
2710  C<< Tracer::CGITrace($cgi); >>      my @data = Tracer::GetLine($handle);
2711    
2712  Set up tracing for a CGI script. See L</ScriptSetup> for more information.  Read a line of data from a tab-delimited file.
2713    
2714  =over 4  =over 4
2715    
2716  =item cgi  =item handle
2717    
2718    Open file handle from which to read.
2719    
2720    =item RETURN
2721    
2722  Ths CGI query object for this script.  Returns a list of the fields in the record read. The fields are presumed to be
2723    tab-delimited. If we are at the end of the file, then an empty list will be
2724    returned. If an empty line is read, a single list item consisting of a null
2725    string will be returned.
2726    
2727  =back  =back
2728    
2729  =cut  =cut
2730    
2731  sub CGITrace {  sub GetLine {
2732      # Get the parameters.      # Get the parameters.
2733      my ($cgi) = @_;      my ($handle) = @_;
2734      # Default to no tracing except errors.      # Declare the return variable.
2735      my ($tracing, $dest) = ("0", "WARN");      my @retVal = ();
2736      # Check for emergency tracing.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2737      my $ip = EmergencyIP($cgi);      # Read from the file.
2738      my $emergencyFile = EmergencyFileName($ip);      my $line = <$handle>;
2739      if (-e $emergencyFile) {      # Only proceed if we found something.
2740          # We have the file. Read in the data.      if (defined $line) {
2741          my @tracing = GetFile($emergencyFile);          # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2742          # Pull off the time limit.          # upload control and have a nonstandard EOL combination.
2743          my $expire = shift @tracing;          $line =~ s/(\r|\n)+$//;
2744          # Convert it to seconds.          # Here we do some fancy tracing to help in debugging complicated EOL marks.
2745          $expire *= 3600;          if (T(File => 4)) {
2746          # Check the file data.              my $escapedLine = $line;
2747          my $stat = stat($emergencyFile);              $escapedLine =~ s/\n/\\n/g;
2748          my ($now) = gettimeofday;              $escapedLine =~ s/\r/\\r/g;
2749          if ($now - $stat->mtime > $expire) {              $escapedLine =~ s/\t/\\t/g;
2750              # Delete the expired file.              Trace("Line read: -->$escapedLine<--");
2751              unlink $emergencyFile;          }
2752            # If the line is empty, return a single empty string; otherwise, parse
2753            # it into fields.
2754            if ($line eq "") {
2755                push @retVal, "";
2756          } else {          } else {
2757              # Emergency tracing is on. Pull off the destination and              push @retVal, split /\t/,$line;
             # the trace level;  
             $dest = shift @tracing;  
             my $level = shift @tracing;  
             # Convert the destination to a real tracing destination.  
             # temp directory.  
             $dest = EmergencyTracingDest($ip, $dest);  
             # Insure Tracer is specified.  
             my %moduleHash = map { $_ => 1 } @tracing;  
             $moduleHash{Tracer} = 1;  
             # Set the trace parameter.  
             $tracing = join(" ", $level, sort keys %moduleHash);  
             # Make sure the script knows tracing is on.  
             $cgi->param(-name => 'Trace', -value => $tracing);  
             $cgi->param(-name => 'TF', -value => (($dest =~ /^>/) ? 1 : 0));  
2758          }          }
2759      } elsif ($cgi->param('Trace')) {      } else {
2760          # Here the user has requested tracing via a form.          # Trace the reason the read failed.
2761          $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");          Trace("End of file: $!") if T(File => 3);
         $tracing = $cgi->param('Trace') . " Tracer";  
2762      }      }
2763      # Setup the tracing we've determined from all the stuff above.      # Return the result.
2764      TSetup($tracing, $dest);      return @retVal;
     # Trace the parameter and environment data.  
     TraceParms($cgi);  
2765  }  }
2766    
2767  =head3 EmergencyFileName  =head3 PutLine
2768    
2769  C<< my $fileName = Tracer::EmergencyFileName($ip); >>      Tracer::PutLine($handle, \@fields, $eol);
2770    
2771  Return the emergency tracing file name. This is the file that specifies  Write a line of data to a tab-delimited file. The specified field values will be
2772  the tracing information.  output in tab-separated form, with a trailing new-line.
2773    
2774  =over 4  =over 4
2775    
2776  =item ip  =item handle
2777    
2778    Output file handle.
2779    
2780    =item fields
2781    
2782  IP address of the user who wants tracing, as taken from the C<< $cgi->remote_host() >>  List of field values.
 method.  
2783    
2784  =item RETURN  =item eol (optional)
2785    
2786  Returns the name of the file to contain the emergency tracing information.  End-of-line character (default is "\n").
2787    
2788  =back  =back
2789    
2790  =cut  =cut
2791    
2792  sub EmergencyFileName {  sub PutLine {
2793      # Get the parameters.      # Get the parameters.
2794      my ($ip) = @_;      my ($handle, $fields, $eol) = @_;
2795      # Compute the emergency tracing file name.      # Write the data.
2796      return "$FIG_Config::temp/Emergency$ip.txt";      print $handle join("\t", @{$fields}) . ($eol || "\n");
2797  }  }
2798    
 =head3 EmergencyFileTarget  
   
 C<< my $fileName = Tracer::EmergencyFileTarget($ip); >>  
2799    
2800  Return the emergency tracing target file name. This is the file that receives  =head3 PrintLine
 the tracing output for file-based tracing.  
2801    
2802  =over 4      Tracer::PrintLine($line);
2803    
2804  =item ip  Print a line of text with a trailing new-line.
2805    
2806  IP address of the user who wants tracing, as taken from the C<< $cgi->remote_host() >>  =over 4
 method.  
2807    
2808  =item RETURN  =item line
2809    
2810  Returns the name of the file to contain the emergency tracing information.  Line of text to print.
2811    
2812  =back  =back
2813    
2814  =cut  =cut
2815    
2816  sub EmergencyFileTarget {  sub PrintLine {
2817      # Get the parameters.      # Get the parameters.
2818      my ($ip) = @_;      my ($line) = @_;
2819      # Compute the emergency tracing file name.      # Print the line.
2820      return "$FIG_Config::temp/Emergency$ip.log";      print "$line\n";
2821  }  }
2822    
 =head3 EmergencyTracingDest  
2823    
2824  C<< my $dest = Tracer::EmergencyTracingDest($ip, $myDest); >>  =head2 Other Useful Methods
2825    
2826  This method converts an emergency tracing destination to a real  =head3 ParseParm
 tracing destination. The main difference is that if the  
 destination is C<FILE> or C<APPEND>, we convert it to file  
 output.  
2827    
2828  =over 4      my $listValue = Tracer::ParseParm($string);
2829    
2830  =item ip  Convert a parameter into a list reference. If the parameter is undefined,
2831    an undefined value will be returned. Otherwise, it will be parsed as a
2832    comma-separated list of values.
2833    
2834  IP address of the user who wants tracing, as taken from the C<< $cgi->remote_host() >>  =over 4
 method.  
2835    
2836  =item myDest  =item string
2837    
2838  Destination from the emergency tracing file.  Incoming string.
2839    
2840  =item RETURN  =item RETURN
2841    
2842  Returns a destination that can be passed into L</TSetup>.  Returns a reference to a list of values, or C<undef> if the incoming value
2843    was undefined.
2844    
2845  =back  =back
2846    
2847  =cut  =cut
2848    
2849  sub EmergencyTracingDest {  sub ParseParm {
2850      # Get the parameters.      # Get the parameters.
2851      my ($ip, $myDest) = @_;      my ($string) = @_;
2852      # Declare the return variable.      # Declare the return variable.
2853      my $retVal;      my $retVal;
2854      # Process according to the destination value.      # Check for data.
2855      if ($myDest eq 'FILE') {      if (defined $string) {
2856          $retVal = ">" . EmergencyFileTarget($ip);          # We have some, so split it into a list.
2857      } elsif ($myDest eq 'APPEND') {          $retVal = [ split /\s*,\s*/, $string];
         $retVal = ">>" . EmergencyFileTarget($ip);  
     } else {  
         $retVal = $myDest;  
2858      }      }
2859      # Return the result.      # Return the result.
2860      return $retVal;      return $retVal;
2861  }  }
2862    
2863  =head3 Emergency  =head3 Now
   
 C<< Emergency($cgi, $hours, $dest, $level, @modules); >>  
2864    
2865  Turn on emergency tracing. This method can only be invoked over the web and is      my $string = Tracer::Now();
 should not be called if debug mode is off. The caller specifies the duration of the  
 emergency in hours, the desired tracing destination, the trace level,  
 and a list of the trace modules to activate. For the duration, when a user  
 from the specified remote web location invokes a Sprout CGI script, tracing  
 will be turned on automatically. See L</TSetup> for more about tracing  
 setup and L</ScriptSetup> for more about emergency tracing.  
2866    
2867  =over 4  Return a displayable time stamp containing the local time. Whatever format this
2868    method produces must be parseable by L</ParseDate>.
2869    
2870  =item cgi  =cut
2871    
2872  A CGI query object.  sub Now {
2873        return DisplayTime(time);
2874    }
2875    
2876  =item hours  =head3 DisplayTime
2877    
2878  Number of hours to keep emergency tracing alive.      my $string = Tracer::DisplayTime($time);
2879    
2880  =item dest  Convert a time value to a displayable time stamp. Whatever format this
2881    method produces must be parseable by L</ParseDate>.
2882    
2883  Tracing destination. If no path information is specified for a file  =over 4
 destination, it is put in the FIG temporary directory.  
2884    
2885  =item level  =item time
2886    
2887  Tracing level. A higher level means more trace messages.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2888    
2889  =item modules  =item RETURN
2890    
2891  A list of the tracing modules to activate.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2892    
2893  =back  =back
2894    
2895  =cut  =cut
2896    
2897  sub Emergency {  sub DisplayTime {
2898      # Get the parameters.      my ($time) = @_;
2899      my ($cgi, $hours, $dest, $level, @modules) = @_;      my $retVal = "(n/a)";
2900      # Get the IP address.      if (defined $time) {
2901      my $ip = EmergencyIP($cgi);          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2902      # Create the emergency file.          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2903      my $specFile = EmergencyFileName($ip);                    _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2904      my $outHandle = Open(undef, ">$specFile");      }
2905      print $outHandle join("\n",$hours, $dest, $level, @modules, "");      return $retVal;
2906  }  }
2907    
2908  =head3 EmergencyIP  # Pad a number to 2 digits.
2909    sub _p2 {
2910        my ($value) = @_;
2911        $value = "0$value" if ($value < 10);
2912        return $value;
2913    }
2914    
2915    =head3 Escape
2916    
2917  C<< my $ip = EmergencyIP($cgi); >>      my $codedString = Tracer::Escape($realString);
2918    
2919  Return the IP address to be used for emergency tracing. If at smoe point we need  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2920  to change the way we compute the IP address, or we decide to use something else,  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2921  all we need to do is change this method.  result is to reverse the effect of L</UnEscape>.
2922    
2923  =over 4  =over 4
2924    
2925  =item cgi  =item realString
2926    
2927  CGI query object.  String to escape.
2928    
2929  =item RETURN  =item RETURN
2930    
2931  Returns the IP address to be used for labelling emergency tracing.  Escaped equivalent of the real string.
2932    
2933  =back  =back
2934    
2935  =cut  =cut
2936    
2937  sub EmergencyIP {  sub Escape {
2938      # Get the parameters.      # Get the parameter.
2939      my ($cgi) = @_;      my ($realString) = @_;
2940        # Initialize the return variable.
2941        my $retVal = "";
2942        # Loop through the parameter string, looking for sequences to escape.
2943        while (length $realString > 0) {
2944            # Look for the first sequence to escape.
2945            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2946                # Here we found it. The text preceding the sequence is in $1. The sequence
2947                # itself is in $2. First, move the clear text to the return variable.
2948                $retVal .= $1;
2949                # Strip the processed section off the real string.
2950                $realString = substr $realString, (length $2) + (length $1);
2951                # Get the matched character.
2952                my $char = $2;
2953                # If we have a CR, we are done.
2954                if ($char ne "\r") {
2955                    # It's not a CR, so encode the escape sequence.
2956                    $char =~ tr/\t\n/tn/;
2957                    $retVal .= "\\" . $char;
2958                }
2959            } else {
2960                # Here there are no more escape sequences. The rest of the string is
2961                # transferred unmodified.
2962                $retVal .= $realString;
2963                $realString = "";
2964            }
2965        }
2966      # Return the result.      # Return the result.
2967      return $cgi->remote_addr();      return $retVal;
2968  }  }
2969    
2970    =head3 UnEscape
2971    
2972  =head3 TraceParms      my $realString = Tracer::UnEscape($codedString);
   
 C<< Tracer::TraceParms($cgi); >>  
2973    
2974  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2975  at level CGI => 4.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2976    be deleted.
2977    
2978  =over 4  =over 4
2979    
2980  =item cgi  =item codedString
2981    
2982  CGI query object containing the parameters to trace.  String to un-escape.
2983    
2984    =item RETURN
2985    
2986    Returns a copy of the original string with the escape sequences converted to their actual
2987    values.
2988    
2989  =back  =back
2990    
2991  =cut  =cut
2992    
2993  sub TraceParms {  sub UnEscape {
2994      # Get the parameters.      # Get the parameter.
2995      my ($cgi) = @_;      my ($codedString) = @_;
2996      if (T(CGI => 3)) {      # Initialize the return variable.
2997          # Here we want to trace the parameter data.      my $retVal = "";
2998          my @names = $cgi->param;      # Only proceed if the incoming string is nonempty.
2999          for my $parmName (sort @names) {      if (defined $codedString) {
3000              # Note we skip the Trace parameters, which are for our use only.          # Loop through the parameter string, looking for escape sequences. We can't do
3001              if ($parmName ne 'Trace' && $parmName ne 'TF') {          # translating because it causes problems with the escaped slash. ("\\t" becomes
3002                  my @values = $cgi->param($parmName);          # "\<tab>" no matter what we do.)
3003                  Trace("CGI: $parmName = " . join(", ", @values));          while (length $codedString > 0) {
3004              }              # Look for the first escape sequence.
3005                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
3006                    # Here we found it. The text preceding the sequence is in $1. The sequence
3007                    # itself is in $2. First, move the clear text to the return variable.
3008                    $retVal .= $1;
3009                    $codedString = substr $codedString, (2 + length $1);
3010                    # Get the escape value.
3011                    my $char = $2;
3012                    # If we have a "\r", we are done.
3013                    if ($char ne 'r') {
3014                        # Here it's not an 'r', so we convert it.
3015                        $char =~ tr/\\tn/\\\t\n/;
3016                        $retVal .= $char;
3017          }          }
3018          # Display the request method.              } else {
3019          my $method = $cgi->request_method();                  # Here there are no more escape sequences. The rest of the string is
3020          Trace("Method: $method");                  # transferred unmodified.
3021                    $retVal .= $codedString;
3022                    $codedString = "";
3023      }      }
     if (T(CGI => 4)) {  
         # Here we want the environment data too.  
         for my $envName (sort keys %ENV) {  
             Trace("ENV: $envName = $ENV{$envName}");  
3024          }          }
3025      }      }
3026        # Return the result.
3027        return $retVal;
3028  }  }
3029    
3030  =head3 ScriptFinish  =head3 Percent
3031    
3032  C<< ScriptFinish($webData, $varHash); >>      my $percent = Tracer::Percent($number, $base);
3033    
3034  Output a web page at the end of a script. Either the string to be output or the  Returns the percent of the base represented by the given number. If the base
3035  name of a template file can be specified. If the second parameter is omitted,  is zero, returns zero.
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
3036    
3037  A typical standard script would loook like the following.  =over 4
3038    
3039      BEGIN {  =item number
3040          # Print the HTML header.  
3041          print "CONTENT-TYPE: text/html\n\n";  Percent numerator.
3042    
3043    =item base
3044    
3045    Percent base.
3046    
3047    =item RETURN
3048    
3049    Returns the percentage of the base represented by the numerator.
3050    
3051    =back
3052    
3053    =cut
3054    
3055    sub Percent {
3056        # Get the parameters.
3057        my ($number, $base) = @_;
3058        # Declare the return variable.
3059        my $retVal = 0;
3060        # Compute the percent.
3061        if ($base != 0) {
3062            $retVal = $number * 100 / $base;
3063        }
3064        # Return the result.
3065        return $retVal;
3066      }      }
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
3067    
3068      my ($cgi, $varHash) = ScriptSetup();  =head3 Constrain
3069      eval {  
3070          # ... get data from $cgi, put it in $varHash ...      my $constrained = Constrain($value, $min, $max);
3071      };  
3072      if ($@) {  Modify a numeric value to bring it to a point in between a maximum and a minimum.
3073          Trace("Script Error: $@") if T(0);  
3074    =over 4
3075    
3076    =item value
3077    
3078    Value to constrain.
3079    
3080    =item min (optional)
3081    
3082    Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3083    
3084    =item max (optional)
3085    
3086    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3087    
3088    =item RETURN
3089    
3090    Returns the incoming value, constrained according to the other parameters.
3091    
3092    =back
3093    
3094    =cut
3095    
3096    sub Constrain {
3097        # Get the parameters.
3098        my ($value, $min, $max) = @_;
3099        # Declare the return variable.
3100        my $retVal = $value;
3101        # Apply the minimum constraint.
3102        if (defined $min && $retVal < $min) {
3103            $retVal = $min;
3104        }
3105        # Apply the maximum constraint.
3106        if (defined $max && $retVal > $max) {
3107            $retVal = $max;
3108        }
3109        # Return the result.
3110        return $retVal;
3111      }      }
     ScriptFinish("Html/MyTemplate.html", $varHash);  
3112    
3113  The idea here is that even if the script fails, you'll see trace messages and  =head3 Min
3114  useful output.  
3115        my $min = Min($value1, $value2, ... $valueN);
3116    
3117    Return the minimum argument. The arguments are treated as numbers.
3118    
3119  =over 4  =over 4
3120    
3121  =item webData  =item $value1, $value2, ... $valueN
3122    
3123  A string containing either the full web page to be written to the output or the  List of numbers to compare.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3124    
3125  =item varHash (optional)  =item RETURN
3126    
3127  If specified, then a reference to a hash mapping variable names for a template  Returns the lowest number in the list.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3128    
3129  =back  =back
3130    
3131  =cut  =cut
3132    
3133  sub ScriptFinish {  sub Min {
3134      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3135      my ($webData, $varHash) = @_;      my ($retVal, @values) = @_;
3136      # Check for a template file situation.      # Loop through the remaining parameters, looking for the lowest.
3137      my $outputString;      for my $value (@values) {
3138      if (defined $varHash) {          if ($value < $retVal) {
3139          # Here we have a template file. We need to determine the template type.              $retVal = $value;
         my $template;  
         if ($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 ne "NONE" && $TraceLevel > 0) {  
         # 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;  
         }  
         # If the trace messages were queued, we unroll them. Otherwise, we display the  
         # destination.  
         my $traceHtml;  
         if ($Destination eq "QUEUE") {  
             $traceHtml = QTrace('Html');  
         } elsif ($Destination =~ /^>>(.+)$/) {  
             # Here the tracing output it to a file. We code it as a hyperlink so the user  
             # can copy the file name into the clipboard easily.  
             my $actualDest = $1;  
             $traceHtml = "<p>Tracing output to <a href=\"$actualDest\">$actualDest</a>.</p>\n";  
         } else {  
             # Here we have one of the special destinations.  
             $traceHtml = "<P>Tracing output type is $Destination.</p>\n";  
3140          }          }
         substr $outputString, $pos, 0, $traceHtml;  
3141      }      }
3142      # Write the output string.      # Return the minimum found.
3143      print $outputString;      return $retVal;
3144  }  }
3145    
3146  =head3 Insure  =head3 Max
3147    
3148  C<< Insure($dirName); >>      my $max = Max($value1, $value2, ... $valueN);
3149    
3150  Insure a directory is present.  Return the maximum argument. The arguments are treated as numbers.
3151    
3152  =over 4  =over 4
3153    
3154  =item dirName  =item $value1, $value2, ... $valueN
3155    
3156  Name of the directory to check. If it does not exist, it will be created.  List of numbers to compare.
3157    
3158    =item RETURN
3159    
3160    Returns the highest number in the list.
3161    
3162  =back  =back
3163    
3164  =cut  =cut
3165    
3166  sub Insure {  sub Max {
3167      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
3168      if (! -d $dirName) {      my ($retVal, @values) = @_;
3169          Trace("Creating $dirName directory.") if T(2);      # Loop through the remaining parameters, looking for the highest.
3170          eval { mkpath $dirName; };      for my $value (@values) {
3171          if ($@) {          if ($value > $retVal) {
3172              Confess("Error creating $dirName: $@");              $retVal = $value;
3173          }          }
3174      }      }
3175        # Return the maximum found.
3176        return $retVal;
3177  }  }
3178    
 =head3 ChDir  
3179    
3180  C<< ChDir($dirName); >>  =head3 Strip
3181    
3182        my $string = Tracer::Strip($line);
3183    
3184  Change to the specified directory.  Strip all line terminators off a string. This is necessary when dealing with files
3185    that may have been transferred back and forth several times among different
3186    operating environments.
3187    
3188  =over 4  =over 4
3189    
3190  =item dirName  =item line
3191    
3192  Name of the directory to which we want to change.  Line of text to be stripped.
3193    
3194    =item RETURN
3195    
3196    The same line of text with all the line-ending characters chopped from the end.
3197    
3198  =back  =back
3199    
3200  =cut  =cut
3201    
3202  sub ChDir {  sub Strip {
3203      my ($dirName) = @_;      # Get a copy of the parameter string.
3204      if (! -d $dirName) {      my ($string) = @_;
3205          Confess("Cannot change to directory $dirName: no such directory.");      my $retVal = (defined $string ? $string : "");
3206      } else {      # Strip the line terminator characters.
3207          Trace("Changing to directory $dirName.") if T(4);      $retVal =~ s/(\r|\n)+$//g;
3208          my $okFlag = chdir $dirName;      # Return the result.
3209          if (! $okFlag) {      return $retVal;
             Confess("Error switching to directory $dirName.");  
         }  
     }  
3210  }  }
3211    
3212  =head3 SendSMS  =head3 Pad
3213    
3214  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3215    
3216  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  Pad a string to a specified length. The pad character will be a
3217  user name, password, and API ID for the relevant account in the hash reference variable  space, and the padding will be on the right side unless specified
3218  I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For  in the third parameter.
 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  
3219    
3220      $phone =  { user => 'BruceTheHumanPet',  =over 4
                 password => 'silly',  
                 api_id => '2561022' };  
3221    
3222  The original purpose of this method was to insure Bruce would be notified immediately when the  =item string
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3223    
3224  The message ID will be returned if successful, and C<undef> if an error occurs.  String to be padded.
3225    
3226  =over 4  =item len
3227    
3228  =item phoneNumber  Desired length of the padded string.
3229    
3230  Phone number to receive the message, in international format. A United States phone number  =item left (optional)
 would be prefixed by "1". A British phone number would be prefixed by "44".  
3231    
3232  =item msg  TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3233    
3234  Message to send to the specified phone.  =item padChar (optional)
3235    
3236    Character to use for padding. The default is a space.
3237    
3238  =item RETURN  =item RETURN
3239    
3240  Returns the message ID if successful, and C<undef> if the message could not be sent.  Returns a copy of the original string with the pad character added to the
3241    specified end so that it achieves the desired length.
3242    
3243  =back  =back
3244    
3245  =cut  =cut
3246    
3247  sub SendSMS {  sub Pad {
3248      # Get the parameters.      # Get the parameters.
3249      my ($phoneNumber, $msg) = @_;      my ($string, $len, $left, $padChar) = @_;
3250      # Declare the return variable. If we do not change it, C<undef> will be returned.      # Compute the padding character.
3251      my $retVal;      if (! defined $padChar) {
3252      # Only proceed if we have phone support.          $padChar = " ";
3253      if (! defined $FIG_Config::phone) {      }
3254          Trace("Phone support not present in FIG_Config.") if T(1);      # Compute the number of spaces needed.
3255      } else {      my $needed = $len - length $string;
3256          # Get the phone data.      # Copy the string into the return variable.
3257          my $parms = $FIG_Config::phone;      my $retVal = $string;
3258          # Get the Clickatell URL.      # Only proceed if padding is needed.
3259          my $url = "http://api.clickatell.com/http/";      if ($needed > 0) {
3260          # Create the user agent.          # Create the pad string.
3261          my $ua = LWP::UserAgent->new;          my $pad = $padChar x $needed;
3262          # Request a Clickatell session.          # Affix it to the return value.
3263          my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},          if ($left) {
3264                                       password => $parms->{password},              $retVal = $pad . $retVal;
                                      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+(.*)$/) {