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revision 1.84, Thu May 3 12:28:00 2007 UTC revision 1.108, Wed Sep 3 20:33:22 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 EmergencyKey ETracing 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 35  Line 36 
36      use Time::HiRes 'gettimeofday';      use Time::HiRes 'gettimeofday';
37      use URI::Escape;      use URI::Escape;
38      use Time::Local;      use Time::Local;
39        use POSIX qw(strftime);
40        use Time::Zone;
41        use Fcntl ':flock';
42    
43    
44  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
45    
# Line 159  Line 164 
164    
165  Sometimes, you need a way for tracing to happen automatically without putting parameters  Sometimes, you need a way for tracing to happen automatically without putting parameters
166  in a form or on the command line. Emergency tracing does this. You invoke emergency tracing  in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
167  from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.  from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
168  Emergency tracing requires you specify a tracing key. For command-line tools, the key is  that you specify a tracing key. For command-line tools, the key is
169  taken from the C<TRACING> environment variable. For web services, the key is taken from  taken from the C<TRACING> environment variable. For web services, the key is taken from
170  a cookie. Either way, the key tells the tracing facility who you are, so that you control  a cookie. Either way, the key tells the tracing facility who you are, so that you control
171  the tracing in your environment without stepping on other users.  the tracing in your environment without stepping on other users.
# Line 183  Line 188 
188    
189  The web script will look for the tracing key in the cookies, and the command-line  The web script will look for the tracing key in the cookies, and the command-line
190  script will look for it in the C<TRACING> environment variable. If you are  script will look for it in the C<TRACING> environment variable. If you are
191  using the L</StandardScript> or L</StandardSetup> methods, emergency tracing  using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
192  will be configured automatically.  will be configured automatically.
193    
 NOTE: to configure emergency tracing from the command line instead of the Debugging  
 Control Panel (see below), use the C<trace.pl> script.  
   
 =head3 Debugging Control Panel  
   
 The debugging control panel provides several tools to assist in development of  
 SEED and Sprout software. You access the debugging control panel from the URL  
 C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,  
 for example, the panel access point for the development NMPDR system is  
 C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to  
 find out what the password is. From this page, you can also specify a tracing  
 key. If you don't specify a key, one will be generated for you.  
   
 =head4 Emergency Tracing Form  
   
 At the bottom of the debugging control panel is a form that allows you to  
 specify a trace level and tracing categories. Special and common categories  
 are listed with check boxes. You can hold your mouse over a check box to see  
 what its category does. In general, however, a category name is the same as  
 the name of the package in which the trace message occurs.  
   
 Additional categories can be entered in an input box, delimited by spaces or commas.  
   
 The B<Activate> button turns on Emergency tracing at the level you specify with the  
 specified categories active. The B<Terminate> button turns tracing off. The  
 B<Show File> button displays the current contents of the trace file. The tracing  
 form at the bottom of the control panel is designed for emergency tracing, so it  
 will only affect programs that call L</ETracing>, L</StandardScript>,  
 or L</StandardSetup>.  
   
 =head4 Script Form  
   
 The top form of the debugging control panel allows you to enter a tiny script and  
 have the output generated in a formatted table. Certain object variables are  
 predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),  
 and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.  
   
 The last line of the script must be a scalar, but it can be a reference to a hash,  
 a list, a list of lists, and various other combinations. If you select the appropriate  
 data type in the dropdown box, the output will be formatted accordingly. The form  
 also has controls for specifying tracing. These controls override any emergency  
 tracing in effect.  
   
 =head4 Database Query Forms  
   
 The forms between the script form and the emergency tracing form allow you to  
 make queries against the database. The FIG query form allows simple queries against  
 a single FIG table. The Sprout query form uses the B<GetAll> method to do a  
 multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>  
 package, and it takes five parameters.  
   
     GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);  
   
 Each of the five parameters corresponds to a text box on the query form:  
   
 =over 4  
   
 =item Objects  
   
 Comma-separated list containing the names of the entity and relationship objects to be retrieved.  
   
 =item Filter  
   
 WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  
 be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form  
 B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a  
 field, I<objectName> is the name of the entity or relationship object containing the field, and  
 I<number> is the 1-based position of the object in the object list. Any parameters  
 specified in the filter clause should be specified in the B<Params> field.  
 The fields in a filter clause can come from primary entity relations,  
 relationship relations, or secondary entity relations; however, all of the  
 entities and relationships involved must be included in the list of object names.  
   
 =item Params  
   
 List of the parameters to be substituted in for the parameters marks in the filter clause. This  
 is a comma-separated list without any quoting or escaping.  
   
 =item fields  
   
 Comma-separated list of the fields to be returned in each element of the list returned. Fields  
 are specified in the same manner as in the filter clause.  
   
 =item count  
   
 Maximum number of records to return. If omitted or 0, all available records will be returned.  
   
 =back  
   
 B<GetAll> automatically joins together the entities and relationships listed in the object  
 names. This simplifies the coding of the filter clause, but it means that some queries are  
 not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation  
 that has yet to be addressed.  
   
194  =cut  =cut
195    
196  # Declare the configuration variables.  # Declare the configuration variables.
197    
198  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
199  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
200                              # standard output                              # standard output
201  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
202                              # hash of active category names                              # hash of active category names
203    my @LevelNames = qw(error warn notice info detail);
204  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
205                              # messages                              # messages
206  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
207  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
208    my $LastLevel = 0;          # level of the last test call
209  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
210  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
211    my $SavedCGI;               # CGI object passed to ETracing
212    my $CommandLine;            # Command line passed to StandardSetup
213    umask 2;                    # Fix the damn umask so everything is group-writable.
214    
215    =head2 Tracing Methods
216    
217    =head3 Setups
218    
219        my $count = Tracer::Setups();
220    
221    Return the number of times L</TSetup> has been called.
222    
223    This method allows for the creation of conditional tracing setups where, for example, we
224    may want to set up tracing if nobody else has done it before us.
225    
226    =cut
227    
228  =head2 Public Methods  sub Setups {
229        return $SetupCount;
230    }
231    
232  =head3 TSetup  =head3 TSetup
233    
234  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
235    
236  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
237  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 350  Line 281 
281          }          }
282      }      }
283      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
284      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
285      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
286        # the standard output (tee mode).
287      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
288          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
289              $TeeFlag = 1;              $TeeFlag = 1;
290              $target = substr($target, 1);              $target = substr($target, 1);
291          }          }
292          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
293                # We need to initialize the file (which clears it).
294              open TRACEFILE, $target;              open TRACEFILE, $target;
295              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
296              close TRACEFILE;              close TRACEFILE;
297                # Set to append mode now that the file has been cleared.
298              $Destination = ">$target";              $Destination = ">$target";
299          } else {          } else {
300              $Destination = $target;              $Destination = $target;
# Line 372  Line 306 
306      $SetupCount++;      $SetupCount++;
307  }  }
308    
309  =head3 StandardSetup  =head3 SetLevel
   
 C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>  
310    
311  This method performs standard command-line parsing and tracing setup. The return      Tracer::SetLevel($newLevel);
 values are a hash of the command-line options and a list of the positional  
 parameters. Tracing is automatically set up and the command-line options are  
 validated.  
312    
313  This is a complex method that does a lot of grunt work. The parameters can  Modify the trace level. A higher trace level will cause more messages to appear.
 be more easily understood, however, once they are examined individually.  
314    
315  The I<categories> parameter is the most obtuse. It is a reference to a list of  =over 4
 special-purpose tracing categories. Most tracing categories are PERL package  
 names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,  
 B<ERDB>, and B<SproutLoad> packages, you would specify the categories  
316    
317      ["Sprout", "SproutLoad", "ERDB"]  =item newLevel
318    
319  This would cause trace messages in the specified three packages to appear in  Proposed new trace level.
 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.  
320    
321  =over 4  =back
322    
323  =item SQL  =cut
324    
325  Traces SQL commands and activity.  sub SetLevel {
326        $TraceLevel = $_[0];
327    }
328    
329  =item Tracer  =head3 ParseDate
330    
331  Traces error messages and call stacks.      my $time = Tracer::ParseDate($dateString);
332    
333  =back  Convert a date into a PERL time number. This method expects a date-like string
334    and parses it into a number. The string must be vaguely date-like or it will
335    return an undefined value. Our requirement is that a month and day be
336    present and that three pieces of the date string (time of day, month and day,
337    year) be separated by likely delimiters, such as spaces, commas, and such-like.
338    
339  C<SQL> is only turned on if the C<-sql> option is specified in the command line.  If a time of day is present, it must be in military time with two digits for
340  The trace level is specified using the C<-trace> command-line option. For example,  everything but the hour.
 the following command line for C<TransactFeatures> turns on SQL tracing and runs  
 all tracing at level 3.  
341    
342      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  The year must be exactly four digits.
343    
344  Standard tracing is output to the standard output and echoed to the file  Additional stuff can be in the string. We presume it's time zones or weekdays or something
345  C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the  equally innocuous. This means, however, that a sufficiently long sentence with date-like
346  process ID. You can also specify the C<user> parameter to put a user ID  parts in it may be interpreted as a date. Hopefully this will not be a problem.
 instead of a process ID in the trace file name. So, for example  
347    
348  The default trace level is 2. To get all messages, specify a trace level of 4.  It should be guaranteed that this method will parse the output of the L</Now> function.
 For a genome-by-genome update, use 3.  
349    
350      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  The parameters are as follows.
351    
352  would send the trace output to C<traceBruce.log> in the temporary directory.  =over 4
353    
354  The I<options> parameter is a reference to a hash containing the command-line  =item dateString
 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.  
355    
356  You can specify a different default trace level by setting C<$options->{trace}>  The date string to convert.
 prior to calling this method.  
357    
358  An example at this point would help. Consider, for example, the command-line utility  =item RETURN
 C<TransactFeatures>. It accepts a list of positional parameters plus the options  
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
359    
360      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
361                          { safe => [0, "use database transactions"],  the date string is invalid. A valid date string must contain a month and day.
                           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);  
362    
363    =back
364    
365  The call to C<ParseCommand> specifies the default values for the options and  =cut
 stores the actual options in a hash that is returned as C<$options>. The  
 positional parameters are returned in C<@parameters>.  
366    
367  The following is a sample command line for C<TransactFeatures>.  # Universal month conversion table.
368    use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
369                                Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
370                                Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
371                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
372                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
373                                Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
374                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
375                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
376                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
377                                Oct =>  9, October  =>   9, '10' =>  9,
378                                Nov => 10, November =>  10, '11' => 10,
379                                Dec => 11, December =>  11, '12' => 11
380                            };
381    
382      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  sub ParseDate {
383        # Get the parameters.
384        my ($dateString) = @_;
385        # Declare the return variable.
386        my $retVal;
387        # Find the month and day of month. There are two ways that can happen. We check for the
388        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
389        # won't be fooled into thinking the month is Sunday.
390        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
391            my ($mon, $mday) = (MONTHS->{$1}, $2);
392            # Insist that the month and day are valid.
393            if (defined($mon) && $2 >= 1 && $2 <= 31) {
394                # Find the time.
395                my ($hour, $min, $sec) = (0, 0, 0);
396                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
397                    ($hour, $min, $sec) = ($1, $2, $3);
398                }
399                # Find the year.
400                my $year;
401                if ($dateString =~ /\b(\d{4})\b/) {
402                    $year = $1;
403                } else {
404                    # Get the default year, which is this one. Note we must convert it to
405                    # the four-digit value expected by "timelocal".
406                    (undef, undef, undef, undef, undef, $year) = localtime();
407                    $year += 1900;
408                }
409                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
410            }
411        }
412        # Return the result.
413        return $retVal;
414    }
415    
416  Single and double hyphens are equivalent. So, you could also code the  =head3 LogErrors
 above command as  
417    
418      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl      Tracer::LogErrors($fileName);
419    
420  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  Route the standard error output to a log file.
 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<$options> hash would be  
421    
422      { trace => 2, sql => 0, safe => 0,  =over 4
       noAlias => 1, start => ' ', tblFiles => 0 }  
423    
424  Use of C<StandardSetup> in this way provides a simple way of performing  =item fileName
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
425    
426  If the C<background> option is specified on the command line, then the  Name of the file to receive the error output.
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
427    
428      -user=Bruce -background  =back
429    
430  then the trace output would go to C<traceBruce.log>, the standard output to  =cut
 C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to  
 simplify starting a command in the background.  
431    
432  The user name is also used as the tracing key for L</Emergency Tracing>.  sub LogErrors {
433  Specifying a value of C<E> for the trace level causes emergency tracing to      # Get the file name.
434  be used instead of custom tracing. If the user name is not specified,      my ($fileName) = @_;
435  the tracing key is taken from the C<Tracing> environment variable. If there      # Open the file as the standard error output.
436  is no value for that variable, the tracing key will be computed from the PID.      open STDERR, '>', $fileName;
437    }
438    
439  Finally, if the special option C<-help> is specified, the option  =head3 Trace
 names will be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
440    
441      TransactFeatures -help      Trace($message);
442    
443  he would see the following output.  Write a trace message to the target location specified in L</TSetup>. If there has not been
444    any prior call to B<TSetup>.
445    
446      TransactFeatures [options] <command> <transactionDirectory> <IDfile>  =over 4
         -trace    tracing level (default E)  
         -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  
447    
448  The caller has the option of modifying the tracing scheme by placing a value  =item message
 for C<trace> in the incoming options hash. The default value can be overridden,  
 or the tracing to the standard output can be turned off by suffixing a minus  
 sign to the trace level. So, for example,  
449    
450      { trace => [0, "tracing level (default 0)"],  Message to write.
        ...  
451    
452  would set the default trace level to 0 instead of E, while  =back
453    
454      { trace => ["2-", "tracing level (default 2)"],  =cut
        ...  
455    
456  would set the default to 2, but trace only to the log file, not to the  sub Trace {
457  standard output.      # Get the parameters.
458        my ($message) = @_;
459        # Strip off any line terminators at the end of the message. We will add
460        # new-line stuff ourselves.
461        my $stripped = Strip($message);
462        # Compute the caller information.
463        my ($callPackage, $callFile, $callLine) = caller();
464        my $callFileTitle = basename($callFile);
465        # Check the caller.
466        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
467        # Get the timestamp.
468        my $timeStamp = Now();
469        # Build the prefix.
470        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
471        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
472        # Format the message.
473        my $formatted = "$prefix $stripped";
474        # Process according to the destination.
475        if ($Destination eq "TEXT") {
476            # Write the message to the standard output.
477            print "$formatted\n";
478        } elsif ($Destination eq "ERROR") {
479            # Write the message to the error output. Here, we want our prefix fields.
480            print STDERR "$formatted\n";
481        } elsif ($Destination eq "WARN") {
482            # Emit the message to the standard error output. It is presumed that the
483            # error logger will add its own prefix fields, the notable exception being
484            # the caller info.
485            print STDERR "$callerInfo$stripped\n";
486        } elsif ($Destination eq "QUEUE") {
487            # Push the message into the queue.
488            push @Queue, "$formatted";
489        } elsif ($Destination eq "HTML") {
490            # Convert the message to HTML and write it to the standard output.
491            my $escapedMessage = CGI::escapeHTML($stripped);
492            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
493        } elsif ($Destination =~ m/^>>/) {
494            # Write the trace message to an output file.
495            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
496            print TRACING "$formatted\n";
497            close TRACING;
498            # If the Tee flag is on, echo it to the standard output.
499            if ($TeeFlag) {
500                print "$formatted\n";
501            }
502        }
503    }
504    
505  The parameters to this method are as follows.  =head3 T
506    
507  =over 4      my $switch = T($category, $traceLevel);
508    
509  =item categories      or
510    
511  Reference to a list of tracing category names. These should be names of      my $switch = T($traceLevel);
 packages whose internal workings will need to be debugged to get the  
 command working.  
512    
513  =item options  Return TRUE if the trace level is at or above a specified value and the specified category
514    is active, else FALSE. If no category is specified, the caller's package name is used.
515    
516  Reference to a hash containing the legal options for the current command mapped  =over 4
 to their default values and descriptions. The user can override the defaults  
 by specifying the options as command-line switches prefixed by a hyphen.  
 Tracing-related options may be added to this hash. If the C<-h> option is  
 specified on the command line, the option descriptions will be used to  
 explain the options. To turn off tracing to the standard output, add a  
 minus sign to the value for C<trace> (see above).  
517    
518  =item parmHelp  =item category
519    
520  A string that vaguely describes the positional parameters. This is used  Category to which the message belongs. If not specified, the caller's package name is
521  if the user specifies the C<-h> option.  used.
522    
523  =item argv  =item traceLevel
524    
525  List of command line parameters, including the option switches, which must  Relevant tracing level.
 precede the positional parameters and be prefixed by a hyphen.  
526    
527  =item RETURN  =item RETURN
528    
529  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.  
530    
531  =back  =back
532    
533  =cut  =cut
534    
535  sub StandardSetup {  sub T {
536        # Declare the return variable.
537        my $retVal = 0;
538        # Only proceed if tracing is turned on.
539        if ($Destination ne "NONE") {
540      # Get the parameters.      # Get the parameters.
541      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
542      # Get the default tracing key.          if (!defined $traceLevel) {
543      my $tkey = EmergencyKey();              # Here we have no category, so we need to get the calling package.
544      # Add the tracing options.              # The calling package is normally the first parameter. If it is
545      if (! exists $options->{trace}) {              # omitted, the first parameter will be the tracelevel. So, the
546          $options->{trace} = ['E', "tracing level (E for emergency tracing)"];              # first thing we do is shift the so-called category into the
547      }              # $traceLevel variable where it belongs.
548      $options->{sql} = [0, "turn on SQL tracing"];              $traceLevel = $category;
549      $options->{help} = [0, "display command-line options"];              my ($package, $fileName, $line) = caller;
550      $options->{user} = [$tkey, "tracing key"];              # If there is no calling package, we default to "main".
551      $options->{background} = [0, "spool standard and error output"];              if (!$package) {
552      # Create a parsing hash from the options hash. The parsing hash                  $category = "main";
     # contains the default values rather than the default value  
     # and the description. While we're at it, we'll memorize the  
     # 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, ">$errFileName";  
     }  
     # Now we want to set up tracing. First, we need to know if the user  
     # wants emergency tracing.  
     if ($retOptions->{trace} eq 'E') {  
         ETracing($retOptions->{user});  
553      } else {      } else {
554          # Here the tracing is controlled from the command line.                  my @cats = split /::/, $package;
555          my @cats = @{$categories};                  $category = $cats[$#cats];
         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";  
556              }              }
             # 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";  
             } else {  
                 $traceMode = "WARN";  
557              }              }
558            # Save the category name and level.
559            $LastCategory = $category;
560            $LastLevel = $traceLevel;
561            # Convert it to lower case before we hash it.
562            $category = lc $category;
563            # Validate the trace level.
564            if (ref $traceLevel) {
565                Confess("Bad trace level.");
566            } elsif (ref $TraceLevel) {
567                Confess("Bad trace config.");
568          }          }
569          # Now set up the tracing.          # Make the check. Note that level 0 shows even if the category is turned off.
570          TSetup("$traceLevel $cats", $traceMode);          $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
571      }      }
572      # Check for the "h" option. If it is specified, dump the command-line      # Return the computed result.
573      # options and exit the program.      return $retVal;
     if ($retOptions->{help}) {  
         $0 =~ m#[/\\](\w+)(\.pl)?$#i;  
         print "$1 [options] $parmHelp\n";  
         for my $key (sort keys %{$options}) {  
             my $name = Pad($key, $longestName, 0, ' ');  
             my $desc = $options->{$key}->[1];  
             if ($options->{$key}->[0]) {  
                 $desc .= " (default " . $options->{$key}->[0] . ")";  
574              }              }
575              print "  $name $desc\n";  
576    =head3 QTrace
577    
578        my $data = QTrace($format);
579    
580    Return the queued trace data in the specified format.
581    
582    =over 4
583    
584    =item format
585    
586    C<html> to format the data as an HTML list, C<text> to format it as straight text.
587    
588    =back
589    
590    =cut
591    
592    sub QTrace {
593        # Get the parameter.
594        my ($format) = @_;
595        # Create the return variable.
596        my $retVal = "";
597        # Only proceed if there is an actual queue.
598        if (@Queue) {
599            # Process according to the format.
600            if ($format =~ m/^HTML$/i) {
601                # Convert the queue into an HTML list.
602                $retVal = "<ul>\n";
603                for my $line (@Queue) {
604                    my $escapedLine = CGI::escapeHTML($line);
605                    $retVal .= "<li>$escapedLine</li>\n";
606          }          }
607          exit(0);              $retVal .= "</ul>\n";
608            } elsif ($format =~ m/^TEXT$/i) {
609                # Convert the queue into a list of text lines.
610                $retVal = join("\n", @Queue) . "\n";
611      }      }
612      # Trace the options, if applicable.          # Clear the queue.
613      if (T(3)) {          @Queue = ();
         my @parms = grep { $retOptions->{$_} } keys %{$retOptions};  
         Trace("Selected options: " . join(", ", sort @parms) . ".");  
614      }      }
615      # Return the parsed parameters.      # Return the formatted list.
616      return ($retOptions, @retParameters);      return $retVal;
617  }  }
618    
619  =head3 Setups  =head3 Confess
620    
621  C<< my $count = Tracer::Setups(); >>      Confess($message);
622    
623  Return the number of times L</TSetup> has been called.  Trace the call stack and abort the program with the specified message. When used with
624    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
625    So, for example
626    
627  This method allows for the creation of conditional tracing setups where, for example, we      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
628  may want to set up tracing if nobody else has done it before us.  
629    Will abort the program with a stack trace if the value of C<$recNum> is negative.
630    
631    =over 4
632    
633    =item message
634    
635    Message to include in the trace.
636    
637    =back
638    
639  =cut  =cut
640    
641  sub Setups {  sub Confess {
642      return $SetupCount;      # Get the parameters.
643        my ($message) = @_;
644        # Set up the category and level.
645        $LastCategory = "(confess)";
646        $LastLevel = 0;
647        if (! defined($FIG_Config::no_tool_hdr)) {
648            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
649            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
650            # Only proceed if the tool header file is actually present.
651            if (-f $toolHeaderFile) {
652                my $fh;
653                if (open $fh, "<$toolHeaderFile") {
654                    my @lines = <$fh>;
655                    Trace("Tool header has " . scalar(@lines) . " lines.");
656                }
657            }
658        }
659        # Trace the call stack.
660        Cluck($message);
661        # Abort the program.
662        croak(">>> $message");
663  }  }
664    
665  =head3 Open  =head3 SaveCGI
   
 C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  
666    
667  Open a file.      Tracer::SaveCGI($cgi);
668    
669  The I<$fileSpec> is essentially the second argument of the PERL C<open>  This method saves the CGI object but does not activate emergency tracing.
670  function. The mode is specified using Unix-like shell information. So, for  It is used to allow L</Warn> to work in situations where emergency
671  example,  tracing is contra-indicated (e.g. the wiki).
672    
673      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =over 4
674    
675  would open for output appended to the specified file, and  =item cgi
676    
677      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  Active CGI query object.
678    
679  would open a pipe that sorts the records written and removes duplicates. Note  =back
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
680    
681      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =cut
682    
683  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  sub SaveCGI {
684  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a      $SavedCGI = $_[0];
685  failed open will throw an exception and the third parameter will be used to construct  }
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
686    
687      Could not open "/usr/spool/news/twitlog"  =head3 Warn
688    
689  Note that the mode characters are automatically cleaned from the file name.      Warn($message, @options);
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
690    
691      Could not open "/usr/spool/news/twitlog": file not found.  This method traces an important message. If an RSS feed is configured
692    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
693    then the message will be echoed to the feed. In general, a tracing
694    destination of C<WARN> indicates that the caller is running as a web
695    service in a production environment; however, this is not a requirement.
696    
697  In some versions of PERL the only error message we get is a number, which  To force warnings into the RSS feed even when the tracing destination
698  corresponds to the C++ C<errno> value.  is not C<WARN>, simply specify the C<Feed> tracing module. This can be
699    configured automatically when L</StandardSetup> is used.
700    
701      Could not open "/usr/spool/news/twitlog": 6.  The L</Cluck> method calls this one for its final message. Since
702    L</Confess> calls L</Cluck>, this means that any error which is caught
703    and confessed will put something in the feed. This insures that someone
704    will be alerted relatively quickly when a failure occurs.
705    
706  =over 4  =over 4
707    
708  =item fileHandle  =item message
709    
710  File handle. If this parameter is C<undef>, a file handle will be generated  Message to be traced.
 and returned as the value of this method.  
711    
712  =item fileSpec  =item options
713    
714  File name and mode, as per the PERL C<open> function.  A list containing zero or more options.
715    
716  =item message (optional)  =back
717    
718  Error message to use if the open fails. If omitted, a standard error message  The permissible options are as follows.
 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>.  
719    
720  =item RETURN  =over 4
721    
722  Returns the name of the file handle assigned to the file, or C<undef> if the  =item noStack
723  open failed.  
724    If specified, then the stack trace is not included in the output.
725    
726  =back  =back
727    
728  =cut  =cut
729    
730  sub Open {  sub Warn {
731      # Get the parameters.      # Get the parameters.
732      my ($fileHandle, $fileSpec, $message) = @_;      my $message = shift @_;
733      # Attempt to open the file.      my %options = map { $_ => 1 } @_;
734      my $rv = open $fileHandle, $fileSpec;      # Save $@;
735      # If the open failed, generate an error message.      my $savedError = $@;
736      if (! $rv) {      # Trace the message.
737          # Save the system error message.      Trace($message);
738          my $sysMessage = $!;      # This will contain the lock handle. If it's defined, it means we need to unlock.
739          # See if we need a default message.      my $lock;
740          if (!$message) {      # Check for feed forcing.
741              # Clean any obvious mode characters and leading spaces from the      my $forceFeed = exists $Categories{feed};
742              # filename.      # An error here would be disastrous. Note that if debug mode is specified,
743              my ($fileName) = FindNamePart($fileSpec);      # we do this stuff even in a test environment.
744              $message = "Could not open \"$fileName\"";      eval {
745            # Do we need to put this in the RSS feed?
746            if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
747                # Yes. We now need to compute the date, the link, and the title.
748                # First, the date, in a very specific format.
749                my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
750                    (tz_local_offset() / 30);
751                # Environment data goes in here. We start with the date.
752                my $environment = "$date.  ";
753                # If we need to recap the message (because it's too long to be a title), we'll
754                # put it in here.
755                my $recap;
756                # Copy the message and remove excess space.
757                my $title = $message;
758                $title =~ s/\s+/ /gs;
759                # If it's too long, we have to split it up.
760                if (length $title > 60) {
761                    # Put the full message in the environment string.
762                    $recap = $title;
763                    # Excerpt it as the title.
764                    $title = substr($title, 0, 50) . "...";
765                }
766                # If we have a CGI object, then this is a web error. Otherwise, it's
767                # command-line.
768                if (defined $SavedCGI) {
769                    # We're in a web service. The environment is the user's IP, and the link
770                    # is the URL that got us here.
771                    my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
772                    $environment .= "Event Reported at IP address $key process $$.";
773                    my $url = $SavedCGI->self_url();
774                    # We need the user agent string and (if available) the referrer.
775                    # The referrer will be the link.
776                    $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
777                    if ($ENV{HTTP_REFERER}) {
778                        my $link = $ENV{HTTP_REFERER};
779                        $environment .= " referred from <a href=\"$link\">$link</a>.";
780                    } else {
781                        $environment .= " referrer unknown.";
782                    }
783                    # Close off the sentence with the original link.
784                    $environment .= " URL of event is <a href=\"$url\">$url</a>.";
785                } else {
786                    # No CGI object, so we're a command-line tool. Use the tracing
787                    # key and the PID as the user identifier, and add the command.
788                    my $key = EmergencyKey();
789                    $environment .= "Event Reported by $key process $$.";
790                    if ($CommandLine) {
791                        # We're in a StandardSetup script, so we have the real command line.
792                        $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
793                    } elsif ($ENV{_}) {
794                        # We're in a BASH script, so the command has been stored in the _ variable.
795                        $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
796                    }
797                }
798                # Build a GUID. We use the current time, the title, and the process ID,
799                # then digest the result.
800                my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
801                # Finally, the description. This is a stack trace plus various environmental stuff.
802                # The trace is optional.
803                my $stackTrace;
804                if ($options{noStack}) {
805                    $stackTrace = "";
806                } else {
807                    my @trace = LongMess();
808                    # Only proceed if we got something back.
809                    if (scalar(@trace) > 0) {
810                        $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
811                        $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
812                    }
813                }
814                # We got the stack trace. Now it's time to put it all together.
815                # We have a goofy thing here in that we need to HTML-escape some sections of the description
816                # twice. They will be escaped once here, and then once when written by XML::Simple. They are
817                # unescaped once when processed by the RSS reader, and stuff in the description is treated as
818                # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
819                # our <br>s and <pre>s are used to format the description.
820                $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
821                my $description = "$recap$environment  $stackTrace";
822                # Okay, we have all the pieces. Create a hash of the new event.
823                my $newItem = { title => $title,
824                                description => $description,
825                                category => $LastCategory,
826                                pubDate => $date,
827                                guid => $guid,
828                              };
829                # We need XML capability for this.
830                require XML::Simple;
831                # The RSS document goes in here.
832                my $rss;
833                # Get the name of the RSS file. It's in the FIG temporary directory.
834                my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
835                # Open the config file and lock it.
836                $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
837                flock $lock, LOCK_EX;
838                # Does it exist?
839                if (-s $fileName) {
840                    # Slurp it in.
841                    $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
842                } else {
843                    my $size = -s $fileName;
844                    # Create an empty channel.
845                    $rss = {
846                        channel => {
847                            title => 'NMPDR Warning Feed',
848                            link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
849                            description => "Important messages regarding the status of the NMPDR.",
850                            generator => "NMPDR Trace Facility",
851                            docs => "http://blogs.law.harvard.edu/tech/rss",
852                            item => []
853                        },
854                    };
855          }          }
856          # Terminate with an error using the supplied message and the              # Get the channel object.
857          # error message from the file system.              my $channel = $rss->{channel};
858          Confess("$message: $!");              # Update the last-build date.
859                $channel->{lastBuildDate} = $date;
860                # Get the item array.
861                my $items = $channel->{item};
862                # Insure it has only 100 entries.
863                while (scalar @{$items} > 100) {
864                    pop @{$items};
865                }
866                # Add our new item at the front.
867                unshift @{$items}, $newItem;
868                # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
869                # the requirements for those.
870                my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
871                # Here we put in the root and declaration. The problem is that the root has to have the version attribute
872                # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
873                $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
874                # We don't use Open here because we can't afford an error.
875                if (open XMLOUT, ">$fileName") {
876                    print XMLOUT $xml;
877                    close XMLOUT;
878      }      }
879      # Return the file handle.          }
880      return $fileHandle;      };
881        if ($@) {
882            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
883            # (which is a good thing).
884            my $error = $@;
885            Trace("Feed Error: $error") if T(Feed => 0);
886        }
887        # Be sure to unlock.
888        if ($lock) {
889            flock $lock, LOCK_UN;
890            undef $lock;
891        }
892        # Restore the error message.
893        $@ = $savedError;
894  }  }
895    
 =head3 FindNamePart  
   
 C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>  
   
 Extract the portion of a file specification that contains the file name.  
   
 A file specification is the string passed to an C<open> call. It specifies the file  
 mode and name. In a truly complex situation, it can specify a pipe sequence. This  
 method assumes that the file name is whatever follows the first angle bracket  
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
   
     >>/usr/fig/myfile.txt  
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
896    
 If the method cannot find a file name using its normal methods, it will return the  
 whole incoming string.  
897    
 =over 4  
898    
899  =item fileSpec  =head3 Assert
900    
901  File specification string from which the file name is to be extracted.      Assert($condition1, $condition2, ... $conditionN);
902    
903  =item RETURN  Return TRUE if all the conditions are true. This method can be used in conjunction with
904    the OR operator and the L</Confess> method as a debugging assert.
905    So, for example
906    
907  Returns a three-element list. The first element contains the file name portion of      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
 the specified string, or the whole string if a file name cannot be found via normal  
 methods. The second element contains the start position of the file name portion and  
 the third element contains the length.  
908    
909  =back  Will abort the program with a stack trace if the value of C<$recNum> is negative.
910    
911  =cut  =cut
912  #: Return Type $;  sub Assert {
913  sub FindNamePart {      my $retVal = 1;
914      # Get the parameters.      LOOP: for my $condition (@_) {
915      my ($fileSpec) = @_;          if (! $condition) {
916      # Default to the whole input string.              $retVal = 0;
917      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);              last LOOP;
     # Parse out the file name if we can.  
     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {  
         $retVal = $2;  
         $len = length $retVal;  
         $pos = (length $fileSpec) - (length $3) - $len;  
918      }      }
919      # Return the result.      }
920      return ($retVal, $pos, $len);      return $retVal;
921  }  }
922    
923  =head3 OpenDir  =head3 Cluck
   
 C<< my @files = OpenDir($dirName, $filtered, $flag); >>  
   
 Open a directory and return all the file names. This function essentially performs  
 the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  
 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  
 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be  
 filtered out of the return list. If the directory does not open and I<$flag> is not  
 set, an exception is thrown. So, for example,  
   
     my @files = OpenDir("/Volumes/fig/contigs", 1);  
   
 is effectively the same as  
924    
925      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");      Cluck($message);
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
926    
927  Similarly, the following code  Trace the call stack. Note that for best results, you should qualify the call with a
928    trace condition. For example,
929    
930      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);      Cluck("Starting record parse.") if T(3);
931    
932  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  will only trace the stack if the trace level for the package is 3 or more.
 automatically returns an empty list if the directory fails to open.  
933    
934  =over 4  =over 4
935    
936  =item dirName  =item message
937    
938  Name of the directory to open.  Message to include in the trace.
939    
940  =item filtered  =back
941    
942  TRUE if files whose names begin with a period (C<.>) should be automatically removed  =cut
 from the list, else FALSE.  
943    
944  =item flag  sub Cluck {
945        # Get the parameters.
946        my ($message) = @_;
947        # Trace what's happening.
948        Trace("Stack trace for event: $message");
949        # Get the stack trace.
950        my @trace = LongMess();
951        # Convert the trace to a series of messages.
952        for my $line (@trace) {
953            # Replace the tab at the beginning with spaces.
954            $line =~ s/^\t/    /;
955            # Trace the line.
956            Trace($line);
957        }
958        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
959        Warn($message);
960    }
961    
962  TRUE if a failure to open is okay, else FALSE  =head3 LongMess
963    
964  =back      my @lines = Tracer::LongMess();
965    
966    Return a stack trace with all tracing methods removed. The return will be in the form of a list
967    of message strings.
968    
969  =cut  =cut
970  #: Return Type @;  
971  sub OpenDir {  sub LongMess {
     # Get the parameters.  
     my ($dirName, $filtered, $flag) = @_;  
972      # Declare the return variable.      # Declare the return variable.
973      my @retVal = ();      my @retVal = ();
974      # Open the directory.      my $confession = longmess("");
975      if (opendir(my $dirHandle, $dirName)) {      for my $line (split /\s*\n/, $confession) {
976          # The directory opened successfully. Get the appropriate list according to the          unless ($line =~ /Tracer\.pm/) {
977          # strictures of the filter parameter.              # Here we have a line worth keeping. Push it onto the result list.
978          if ($filtered) {              push @retVal, $line;
             @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;  
         } else {  
             @retVal = readdir $dirHandle;  
979          }          }
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
980      }      }
981      # Return the result.      # Return the result.
982      return @retVal;      return @retVal;
983  }  }
984    
985  =head3 SetLevel  =head3 ETracing
986    
987  C<< Tracer::SetLevel($newLevel); >>      ETracing($parameter);
988    
989  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
990    on automatically for any program that calls this method. The emergency
991    tracing parameters are stored in a a file identified by a tracing key.
992    If this method is called with a CGI object, then the tracing key is
993    taken from a cookie. If it is called with no parameters, then the tracing
994    key is taken from an environment variable. If it is called with a string,
995    the tracing key is that string.
996    
997  =over 4  =over 4
998    
999  =item newLevel  =item parameter
1000    
1001  Proposed new trace level.  A parameter from which the tracing key is computed. If it is a scalar,
1002    that scalar is used as the tracing key. If it is a CGI object, the
1003    tracing key is taken from the C<IP> cookie. If it is omitted, the
1004    tracing key is taken from the C<TRACING> environment variable. If it
1005    is a CGI object and emergency tracing is not on, the C<Trace> and
1006    C<TF> parameters will be used to determine the type of tracing.
1007    
1008  =back  =back
1009    
1010  =cut  =cut
1011    
1012  sub SetLevel {  sub ETracing {
1013      $TraceLevel = $_[0];      # Get the parameter.
1014        my ($parameter) = @_;
1015        # Check for CGI mode.
1016        if (defined $parameter && ref $parameter eq 'CGI') {
1017            $SavedCGI = $parameter;
1018        } else {
1019            $SavedCGI = undef;
1020        }
1021        # Default to no tracing except errors.
1022        my ($tracing, $dest) = ("0", "WARN");
1023        # Check for emergency tracing.
1024        my $tkey = EmergencyKey($parameter);
1025        my $emergencyFile = EmergencyFileName($tkey);
1026        if (-e $emergencyFile) {
1027            # We have the file. Read in the data.
1028            my @tracing = GetFile($emergencyFile);
1029            # Pull off the time limit.
1030            my $expire = shift @tracing;
1031            # Convert it to seconds.
1032            $expire *= 3600;
1033            # Check the file data.
1034            my $stat = stat($emergencyFile);
1035            my ($now) = gettimeofday;
1036            if ($now - $stat->mtime > $expire) {
1037                # Delete the expired file.
1038                unlink $emergencyFile;
1039            } else {
1040                # Emergency tracing is on. Pull off the destination and
1041                # the trace level;
1042                $dest = shift @tracing;
1043                my $level = shift @tracing;
1044                # Convert the destination to a real tracing destination.
1045                # temp directory.
1046                $dest = EmergencyTracingDest($tkey, $dest);
1047                # Insure Tracer is specified.
1048                my %moduleHash = map { $_ => 1 } @tracing;
1049                $moduleHash{Tracer} = 1;
1050                # Set the trace parameter.
1051                $tracing = join(" ", $level, sort keys %moduleHash);
1052            }
1053        } elsif (defined $SavedCGI) {
1054            # There's no emergency tracing, but we have a CGI object, so check
1055            # for tracing from the form parameters.
1056            if ($SavedCGI->param('Trace')) {
1057                # Here the user has requested tracing via a form.
1058                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1059                $tracing = $SavedCGI->param('Trace') . " Tracer";
1060            }
1061        }
1062        # Setup the tracing we've determined from all the stuff above.
1063        TSetup($tracing, $dest);
1064        # Check to see if we're a web script.
1065        if (defined $SavedCGI) {
1066            # Yes we are. Trace the form and environment data.
1067            TraceParms($SavedCGI);
1068            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1069            # emitted by the script in its raw form.
1070            if (T(Raw => 3)) {
1071                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1072  }  }
   
 =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;  
1073  }  }
   
 # Pad a number to 2 digits.  
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
1074  }  }
1075    
1076  =head3 ParseTraceDate  =head3 EmergencyFileName
1077    
1078  C<< my $time = Tracer::ParseTraceDate($dateString); >>      my $fileName = Tracer::EmergencyFileName($tkey);
1079    
1080  Convert a date from the trace file into a PERL timestamp.  Return the emergency tracing file name. This is the file that specifies
1081    the tracing information.
1082    
1083  =over 4  =over 4
1084    
1085  =item dateString  =item tkey
1086    
1087  The date string from the trace file. The format of the string is determined by the  Tracing key for the current program.
 L</Now> method.  
1088    
1089  =item RETURN  =item RETURN
1090    
1091  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if  Returns the name of the file to contain the emergency tracing information.
 the time string is invalid.  
1092    
1093  =back  =back
1094    
1095  =cut  =cut
1096    
1097  sub ParseTraceDate {  sub EmergencyFileName {
1098      # Get the parameters.      # Get the parameters.
1099      my ($dateString) = @_;      my ($tkey) = @_;
1100      # Declare the return variable.      # Compute the emergency tracing file name.
1101      my $retVal;      return "$FIG_Config::temp/Emergency$tkey.txt";
     # Parse the date.  
     if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {  
         # Create a time object. Note we need to convert the day, month,  
         # and year to a different base. Years count from 1900, and  
         # the internal month value is relocated to January = 0.  
         $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);  
     }  
     # Return the result.  
     return $retVal;  
1102  }  }
1103    
1104  =head3 LogErrors  =head3 EmergencyFileTarget
1105    
1106  C<< Tracer::LogErrors($fileName); >>      my $fileName = Tracer::EmergencyFileTarget($tkey);
1107    
1108  Route the standard error output to a log file.  Return the emergency tracing target file name. This is the file that receives
1109    the tracing output for file-based tracing.
1110    
1111  =over 4  =over 4
1112    
1113  =item fileName  =item tkey
1114    
1115  Name of the file to receive the error output.  Tracing key for the current program.
1116    
1117    =item RETURN
1118    
1119    Returns the name of the file to contain the trace output.
1120    
1121  =back  =back
1122    
1123  =cut  =cut
1124    
1125  sub LogErrors {  sub EmergencyFileTarget {
1126      # Get the file name.      # Get the parameters.
1127      my ($fileName) = @_;      my ($tkey) = @_;
1128      # Open the file as the standard error output.      # Compute the emergency tracing file name.
1129      open STDERR, '>', $fileName;      return "$FIG_Config::temp/trace$tkey.log";
1130  }  }
1131    
1132  =head3 ReadOptions  =head3 EmergencyTracingDest
1133    
1134  C<< my %options = Tracer::ReadOptions($fileName); >>      my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1135    
1136  Read a set of options from a file. Each option is encoded in a line of text that has the  This method converts an emergency tracing destination to a real
1137  format  tracing destination. The main difference is that if the
1138    destination is C<FILE> or C<APPEND>, we convert it to file
1139    output. If the destination is C<DUAL>, we convert it to file
1140    and standard output.
1141    
1142  I<optionName>C<=>I<optionValue>C<; >I<comment>  =over 4
1143    
1144  The option name must consist entirely of letters, digits, and the punctuation characters  =item tkey
 C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  
 character is a semi-colon will be ignored. The return hash will map each option name to  
 the corresponding option value.  
1145    
1146  =over 4  Tracing key for this environment.
1147    
1148  =item fileName  =item myDest
1149    
1150  Name of the file containing the option data.  Destination from the emergency tracing file.
1151    
1152  =item RETURN  =item RETURN
1153    
1154  Returns a hash mapping the option names specified in the file to their corresponding option  Returns a destination that can be passed into L</TSetup>.
 value.  
1155    
1156  =back  =back
1157    
1158  =cut  =cut
1159    
1160  sub ReadOptions {  sub EmergencyTracingDest {
1161      # Get the parameters.      # Get the parameters.
1162      my ($fileName) = @_;      my ($tkey, $myDest) = @_;
1163      # Open the file.      # Declare the return variable.
1164      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");      my $retVal = $myDest;
1165      # Count the number of records read.      # Process according to the destination value.
1166      my ($records, $comments) = 0;      if ($myDest eq 'FILE') {
1167      # Create the return hash.          $retVal = ">" . EmergencyFileTarget($tkey);
1168      my %retVal = ();      } elsif ($myDest eq 'APPEND') {
1169      # Loop through the file, accumulating key-value pairs.          $retVal = ">>" . EmergencyFileTarget($tkey);
1170      while (my $line = <CONFIGFILE>) {      } elsif ($myDest eq 'DUAL') {
1171          # Denote we've read a line.          $retVal = "+>" . EmergencyFileTarget($tkey);
1172          $records++;      } elsif ($myDest eq 'WARN') {
1173          # Determine the line type.          $retVal = "WARN";
         if ($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);  
         }  
1174      }      }
1175      # Return the hash created.      # Return the result.
1176      return %retVal;      return $retVal;
1177  }  }
1178    
1179  =head3 GetOptions  =head3 Emergency
   
 C<< Tracer::GetOptions(\%defaults, \%options); >>  
1180    
1181  Merge a specified set of options into a table of defaults. This method takes two hash references      Emergency($key, $hours, $dest, $level, @modules);
 as input and uses the data from the second to update the first. If the second does not exist,  
 there will be no effect. An error will be thrown if one of the entries in the second hash does not  
 exist in the first.  
1182    
1183  Consider the following example.  Turn on emergency tracing. This method is normally invoked over the web from
1184    a debugging console, but it can also be called by the C<trace.pl> script.
1185    The caller specifies the duration of the emergency in hours, the desired tracing
1186    destination, the trace level, and a list of the trace modules to activate.
1187    For the length of the duration, when a program in an environment with the
1188    specified tracing key active invokes a Sprout CGI script, tracing will be
1189    turned on automatically. See L</TSetup> for more about tracing setup and
1190    L</ETracing> for more about emergency tracing.
1191    
1192  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  =over 4
1193    
1194  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  =item tkey
 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<$options> is defined as  
1195    
1196  C<< {databaseType => 'Oracle'} >>  The tracing key. This is used to identify the control file and the trace file.
1197    
1198  an error will occur because the B<databaseType> option does not exist.  =item hours
1199    
1200  =over 4  Number of hours to keep emergency tracing alive.
1201    
1202  =item defaults  =item dest
1203    
1204  Table of default option values.  Tracing destination. If no path information is specified for a file
1205    destination, it is put in the FIG temporary directory.
1206    
1207  =item options  =item level
1208    
1209  Table of overrides, if any.  Tracing level. A higher level means more trace messages.
1210    
1211  =item RETURN  =item modules
1212    
1213  Returns a reference to the default table passed in as the first parameter.  A list of the tracing modules to activate.
1214    
1215  =back  =back
1216    
1217  =cut  =cut
1218    
1219  sub GetOptions {  sub Emergency {
1220      # Get the parameters.      # Get the parameters.
1221      my ($defaults, $options) = @_;      my ($tkey, $hours, $dest, $level, @modules) = @_;
1222      # Check for overrides.      # Create the emergency file.
1223      if ($options) {      my $specFile = EmergencyFileName($tkey);
1224          # Loop through the overrides.      my $outHandle = Open(undef, ">$specFile");
1225          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;  
1226  }  }
1227    
1228  =head3 MergeOptions  =head3 EmergencyKey
1229    
1230  C<< Tracer::MergeOptions(\%table, \%defaults); >>      my $tkey = EmergencyKey($parameter);
1231    
1232  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,
1233  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.  
1234    
1235  =over 4  =over 4
1236    
1237  =item table  =item parameter
1238    
1239  Hash table to be updated with the default values.  Parameter defining the method for finding the tracing key. If it is a scalar,
1240    then it is presumed to be the tracing key itself. If it is a CGI object, then
1241    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1242    taken from the C<TRACING> environment variable.
1243    
1244  =item defaults  =item RETURN
1245    
1246  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.
1247    
1248  =back  =back
1249    
1250  =cut  =cut
1251    
1252  sub MergeOptions {  sub EmergencyKey {
1253      # Get the parameters.      # Get the parameters.
1254      my ($table, $defaults) = @_;      my ($parameter) = @_;
1255      # Loop through the defaults.      # Declare the return variable.
1256      while (my ($key, $value) = each %{$defaults}) {      my $retVal;
1257          if (!exists $table->{$key}) {      # Determine the parameter type.
1258              $table->{$key} = $value;      if (! defined $parameter) {
1259            # Here we're supposed to check the environment. If that fails, we
1260            # get the effective login ID.
1261            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1262        } else {
1263            my $ptype = ref $parameter;
1264            if ($ptype eq 'CGI') {
1265                # Here we were invoked from a web page. Look for a cookie.
1266                $retVal = $parameter->cookie('IP');
1267            } elsif (! $ptype) {
1268                # Here the key was passed in.
1269                $retVal = $parameter;
1270          }          }
1271      }      }
1272        # If no luck finding a key, use the PID.
1273        if (! defined $retVal) {
1274            $retVal = $$;
1275        }
1276        # Return the result.
1277        return $retVal;
1278  }  }
1279    
 =head3 Trace  
1280    
1281  C<< Trace($message); >>  =head3 TraceParms
1282    
1283        Tracer::TraceParms($cgi);
1284    
1285  Write a trace message to the target location specified in L</TSetup>. If there has not been  Trace the CGI parameters at trace level CGI => 3 and the environment variables
1286  any prior call to B<TSetup>.  at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1287    
1288  =over 4  =over 4
1289    
1290  =item message  =item cgi
1291    
1292  Message to write.  CGI query object containing the parameters to trace.
1293    
1294  =back  =back
1295    
1296  =cut  =cut
1297    
1298  sub Trace {  sub TraceParms {
1299      # Get the parameters.      # Get the parameters.
1300      my ($message) = @_;      my ($cgi) = @_;
1301      # Get the timestamp.      if (T(CGI => 2)) {
1302      my $timeStamp = Now();          # Here we trace the GET-style URL for the script.
1303      # Format the message. Note we strip off any line terminators at the end.          Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1304      my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);      }
1305      # Process according to the destination.      if (T(CGI => 3)) {
1306      if ($Destination eq "TEXT") {          # Here we want to trace the parameter data.
1307          # Write the message to the standard output.          my @names = $cgi->param;
1308          print "$formatted\n";          for my $parmName (sort @names) {
1309      } elsif ($Destination eq "ERROR") {              # Note we skip the Trace parameters, which are for our use only.
1310          # Write the message to the error output.              if ($parmName ne 'Trace' && $parmName ne 'TF') {
1311          print STDERR "$formatted\n";                  my @values = $cgi->param($parmName);
1312      } elsif ($Destination eq "QUEUE") {                  Trace("[CGI] $parmName = " . join(", ", @values));
1313          # Push the message into the queue.              }
1314          push @Queue, "$formatted";          }
1315      } elsif ($Destination eq "HTML") {          # Display the request method.
1316          # Convert the message to HTML and write it to the standard output.          my $method = $cgi->request_method();
1317          my $escapedMessage = CGI::escapeHTML($message);          Trace("Method: $method");
1318          print "<p>$formatted</p>\n";      }
1319      } elsif ($Destination eq "WARN") {      if (T(CGI => 4)) {
1320         # Emit the message as a warning.          # Here we want the environment data too.
1321         warn $message;          for my $envName (sort keys %ENV) {
1322      } 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";  
1323          }          }
1324      }      }
1325  }  }
1326    
1327  =head3 T  =head3 TraceImages
1328    
1329  C<< my $switch = T($category, $traceLevel); >>      Tracer::TraceImages($htmlString);
1330    
1331      or  Trace information about all of an html document's images. The tracing
1332    will be for type "IMG" at level 3. The image's source string
1333    will be displayed. This is generally either the URL of the image or
1334    raw data for the image itself. If the source is too long, only the first 300
1335    characters will be shown at trace level 3. The entire source will be shown,
1336    however, at trace level 4. This method is not very smart, and might catch
1337    Javascript code, but it is still useful when debugging the arcane
1338    behavior of images in multiple browser environments.
1339    
1340  C<< my $switch = T($traceLevel); >>  =over 4
1341    
1342  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.  
1343    
1344  =over 4  HTML text for an outgoing web page.
1345    
1346  =item category  =back
1347    
1348  Category to which the message belongs. If not specified, the caller's package name is  =cut
 used.  
1349    
1350  =item traceLevel  sub TraceImages {
1351        # Only proceed if we're at the proper trace level.
1352        if (T(IMG => 3)) {
1353            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1354            # into a variable called "$htmlString". This is because we expect html strings to be
1355            # long, and don't want to copy them any more than we have to.
1356            Trace(length($_[0]) . " characters in web page.");
1357            # Loop through the HTML, culling image tags.
1358            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1359                # Extract the source string and determine whether or not it's too long.
1360                my $srcString = $1;
1361                my $pos = pos($_[0]) - length($srcString);
1362                my $excess = length($srcString) - 300;
1363                # We'll put the display string in here.
1364                my $srcDisplay = $srcString;
1365                # If it's a data string, split it at the comma.
1366                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1367                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1368                # a long string, however, we only show the first 300 characters.
1369                if ($excess > 0 && ! T(IMG => 4)) {
1370                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1371                }
1372                # Output the trace message.
1373                Trace("Image tag at position $pos:\n$srcDisplay");
1374            }
1375        }
1376    }
1377    
1378  Relevant tracing level.  =head2 Command-Line Utility Methods
1379    
1380  =item RETURN  =head3 SendSMS
1381    
1382  TRUE if a message at the specified trace level would appear in the trace, else FALSE.      my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1383    
1384  =back  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1385    user name, password, and API ID for the relevant account in the hash reference variable
1386    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1387    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1388    is C<2561022>, then the FIG_Config file must contain
1389    
1390  =cut      $phone =  { user => 'BruceTheHumanPet',
1391                    password => 'silly',
1392                    api_id => '2561022' };
1393    
1394  sub T {  The original purpose of this method was to insure Bruce would be notified immediately when the
1395      # Declare the return variable.  Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1396      my $retVal = 0;  when you call this method.
1397      # Only proceed if tracing is turned on.  
1398      if ($Destination ne "NONE") {  The message ID will be returned if successful, and C<undef> if an error occurs.
1399    
1400    =over 4
1401    
1402    =item phoneNumber
1403    
1404    Phone number to receive the message, in international format. A United States phone number
1405    would be prefixed by "1". A British phone number would be prefixed by "44".
1406    
1407    =item msg
1408    
1409    Message to send to the specified phone.
1410    
1411    =item RETURN
1412    
1413    Returns the message ID if successful, and C<undef> if the message could not be sent.
1414    
1415    =back
1416    
1417    =cut
1418    
1419    sub SendSMS {
1420          # Get the parameters.          # Get the parameters.
1421          my ($category, $traceLevel) = @_;      my ($phoneNumber, $msg) = @_;
1422          if (!defined $traceLevel) {      # Declare the return variable. If we do not change it, C<undef> will be returned.
1423              # Here we have no category, so we need to get the calling package.      my $retVal;
1424              # The calling package is normally the first parameter. If it is      # Only proceed if we have phone support.
1425              # omitted, the first parameter will be the tracelevel. So, the      if (! defined $FIG_Config::phone) {
1426              # first thing we do is shift the so-called category into the          Trace("Phone support not present in FIG_Config.") if T(1);
1427              # $traceLevel variable where it belongs.      } else {
1428              $traceLevel = $category;          # Get the phone data.
1429              my ($package, $fileName, $line) = caller;          my $parms = $FIG_Config::phone;
1430              # If there is no calling package, we default to "main".          # Get the Clickatell URL.
1431              if (!$package) {          my $url = "http://api.clickatell.com/http/";
1432                  $category = "main";          # Create the user agent.
1433            my $ua = LWP::UserAgent->new;
1434            # Request a Clickatell session.
1435            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1436                                         password => $parms->{password},
1437                                         api_id => $parms->{api_id},
1438                                         to => $phoneNumber,
1439                                         text => $msg});
1440            # Check for an error.
1441            if (! $resp->is_success) {
1442                Trace("Alert failed.") if T(1);
1443            } else {
1444                # Get the message ID.
1445                my $rstring = $resp->content;
1446                if ($rstring =~ /^ID:\s+(.*)$/) {
1447                    $retVal = $1;
1448                } else {
1449                    Trace("Phone attempt failed with $rstring") if T(1);
1450                }
1451            }
1452        }
1453        # Return the result.
1454        return $retVal;
1455    }
1456    
1457    =head3 StandardSetup
1458    
1459        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1460    
1461    This method performs standard command-line parsing and tracing setup. The return
1462    values are a hash of the command-line options and a list of the positional
1463    parameters. Tracing is automatically set up and the command-line options are
1464    validated.
1465    
1466    This is a complex method that does a lot of grunt work. The parameters can
1467    be more easily understood, however, once they are examined individually.
1468    
1469    The I<categories> parameter is the most obtuse. It is a reference to a list of
1470    special-purpose tracing categories. Most tracing categories are PERL package
1471    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1472    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1473    
1474        ["Sprout", "SproutLoad", "ERDB"]
1475    
1476    This would cause trace messages in the specified three packages to appear in
1477    the output. There are two special tracing categories that are automatically
1478    handled by this method. In other words, if you used L</TSetup> you would need
1479    to include these categories manually, but if you use this method they are turned
1480    on automatically.
1481    
1482    =over 4
1483    
1484    =item SQL
1485    
1486    Traces SQL commands and activity.
1487    
1488    =item Tracer
1489    
1490    Traces error messages and call stacks.
1491    
1492    =back
1493    
1494    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1495    The trace level is specified using the C<-trace> command-line option. For example,
1496    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1497    all tracing at level 3.
1498    
1499        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1500    
1501    Standard tracing is output to the standard output and echoed to the file
1502    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1503    process ID. You can also specify the C<user> parameter to put a user ID
1504    instead of a process ID in the trace file name. So, for example
1505    
1506    The default trace level is 2. To get all messages, specify a trace level of 4.
1507    For a genome-by-genome update, use 3.
1508    
1509        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1510    
1511    would send the trace output to C<traceBruce.log> in the temporary directory.
1512    
1513    The I<options> parameter is a reference to a hash containing the command-line
1514    options, their default values, and an explanation of what they mean. Command-line
1515    options may be in the form of switches or keywords. In the case of a switch, the
1516    option value is 1 if it is specified and 0 if it is not specified. In the case
1517    of a keyword, the value is separated from the option name by an equal sign. You
1518    can see this last in the command-line example above.
1519    
1520    You can specify a different default trace level by setting C<$options->{trace}>
1521    prior to calling this method.
1522    
1523    An example at this point would help. Consider, for example, the command-line utility
1524    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1525    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1526    the following code.
1527    
1528        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1529                            { safe => [0, "use database transactions"],
1530                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1531                              start => [' ', "start with this genome"],
1532                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1533                            "<command> <transactionDirectory> <IDfile>",
1534                          @ARGV);
1535    
1536    
1537    The call to C<ParseCommand> specifies the default values for the options and
1538    stores the actual options in a hash that is returned as C<$options>. The
1539    positional parameters are returned in C<@parameters>.
1540    
1541    The following is a sample command line for C<TransactFeatures>.
1542    
1543        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1544    
1545    Single and double hyphens are equivalent. So, you could also code the
1546    above command as
1547    
1548        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1549    
1550    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1551    parameters, and would find themselves in I<@parameters> after executing the
1552    above code fragment. The tracing would be set to level 2, and the categories
1553    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1554    and C<DocUtils> was included because it came in within the first parameter
1555    to this method. The I<$options> hash would be
1556    
1557        { trace => 2, sql => 0, safe => 0,
1558          noAlias => 1, start => ' ', tblFiles => 0 }
1559    
1560    Use of C<StandardSetup> in this way provides a simple way of performing
1561    standard tracing setup and command-line parsing. Note that the caller is
1562    not even aware of the command-line switches C<-trace> and C<-sql>, which
1563    are used by this method to control the tracing. If additional tracing features
1564    need to be added in the future, they can be processed by this method without
1565    upsetting the command-line utilities.
1566    
1567    If the C<background> option is specified on the command line, then the
1568    standard and error outputs will be directed to files in the temporary
1569    directory, using the same suffix as the trace file. So, if the command
1570    line specified
1571    
1572        -user=Bruce -background
1573    
1574    then the trace output would go to C<traceBruce.log>, the standard output to
1575    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1576    simplify starting a command in the background.
1577    
1578    The user name is also used as the tracing key for L</Emergency Tracing>.
1579    Specifying a value of C<E> for the trace level causes emergency tracing to
1580    be used instead of custom tracing. If the user name is not specified,
1581    the tracing key is taken from the C<Tracing> environment variable. If there
1582    is no value for that variable, the tracing key will be computed from the active
1583    login ID.
1584    
1585    Since the default situation in StandardSetup is to trace to the standard
1586    output, errors that occur in command-line scripts will not generate
1587    RSS events. To force the events, use the C<warn> option.
1588    
1589        TransactFeatures -background -warn register ../xacts IDs.tbl
1590    
1591    Finally, if the special option C<-help> is specified, the option
1592    names will be traced at level 0 and the program will exit without processing.
1593    This provides a limited help capability. For example, if the user enters
1594    
1595        TransactFeatures -help
1596    
1597    he would see the following output.
1598    
1599        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1600            -trace    tracing level (default E)
1601            -sql      trace SQL commands
1602            -safe     use database transactions
1603            -noAlias  do not expect aliases in CHANGE transactions
1604            -start    start with this genome
1605            -tblFiles output TBL files containing the corrected IDs
1606    
1607    The caller has the option of modifying the tracing scheme by placing a value
1608    for C<trace> in the incoming options hash. The default value can be overridden,
1609    or the tracing to the standard output can be turned off by suffixing a minus
1610    sign to the trace level. So, for example,
1611    
1612        { trace => [0, "tracing level (default 0)"],
1613           ...
1614    
1615    would set the default trace level to 0 instead of E, while
1616    
1617        { trace => ["2-", "tracing level (default 2)"],
1618           ...
1619    
1620    would set the default to 2, but trace only to the log file, not to the
1621    standard output.
1622    
1623    The parameters to this method are as follows.
1624    
1625    =over 4
1626    
1627    =item categories
1628    
1629    Reference to a list of tracing category names. These should be names of
1630    packages whose internal workings will need to be debugged to get the
1631    command working.
1632    
1633    =item options
1634    
1635    Reference to a hash containing the legal options for the current command mapped
1636    to their default values and descriptions. The user can override the defaults
1637    by specifying the options as command-line switches prefixed by a hyphen.
1638    Tracing-related options may be added to this hash. If the C<-h> option is
1639    specified on the command line, the option descriptions will be used to
1640    explain the options. To turn off tracing to the standard output, add a
1641    minus sign to the value for C<trace> (see above).
1642    
1643    =item parmHelp
1644    
1645    A string that vaguely describes the positional parameters. This is used
1646    if the user specifies the C<-h> option.
1647    
1648    =item argv
1649    
1650    List of command line parameters, including the option switches, which must
1651    precede the positional parameters and be prefixed by a hyphen.
1652    
1653    =item RETURN
1654    
1655    Returns a list. The first element of the list is the reference to a hash that
1656    maps the command-line option switches to their values. These will either be the
1657    default values or overrides specified on the command line. The remaining
1658    elements of the list are the position parameters, in order.
1659    
1660    =back
1661    
1662    =cut
1663    
1664    sub StandardSetup {
1665        # Get the parameters.
1666        my ($categories, $options, $parmHelp, @argv) = @_;
1667        # Get the default tracing key.
1668        my $tkey = EmergencyKey();
1669        # Save the command line.
1670        $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1671        # Add the tracing options.
1672        if (! exists $options->{trace}) {
1673            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1674        }
1675        $options->{sql} = [0, "turn on SQL tracing"];
1676        $options->{help} = [0, "display command-line options"];
1677        $options->{user} = [$tkey, "tracing key"];
1678        $options->{background} = [0, "spool standard and error output"];
1679        $options->{warn} = [0, "send errors to RSS feed"];
1680        # Create a parsing hash from the options hash. The parsing hash
1681        # contains the default values rather than the default value
1682        # and the description. While we're at it, we'll memorize the
1683        # length of the longest option name.
1684        my $longestName = 0;
1685        my %parseOptions = ();
1686        for my $key (keys %{$options}) {
1687            if (length $key > $longestName) {
1688                $longestName = length $key;
1689            }
1690            $parseOptions{$key} = $options->{$key}->[0];
1691        }
1692        # Parse the command line.
1693        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1694        # Get the logfile suffix.
1695        my $suffix = $retOptions->{user};
1696        # Check for background mode.
1697        if ($retOptions->{background}) {
1698            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1699            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1700            open STDOUT, ">$outFileName";
1701            open STDERR, ">$errFileName";
1702            # Check for phone support. If we have phone support and a phone number,
1703            # we want to turn it on.
1704            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1705                $retOptions->{phone} = $ENV{PHONE};
1706            }
1707        }
1708        # Now we want to set up tracing. First, we need to know if the user
1709        # wants emergency tracing.
1710        if ($retOptions->{trace} eq 'E') {
1711            ETracing($retOptions->{user});
1712        } else {
1713            # Here the tracing is controlled from the command line.
1714            my @cats = @{$categories};
1715            if ($retOptions->{sql}) {
1716                push @cats, "SQL";
1717            }
1718            if ($retOptions->{warn}) {
1719                push @cats, "Feed";
1720            }
1721            # Add the default categories.
1722            push @cats, "Tracer";
1723            # Next, we create the category string by joining the categories.
1724            my $cats = join(" ", @cats);
1725            # Check to determine whether or not the caller wants to turn off tracing
1726            # to the standard output.
1727            my $traceLevel = $retOptions->{trace};
1728            my $textOKFlag = 1;
1729            if ($traceLevel =~ /^(.)-/) {
1730                $traceLevel = $1;
1731                $textOKFlag = 0;
1732            }
1733            # Now we set up the trace mode.
1734            my $traceMode;
1735            # Verify that we can open a file in the FIG temporary directory.
1736            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1737            if (open TESTTRACE, ">$traceFileName") {
1738                # Here we can trace to a file.
1739                $traceMode = ">$traceFileName";
1740                if ($textOKFlag) {
1741                    # Echo to standard output if the text-OK flag is set.
1742                    $traceMode = "+$traceMode";
1743                }
1744                # Close the test file.
1745                close TESTTRACE;
1746            } else {
1747                # Here we can't trace to a file. Complain about this.
1748                warn "Could not open trace file $traceFileName: $!\n";
1749                # We trace to the standard output if it's
1750                # okay, and the error log otherwise.
1751                if ($textOKFlag) {
1752                    $traceMode = "TEXT";
1753              } else {              } else {
1754                  $category = $package;                  $traceMode = "WARN";
1755              }              }
1756          }          }
1757          # Save the category name.          # Now set up the tracing.
1758          $LastCategory = $category;          TSetup("$traceLevel $cats", $traceMode);
         # Convert it to lower case before we hash it.  
         $category = lc $category;  
         # Use the category and tracelevel to compute the result.  
         if (ref $traceLevel) {  
             Confess("Bad trace level.");  
         } elsif (ref $TraceLevel) {  
             Confess("Bad trace config.");  
1759          }          }
1760          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));      # Check for the "help" option. If it is specified, dump the command-line
1761        # options and exit the program.
1762        if ($retOptions->{help}) {
1763            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1764            print "$1 [options] $parmHelp\n";
1765            for my $key (sort keys %{$options}) {
1766                my $name = Pad($key, $longestName, 0, ' ');
1767                my $desc = $options->{$key}->[1];
1768                if ($options->{$key}->[0]) {
1769                    $desc .= " (default " . $options->{$key}->[0] . ")";
1770      }      }
1771      # Return the computed result.              print "  $name $desc\n";
1772      return $retVal;          }
1773            exit(0);
1774        }
1775        # Trace the options, if applicable.
1776        if (T(3)) {
1777            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1778            Trace("Selected options: " . join(", ", sort @parms) . ".");
1779        }
1780        # Return the parsed parameters.
1781        return ($retOptions, @retParameters);
1782  }  }
1783    
1784  =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 and 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<$options> will be  
1785    
1786  C<< { errors => 0, logFile => 'error.log' } >>      my %options = Tracer::ReadOptions($fileName);
1787    
1788  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
1789    format
1790    
1791  C<< apple orange rutabaga >>  I<optionName>C<=>I<optionValue>C<; >I<comment>
1792    
1793  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
1794  support for quote characters. Options can be specified with single or double hyphens.  C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1795    character is a semi-colon will be ignored. The return hash will map each option name to
1796    the corresponding option value.
1797    
1798  =over 4  =over 4
1799    
1800  =item optionTable  =item fileName
   
 Table of default options.  
   
 =item inputList  
1801    
1802  List of words on the command line.  Name of the file containing the option data.
1803    
1804  =item RETURN  =item RETURN
1805    
1806  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
1807    value.
1808    
1809  =back  =back
1810    
1811  =cut  =cut
1812    
1813  sub ParseCommand {  sub ReadOptions {
1814      # Get the parameters.      # Get the parameters.
1815      my ($optionTable, @inputList) = @_;      my ($fileName) = @_;
1816      # Process any options in the input list.      # Open the file.
1817      my %overrides = ();      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1818      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {      # Count the number of records read.
1819          # Get the current option.      my ($records, $comments) = 0;
1820          my $arg = shift @inputList;      # Create the return hash.
1821          # Pull out the option name.      my %retVal = ();
1822          $arg =~ /^--?([^=]*)/g;      # Loop through the file, accumulating key-value pairs.
1823          my $name = $1;      while (my $line = <CONFIGFILE>) {
1824          # Check for an option value.          # Denote we've read a line.
1825          if ($arg =~ /\G=(.*)$/g) {          $records++;
1826              # Here we have a value for the option.          # Determine the line type.
1827              $overrides{$name} = UnEscape($1);          if ($line =~ /^\s*[\n\r]/) {
1828                # A blank line is a comment.
1829                $comments++;
1830            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1831                # Here we have an option assignment.
1832                retVal{$1} = $2;
1833            } elsif ($line =~ /^\s*;/) {
1834                # Here we have a text comment.
1835                $comments++;
1836          } else {          } else {
1837              # Here there is no value, so we use 1.              # Here we have an invalid line.
1838              $overrides{$name} = 1;              Trace("Invalid option statement in record $records.") if T(0);
         }  
1839      }      }
     # Merge the options into the defaults.  
     GetOptions($optionTable, \%overrides);  
     # Translate the remaining parameters.  
     my @retVal = ();  
     for my $inputParm (@inputList) {  
         push @retVal, UnEscape($inputParm);  
1840      }      }
1841      # Return the results.      # Return the hash created.
1842      return ($optionTable, @retVal);      return %retVal;
1843  }  }
1844    
1845  =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  
1846    
1847  String to escape.      Tracer::GetOptions(\%defaults, \%options);
1848    
1849  =item RETURN  Merge a specified set of options into a table of defaults. This method takes two hash references
1850    as input and uses the data from the second to update the first. If the second does not exist,
1851    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1852    exist in the first.
1853    
1854  Escaped equivalent of the real string.  Consider the following example.
1855    
1856  =back      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1857    
1858  =cut  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1859    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1860    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1861    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1862    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1863    
1864  sub Escape {      {databaseType => 'Oracle'}
     # Get the parameter.  
     my ($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;  
 }  
1865    
1866  =head3 UnEscape  an error will occur because the B<databaseType> option does not exist.
1867    
1868  C<< my $realString = Tracer::UnEscape($codedString); >>  =over 4
1869    
1870  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.  
1871    
1872  =over 4  Table of default option values.
1873    
1874  =item codedString  =item options
1875    
1876  String to un-escape.  Table of overrides, if any.
1877    
1878  =item RETURN  =item RETURN
1879    
1880  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.  
1881    
1882  =back  =back
1883    
1884  =cut  =cut
1885    
1886  sub UnEscape {  sub GetOptions {
1887      # Get the parameter.      # Get the parameters.
1888      my ($codedString) = @_;      my ($defaults, $options) = @_;
1889      # Initialize the return variable.      # Check for overrides.
1890      my $retVal = "";      if ($options) {
1891      # Only proceed if the incoming string is nonempty.          # Loop through the overrides.
1892      if (defined $codedString) {          while (my ($option, $setting) = each %{$options}) {
1893          # Loop through the parameter string, looking for escape sequences. We can't do              # Insure this override exists.
1894          # translating because it causes problems with the escaped slash. ("\\t" becomes              if (!exists $defaults->{$option}) {
1895          # "\<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;  
                 }  
1896              } else {              } else {
1897                  # Here there are no more escape sequences. The rest of the string is                  # Apply the override.
1898                  # transferred unmodified.                  $defaults->{$option} = $setting;
                 $retVal .= $codedString;  
                 $codedString = "";  
1899              }              }
1900          }          }
1901      }      }
1902      # Return the result.      # Return the merged table.
1903      return $retVal;      return $defaults;
1904  }  }
1905    
1906  =head3 ParseRecord  =head3 MergeOptions
1907    
1908  C<< my @fields = Tracer::ParseRecord($line); >>      Tracer::MergeOptions(\%table, \%defaults);
1909    
1910  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
1911  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
1912  These will automatically be converted.  pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1913    checking and no return value.
1914    
1915  =over 4  =over 4
1916    
1917  =item line  =item table
1918    
1919  Line of data containing the tab-delimited fields.  Hash table to be updated with the default values.
1920    
1921  =item RETURN  =item defaults
1922    
1923  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.
1924    
1925  =back  =back
1926    
1927  =cut  =cut
1928    
1929  sub ParseRecord {  sub MergeOptions {
1930      # Get the parameter.      # Get the parameters.
1931      my ($line) = @_;      my ($table, $defaults) = @_;
1932      # Remove the trailing new-line, if any.      # Loop through the defaults.
1933      chomp $line;      while (my ($key, $value) = each %{$defaults}) {
1934      # Split the line read into pieces using the tab character.          if (!exists $table->{$key}) {
1935      my @retVal = split /\t/, $line;              $table->{$key} = $value;
1936      # Trim and fix the escapes in each piece.          }
     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;  
1937      }      }
     # Return the result.  
     return @retVal;  
1938  }  }
1939    
1940  =head3 Merge  =head3 ParseCommand
   
 C<< my @mergedList = Tracer::Merge(@inputList); >>  
   
 Sort a list of strings and remove duplicates.  
   
 =over 4  
1941    
1942  =item inputList      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1943    
1944  List of scalars to sort and merge.  Parse a command line consisting of a list of parameters. The initial parameters may be option
1945    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1946    off and merged into a table of default options. The remainder of the command line is
1947    returned as a list of positional arguments. For example, consider the following invocation.
1948    
1949  =item RETURN      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1950    
1951  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,
1952  removed.  B<errors> and B<logFile>. If @words has the following format
1953    
1954  =back      -logFile=error.log apple orange rutabaga
1955    
1956  =cut  then at the end of the invocation, C<$options> will be
1957    
1958  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;  
 }  
1959    
1960  =head3 Percent  and C<@arguments> will contain
1961    
1962  C<< my $percent = Tracer::Percent($number, $base); >>      apple orange rutabaga
1963    
1964  Returns the percent of the base represented by the given number. If the base  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1965  is zero, returns zero.  support for quote characters. Options can be specified with single or double hyphens.
1966    
1967  =over 4  =over 4
1968    
1969  =item number  =item optionTable
1970    
1971  Percent numerator.  Table of default options.
1972    
1973  =item base  =item inputList
1974    
1975  Percent base.  List of words on the command line.
1976    
1977  =item RETURN  =item RETURN
1978    
1979  Returns the percentage of the base represented by the numerator.  Returns a reference to the option table and a list of the positional arguments.
1980    
1981  =back  =back
1982    
1983  =cut  =cut
1984    
1985  sub Percent {  sub ParseCommand {
1986      # Get the parameters.      # Get the parameters.
1987      my ($number, $base) = @_;      my ($optionTable, @inputList) = @_;
1988      # Declare the return variable.      # Process any options in the input list.
1989      my $retVal = 0;      my %overrides = ();
1990      # Compute the percent.      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1991      if ($base != 0) {          # Get the current option.
1992          $retVal = $number * 100 / $base;          my $arg = shift @inputList;
1993            # Pull out the option name.
1994            $arg =~ /^--?([^=]*)/g;
1995            my $name = $1;
1996            # Check for an option value.
1997            if ($arg =~ /\G=(.*)$/g) {
1998                # Here we have a value for the option.
1999                $overrides{$name} = UnEscape($1);
2000            } else {
2001                # Here there is no value, so we use 1.
2002                $overrides{$name} = 1;
2003      }      }
2004      # Return the result.      }
2005      return $retVal;      # Merge the options into the defaults.
2006        GetOptions($optionTable, \%overrides);
2007        # Translate the remaining parameters.
2008        my @retVal = ();
2009        for my $inputParm (@inputList) {
2010            push @retVal, UnEscape($inputParm);
2011        }
2012        # Return the results.
2013        return ($optionTable, @retVal);
2014  }  }
2015    
2016    
2017    =head2 File Utility Methods
2018    
2019  =head3 GetFile  =head3 GetFile
2020    
2021  C<< my @fileContents = Tracer::GetFile($fileName); >>      my @fileContents = Tracer::GetFile($fileName);
2022    
2023      or      or
2024    
2025  C<< my $fileContents = Tracer::GetFile($fileName); >>      my $fileContents = Tracer::GetFile($fileName);
2026    
2027  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
2028  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 1661  Line 2072 
2072    
2073  =head3 PutFile  =head3 PutFile
2074    
2075  C<< Tracer::PutFile($fileName, \@lines); >>      Tracer::PutFile($fileName, \@lines);
2076    
2077  Write out a file from a list of lines of text.  Write out a file from a list of lines of text.
2078    
# Line 1704  Line 2115 
2115      close $handle;      close $handle;
2116  }  }
2117    
2118  =head3 QTrace  =head3 ParseRecord
2119    
2120  C<< my $data = QTrace($format); >>      my @fields = Tracer::ParseRecord($line);
2121    
2122  Return the queued trace data in the specified format.  Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2123    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2124    These will automatically be converted.
2125    
2126  =over 4  =over 4
2127    
2128  =item format  =item line
2129    
2130  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Line of data containing the tab-delimited fields.
2131    
2132    =item RETURN
2133    
2134    Returns a list of the fields found in the data line.
2135    
2136  =back  =back
2137    
2138  =cut  =cut
2139    
2140  sub QTrace {  sub ParseRecord {
2141      # Get the parameter.      # Get the parameter.
2142      my ($format) = @_;      my ($line) = @_;
2143      # Create the return variable.      # Remove the trailing new-line, if any.
2144      my $retVal = "";      chomp $line;
2145      # Only proceed if there is an actual queue.      # Split the line read into pieces using the tab character.
2146      if (@Queue) {      my @retVal = split /\t/, $line;
2147          # Process according to the format.      # Trim and fix the escapes in each piece.
2148          if ($format =~ m/^HTML$/i) {      for my $value (@retVal) {
2149              # Convert the queue into an HTML list.          # Trim leading whitespace.
2150              $retVal = "<ul>\n";          $value =~ s/^\s+//;
2151              for my $line (@Queue) {          # Trim trailing whitespace.
2152                  my $escapedLine = CGI::escapeHTML($line);          $value =~ s/\s+$//;
2153                  $retVal .= "<li>$escapedLine</li>\n";          # Delete the carriage returns.
2154              }          $value =~ s/\r//g;
2155              $retVal .= "</ul>\n";          # Convert the escapes into their real values.
2156          } elsif ($format =~ m/^TEXT$/i) {          $value =~ s/\\t/"\t"/ge;
2157              # Convert the queue into a list of text lines.          $value =~ s/\\n/"\n"/ge;
             $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
2158      }      }
2159      # Return the formatted list.      # Return the result.
2160      return $retVal;      return @retVal;
2161  }  }
2162    
2163  =head3 Confess  =head3 Merge
2164    
2165  C<< Confess($message); >>      my @mergedList = Tracer::Merge(@inputList);
2166    
2167  Trace the call stack and abort the program with the specified message. When used with  Sort a list of strings and remove duplicates.
2168  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
2169  So, for example  =over 4
2170    
2171    =item inputList
2172    
2173    List of scalars to sort and merge.
2174    
2175    =item RETURN
2176    
2177    Returns a list containing the same elements sorted in ascending order with duplicates
2178    removed.
2179    
2180    =back
2181    
2182    =cut
2183    
2184    sub Merge {
2185        # Get the input list in sort order.
2186        my @inputList = sort @_;
2187        # Only proceed if the list has at least two elements.
2188        if (@inputList > 1) {
2189            # Now we want to move through the list splicing out duplicates.
2190            my $i = 0;
2191            while ($i < @inputList) {
2192                # Get the current entry.
2193                my $thisEntry = $inputList[$i];
2194                # Find out how many elements duplicate the current entry.
2195                my $j = $i + 1;
2196                my $dup1 = $i + 1;
2197                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2198                # If the number is nonzero, splice out the duplicates found.
2199                if ($j > $dup1) {
2200                    splice @inputList, $dup1, $j - $dup1;
2201                }
2202                # Now the element at position $dup1 is different from the element before it
2203                # at position $i. We push $i forward one position and start again.
2204                $i++;
2205            }
2206        }
2207        # Return the merged list.
2208        return @inputList;
2209    }
2210    
2211    =head3 Open
2212    
2213  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2214    
2215  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Open a file.
2216    
2217  =over 4  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2218    function. The mode is specified using Unix-like shell information. So, for
2219    example,
2220    
2221  =item message      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2222    
2223  Message to include in the trace.  would open for output appended to the specified file, and
2224    
2225  =back      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2226    
2227  =cut  would open a pipe that sorts the records written and removes duplicates. Note
2228    the use of file handle syntax in the Open call. To use anonymous file handles,
2229    code as follows.
2230    
2231  sub Confess {      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
     # Get the parameters.  
     my ($message) = @_;  
     # Trace the call stack.  
     Cluck($message);  
     # Abort the program.  
     croak(">>> $message");  
 }  
2232    
2233  =head3 Assert  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2234    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2235    failed open will throw an exception and the third parameter will be used to construct
2236    an error message. If the parameter is omitted, a standard message is constructed
2237    using the file spec.
2238    
2239  C<< Assert($condition1, $condition2, ... $conditionN); >>      Could not open "/usr/spool/news/twitlog"
2240    
2241  Return TRUE if all the conditions are true. This method can be used in conjunction with  Note that the mode characters are automatically cleaned from the file name.
2242  the OR operator and the L</Confess> method as a debugging assert.  The actual error message from the file system will be captured and appended to the
2243  So, for example  message in any case.
2244    
2245  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      Could not open "/usr/spool/news/twitlog": file not found.
2246    
2247  Will abort the program with a stack trace if the value of C<$recNum> is negative.  In some versions of PERL the only error message we get is a number, which
2248    corresponds to the C++ C<errno> value.
2249    
2250  =cut      Could not open "/usr/spool/news/twitlog": 6.
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
2251    
2252  =head3 Cluck  =over 4
2253    
2254  C<< Cluck($message); >>  =item fileHandle
2255    
2256  Trace the call stack. Note that for best results, you should qualify the call with a  File handle. If this parameter is C<undef>, a file handle will be generated
2257  trace condition. For example,  and returned as the value of this method.
2258    
2259  C<< Cluck("Starting record parse.") if T(3); >>  =item fileSpec
2260    
2261  will only trace the stack if the trace level for the package is 3 or more.  File name and mode, as per the PERL C<open> function.
2262    
2263  =over 4  =item message (optional)
2264    
2265  =item message  Error message to use if the open fails. If omitted, a standard error message
2266    will be generated. In either case, the error information from the file system
2267    is appended to the message. To specify a conditional open that does not throw
2268    an error if it fails, use C<0>.
2269    
2270  Message to include in the trace.  =item RETURN
2271    
2272    Returns the name of the file handle assigned to the file, or C<undef> if the
2273    open failed.
2274    
2275  =back  =back
2276    
2277  =cut  =cut
2278    
2279  sub Cluck {  sub Open {
2280      # Get the parameters.      # Get the parameters.
2281      my ($message) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2282      # Trace what's happening.      # Attempt to open the file.
2283      Trace("Stack trace for event: $message");      my $rv = open $fileHandle, $fileSpec;
2284      my $confession = longmess($message);      # If the open failed, generate an error message.
2285      # Convert the confession to a series of trace messages. Note we skip any      if (! $rv) {
2286      # messages relating to calls into Tracer.          # Save the system error message.
2287      for my $line (split /\s*\n/, $confession) {          my $sysMessage = $!;
2288          Trace($line) if ($line !~ /Tracer\.pm/);          # See if we need a default message.
2289            if (!$message) {
2290                # Clean any obvious mode characters and leading spaces from the
2291                # filename.
2292                my ($fileName) = FindNamePart($fileSpec);
2293                $message = "Could not open \"$fileName\"";
2294            }
2295            # Terminate with an error using the supplied message and the
2296            # error message from the file system.
2297            Confess("$message: $!");
2298      }      }
2299        # Return the file handle.
2300        return $fileHandle;
2301  }  }
2302    
2303  =head3 Min  =head3 FindNamePart
2304    
2305  C<< my $min = Min($value1, $value2, ... $valueN); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2306    
2307  Return the minimum argument. The arguments are treated as numbers.  Extract the portion of a file specification that contains the file name.
2308    
2309    A file specification is the string passed to an C<open> call. It specifies the file
2310    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2311    method assumes that the file name is whatever follows the first angle bracket
2312    sequence.  So, for example, in the following strings the file name is
2313    C</usr/fig/myfile.txt>.
2314    
2315        >>/usr/fig/myfile.txt
2316        </usr/fig/myfile.txt
2317        | sort -u > /usr/fig/myfile.txt
2318    
2319    If the method cannot find a file name using its normal methods, it will return the
2320    whole incoming string.
2321    
2322  =over 4  =over 4
2323    
2324  =item $value1, $value2, ... $valueN  =item fileSpec
2325    
2326  List of numbers to compare.  File specification string from which the file name is to be extracted.
2327    
2328  =item RETURN  =item RETURN
2329    
2330  Returns the lowest number in the list.  Returns a three-element list. The first element contains the file name portion of
2331    the specified string, or the whole string if a file name cannot be found via normal
2332    methods. The second element contains the start position of the file name portion and
2333    the third element contains the length.
2334    
2335  =back  =back
2336    
2337  =cut  =cut
2338    #: Return Type $;
2339  sub Min {  sub FindNamePart {
2340      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2341      my ($retVal, @values) = @_;      my ($fileSpec) = @_;
2342      # Loop through the remaining parameters, looking for the lowest.      # Default to the whole input string.
2343      for my $value (@values) {      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2344          if ($value < $retVal) {      # Parse out the file name if we can.
2345              $retVal = $value;      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2346          }          $retVal = $2;
2347            $len = length $retVal;
2348            $pos = (length $fileSpec) - (length $3) - $len;
2349      }      }
2350      # Return the minimum found.      # Return the result.
2351      return $retVal;      return ($retVal, $pos, $len);
2352  }  }
2353    
2354  =head3 Max  =head3 OpenDir
   
 C<< my $max = Max($value1, $value2, ... $valueN); >>  
   
 Return the maximum argument. The arguments are treated as numbers.  
   
 =over 4  
   
 =item $value1, $value2, ... $valueN  
   
 List of numbers to compare.  
2355    
2356  =item RETURN      my @files = OpenDir($dirName, $filtered, $flag);
2357    
2358  Returns the highest number in the list.  Open a directory and return all the file names. This function essentially performs
2359    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2360    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2361    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2362    filtered out of the return list. If the directory does not open and I<$flag> is not
2363    set, an exception is thrown. So, for example,
2364    
2365  =back      my @files = OpenDir("/Volumes/fig/contigs", 1);
2366    
2367  =cut  is effectively the same as
2368    
2369  sub Max {      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2370      # Get the parameters. Note that we prime the return value with the first parameter.      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
     my ($retVal, @values) = @_;  
     # Loop through the remaining parameters, looking for the highest.  
     for my $value (@values) {  
         if ($value > $retVal) {  
             $retVal = $value;  
         }  
     }  
     # Return the maximum found.  
     return $retVal;  
 }  
2371    
2372  =head3 AddToListMap  Similarly, the following code
2373    
2374  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2375    
2376  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2377  is created for the key. Otherwise, the new value is pushed onto the list.  automatically returns an empty list if the directory fails to open.
2378    
2379  =over 4  =over 4
2380    
2381  =item hash  =item dirName
2382    
2383  Reference to the target hash.  Name of the directory to open.
2384    
2385  =item key  =item filtered
2386    
2387  Key for which the value is to be added.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2388    from the list, else FALSE.
2389    
2390  =item value1, value2, ... valueN  =item flag
2391    
2392  List of values to add to the key's value list.  TRUE if a failure to open is okay, else FALSE
2393    
2394  =back  =back
2395    
2396  =cut  =cut
2397    #: Return Type @;
2398  sub AddToListMap {  sub OpenDir {
2399      # Get the parameters.      # Get the parameters.
2400      my ($hash, $key, @values) = @_;      my ($dirName, $filtered, $flag) = @_;
2401      # Process according to whether or not the key already has a value.      # Declare the return variable.
2402      if (! exists $hash->{$key}) {      my @retVal = ();
2403          $hash->{$key} = [@values];      # Open the directory.
2404        if (opendir(my $dirHandle, $dirName)) {
2405            # The directory opened successfully. Get the appropriate list according to the
2406            # strictures of the filter parameter.
2407            if ($filtered) {
2408                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2409      } else {      } else {
2410          push @{$hash->{$key}}, @values;              @retVal = readdir $dirHandle;
2411            }
2412        } elsif (! $flag) {
2413            # Here the directory would not open and it's considered an error.
2414            Confess("Could not open directory $dirName.");
2415      }      }
2416        # Return the result.
2417        return @retVal;
2418  }  }
2419    
 =head3 DebugMode  
2420    
2421  C<< if (Tracer::DebugMode) { ...code... } >>  =head3 Insure
2422    
2423        Insure($dirName, $chmod);
2424    
2425    Insure a directory is present.
2426    
2427    =over 4
2428    
2429    =item dirName
2430    
2431    Name of the directory to check. If it does not exist, it will be created.
2432    
2433    =item chmod (optional)
2434    
2435  Return TRUE if debug mode has been turned on, else abort.  Security privileges to be given to the directory if it is created.
2436    
2437  Certain CGI scripts are too dangerous to exist in the production  =back
 environment. This method provides a simple way to prevent them  
 from working unless they are explicitly turned on by creating a password  
 cookie via the B<SetPassword> script.  If debugging mode  
 is not turned on, an error will occur.  
2438    
2439  =cut  =cut
2440    
2441  sub DebugMode {  sub Insure {
2442      # Declare the return variable.      my ($dirName, $chmod) = @_;
2443      my $retVal = 0;      if (! -d $dirName) {
2444      # Check the debug configuration.          Trace("Creating $dirName directory.") if T(2);
2445      my $password = CGI::cookie("DebugMode");          eval {
2446      my $encrypted = Digest::MD5::md5_hex($password);              mkpath $dirName;
2447      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {              # If we have permissions specified, set them here.
2448          $retVal = 1;              if (defined($chmod)) {
2449      } else {                  chmod $chmod, $dirName;
2450          # Here debug mode is off, so we generate an error.              }
2451          Confess("Cannot use this facility without logging in.");          };
2452            if ($@) {
2453                Confess("Error creating $dirName: $@");
2454            }
2455      }      }
     # Return the determination indicator.  
     return $retVal;  
2456  }  }
2457    
2458  =head3 Strip  =head3 ChDir
2459    
2460  C<< my $string = Tracer::Strip($line); >>      ChDir($dirName);
2461    
2462  Strip all line terminators off a string. This is necessary when dealing with files  Change to the specified directory.
 that may have been transferred back and forth several times among different  
 operating environments.  
2463    
2464  =over 4  =over 4
2465    
2466  =item line  =item dirName
   
 Line of text to be stripped.  
   
 =item RETURN  
2467    
2468  The same line of text with all the line-ending characters chopped from the end.  Name of the directory to which we want to change.
2469    
2470  =back  =back
2471    
2472  =cut  =cut
2473    
2474  sub Strip {  sub ChDir {
2475      # Get a copy of the parameter string.      my ($dirName) = @_;
2476      my ($string) = @_;      if (! -d $dirName) {
2477      my $retVal = (defined $string ? $string : "");          Confess("Cannot change to directory $dirName: no such directory.");
2478      # Strip the line terminator characters.      } else {
2479      $retVal =~ s/(\r|\n)+$//g;          Trace("Changing to directory $dirName.") if T(File => 4);
2480      # Return the result.          my $okFlag = chdir $dirName;
2481      return $retVal;          if (! $okFlag) {
2482                Confess("Error switching to directory $dirName.");
2483            }
2484        }
2485  }  }
2486    
2487  =head3 Pad  =head3 SetPermissions
2488    
2489  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2490    
2491  Pad a string to a specified length. The pad character will be a  Set the permissions for a directory and all the files and folders inside it.
2492  space, and the padding will be on the right side unless specified  In addition, the group ownership will be changed to the specified value.
2493  in the third parameter.  
2494    This method is more vulnerable than most to permission and compatability
2495    problems, so it does internal error recovery.
2496    
2497  =over 4  =over 4
2498    
2499  =item string  =item dirName
2500    
2501  String to be padded.  Name of the directory to process.
2502    
2503  =item len  =item group
2504    
2505  Desired length of the padded string.  Name of the group to be assigned.
2506    
2507  =item left (optional)  =item mask
2508    
2509  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  Permission mask. Bits that are C<1> in this mask will be ORed into the
2510    permission bits of any file or directory that does not already have them
2511    set to 1.
2512    
2513  =item padChar (optional)  =item otherMasks
2514    
2515  Character to use for padding. The default is a space.  Map of search patterns to permission masks. If a directory name matches
2516    one of the patterns, that directory and all its members and subdirectories
2517    will be assigned the new pattern. For example, the following would
2518    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2519    
2520  =item RETURN      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2521    
2522  Returns a copy of the original string with the pad character added to the  The list is ordered, so the following would use 0777 for C<tmp1> and
2523  specified end so that it achieves the desired length.  0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2524    
2525        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2526                                                       '^tmp' => 0666);
2527    
2528    Note that the pattern matches are all case-insensitive, and only directory
2529    names are matched, not file names.
2530    
2531  =back  =back
2532    
2533  =cut  =cut
2534    
2535  sub Pad {  sub SetPermissions {
2536      # Get the parameters.      # Get the parameters.
2537      my ($string, $len, $left, $padChar) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2538      # Compute the padding character.      # Set up for error recovery.
2539      if (! defined $padChar) {      eval {
2540          $padChar = " ";          # Switch to the specified directory.
2541            ChDir($dirName);
2542            # Get the group ID.
2543            my $gid = getgrnam($group);
2544            # Get the mask for tracing.
2545            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2546            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2547            my $fixCount = 0;
2548            my $lookCount = 0;
2549            # @dirs will be a stack of directories to be processed.
2550            my @dirs = (getcwd());
2551            while (scalar(@dirs) > 0) {
2552                # Get the current directory.
2553                my $dir = pop @dirs;
2554                # Check for a match to one of the specified directory names. To do
2555                # that, we need to pull the individual part of the name off of the
2556                # whole path.
2557                my $simpleName = $dir;
2558                if ($dir =~ m!/([^/]+)$!) {
2559                    $simpleName = $1;
2560      }      }
2561      # Compute the number of spaces needed.              Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2562      my $needed = $len - length $string;              # Search for a match.
2563      # Copy the string into the return variable.              my $match = 0;
2564      my $retVal = $string;              my $i;
2565      # Only proceed if padding is needed.              for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2566      if ($needed > 0) {                  my $pattern = $otherMasks[$i];
2567          # Create the pad string.                  if ($simpleName =~ /$pattern/i) {
2568          my $pad = $padChar x $needed;                      $match = 1;
2569          # Affix it to the return value.                  }
2570          if ($left) {              }
2571              $retVal = $pad . $retVal;              # Check for a match. Note we use $i-1 because the loop added 2
2572                # before terminating due to the match.
2573                if ($match && $otherMasks[$i-1] != $mask) {
2574                    # This directory matches one of the incoming patterns, and it's
2575                    # a different mask, so we process it recursively with that mask.
2576                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2577          } else {          } else {
2578              $retVal .= $pad;                  # Here we can process normally. Get all of the non-hidden members.
2579                    my @submems = OpenDir($dir, 1);
2580                    for my $submem (@submems) {
2581                        # Get the full name.
2582                        my $thisMem = "$dir/$submem";
2583                        Trace("Checking member $thisMem.") if T(4);
2584                        $lookCount++;
2585                        if ($lookCount % 1000 == 0) {
2586                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2587          }          }
2588                        # Fix the group.
2589                        chown -1, $gid, $thisMem;
2590                        # Insure this member is not a symlink.
2591                        if (! -l $thisMem) {
2592                            # Get its info.
2593                            my $fileInfo = stat $thisMem;
2594                            # Only proceed if we got the info. Otherwise, it's a hard link
2595                            # and we want to skip it anyway.
2596                            if ($fileInfo) {
2597                                my $fileMode = $fileInfo->mode;
2598                                if (($fileMode & $mask) != $mask) {
2599                                    # Fix this member.
2600                                    $fileMode |= $mask;
2601                                    chmod $fileMode, $thisMem;
2602                                    $fixCount++;
2603      }      }
2604      # Return the result.                              # If it's a subdirectory, stack it.
2605      return $retVal;                              if (-d $thisMem) {
2606                                    push @dirs, $thisMem;
2607                                }
2608                            }
2609                        }
2610                    }
2611                }
2612            }
2613            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2614        };
2615        # Check for an error.
2616        if ($@) {
2617            Confess("SetPermissions error: $@");
2618  }  }
   
 =head3 EOF  
   
 This is a constant that is lexically greater than any useful string.  
   
 =cut  
   
 sub EOF {  
     return "\xFF\xFF\xFF\xFF\xFF";  
2619  }  }
2620    
2621  =head3 TICK  =head3 GetLine
   
 C<< my @results = TICK($commandString); >>  
   
 Perform a back-tick operation on a command. If this is a Windows environment, any leading  
 dot-slash (C<./> will be removed. So, for example, if you were doing  
   
     `./protein.cgi`  
   
 from inside a CGI script, it would work fine in Unix, but would issue an error message  
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
2622    
2623      TICK("./protein.cgi")      my @data = Tracer::GetLine($handle);
2624    
2625  it will work correctly in both environments.  Read a line of data from a tab-delimited file.
2626    
2627  =over 4  =over 4
2628    
2629  =item commandString  =item handle
2630    
2631  The command string to pass to the system.  Open file handle from which to read.
2632    
2633  =item RETURN  =item RETURN
2634    
2635  Returns the standard output from the specified command, as a list.  Returns a list of the fields in the record read. The fields are presumed to be
2636    tab-delimited. If we are at the end of the file, then an empty list will be
2637    returned. If an empty line is read, a single list item consisting of a null
2638    string will be returned.
2639    
2640  =back  =back
2641    
2642  =cut  =cut
2643  #: Return Type @;  
2644  sub TICK {  sub GetLine {
2645      # Get the parameters.      # Get the parameters.
2646      my ($commandString) = @_;      my ($handle) = @_;
2647      # Chop off the dot-slash if this is Windows.      # Declare the return variable.
2648      if ($FIG_Config::win_mode) {      my @retVal = ();
2649          $commandString =~ s!^\./!!;      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2650        # Read from the file.
2651        my $line = <$handle>;
2652        # Only proceed if we found something.
2653        if (defined $line) {
2654            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2655            # upload control and have a nonstandard EOL combination.
2656            $line =~ s/(\r|\n)+$//;
2657            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2658            if (T(File => 4)) {
2659                my $escapedLine = $line;
2660                $escapedLine =~ s/\n/\\n/g;
2661                $escapedLine =~ s/\r/\\r/g;
2662                $escapedLine =~ s/\t/\\t/g;
2663                Trace("Line read: -->$escapedLine<--");
2664      }      }
2665      # Activate the command and return the result.          # If the line is empty, return a single empty string; otherwise, parse
2666      return `$commandString`;          # it into fields.
2667            if ($line eq "") {
2668                push @retVal, "";
2669            } else {
2670                push @retVal, split /\t/,$line;
2671            }
2672        } else {
2673            # Trace the reason the read failed.
2674            Trace("End of file: $!") if T(File => 3);
2675        }
2676        # Return the result.
2677        return @retVal;
2678  }  }
2679    
2680  =head3 ScriptSetup  =head3 PutLine
   
 C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  
2681    
2682  Perform standard tracing and debugging setup for scripts. The value returned is      Tracer::PutLine($handle, \@fields, $eol);
 the CGI object followed by a pre-built variable hash. At the end of the script,  
 the client should call L</ScriptFinish> to output the web page.  
2683    
2684  This method calls L</ETracing> to configure tracing, which allows the tracing  Write a line of data to a tab-delimited file. The specified field values will be
2685  to be configured via the emergency tracing form on the debugging control panel.  output in tab-separated form, with a trailing new-line.
 Tracing will then be turned on automatically for all programs that use the L</ETracing>  
 method, which includes every program that uses this method or L</StandardSetup>.  
2686    
2687  =over 4  =over 4
2688    
2689  =item noTrace (optional)  =item handle
2690    
2691  If specified, tracing will be suppressed. This is useful if the script wants to set up  Output file handle.
 tracing manually.  
2692    
2693  =item RETURN  =item fields
2694    
2695    List of field values.
2696    
2697    =item eol (optional)
2698    
2699  Returns a two-element list consisting of a CGI query object and a variable hash for  End-of-line character (default is "\n").
 the output page.  
2700    
2701  =back  =back
2702    
2703  =cut  =cut
2704    
2705  sub ScriptSetup {  sub PutLine {
2706      # Get the parameters.      # Get the parameters.
2707      my ($noTrace) = @_;      my ($handle, $fields, $eol) = @_;
2708      # Get the CGI query object.      # Write the data.
2709      my $cgi = CGI->new();      print $handle join("\t", @{$fields}) . ($eol || "\n");
     # Set up tracing if it's not suppressed.  
     ETracing($cgi) unless $noTrace;  
     # Create the variable hash.  
     my $varHash = { results => '' };  
     # Return the query object and variable hash.  
     return ($cgi, $varHash);  
2710  }  }
2711    
 =head3 ETracing  
2712    
2713  C<< ETracing($parameter); >>  =head3 PrintLine
2714    
2715  Set up emergency tracing. Emergency tracing is tracing that is turned      Tracer::PrintLine($line);
2716  on automatically for any program that calls this method. The emergency  
2717  tracing parameters are stored in a a file identified by a tracing key.  Print a line of text with a trailing new-line.
 If this method is called with a CGI object, then the tracing key is  
 taken from a cookie. If it is called with no parameters, then the tracing  
 key is taken from an environment variable. If it is called with a string,  
 the tracing key is that string.  
2718    
2719  =over 4  =over 4
2720    
2721  =item parameter  =item line
2722    
2723  A parameter from which the tracing key is computed. If it is a scalar,  Line of text to print.
 that scalar is used as the tracing key. If it is a CGI object, the  
 tracing key is taken from the C<IP> cookie. If it is omitted, the  
 tracing key is taken from the C<TRACING> environment variable. If it  
 is a CGI object and emergency tracing is not on, the C<Trace> and  
 C<TF> parameters will be used to determine the type of tracing.  
2724    
2725  =back  =back
2726    
2727  =cut  =cut
2728    
2729  sub ETracing {  sub PrintLine {
2730      # Get the parameter.      # Get the parameters.
2731      my ($parameter) = @_;      my ($line) = @_;
2732      # Check for CGI mode.      # Print the line.
2733      my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);      print "$line\n";
     # Default to no tracing except errors.  
     my ($tracing, $dest) = ("0", "WARN");  
     # Check for emergency tracing.  
     my $tkey = EmergencyKey($parameter);  
     my $emergencyFile = EmergencyFileName($tkey);  
     if (-e $emergencyFile) {  
         # We have the file. Read in the data.  
         my @tracing = GetFile($emergencyFile);  
         # Pull off the time limit.  
         my $expire = shift @tracing;  
         # Convert it to seconds.  
         $expire *= 3600;  
         # Check the file data.  
         my $stat = stat($emergencyFile);  
         my ($now) = gettimeofday;  
         if ($now - $stat->mtime > $expire) {  
             # Delete the expired file.  
             unlink $emergencyFile;  
         } else {  
             # Emergency tracing is on. Pull off the destination and  
             # the trace level;  
             $dest = shift @tracing;  
             my $level = shift @tracing;  
             # Convert the destination to a real tracing destination.  
             # temp directory.  
             $dest = EmergencyTracingDest($tkey, $dest);  
             # Insure Tracer is specified.  
             my %moduleHash = map { $_ => 1 } @tracing;  
             $moduleHash{Tracer} = 1;  
             # Set the trace parameter.  
             $tracing = join(" ", $level, sort keys %moduleHash);  
         }  
     } elsif (defined $cgi) {  
         # There's no emergency tracing, but we have a CGI object, so check  
         # for tracing from the form parameters.  
         if ($cgi->param('Trace')) {  
             # Here the user has requested tracing via a form.  
             $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");  
             $tracing = $cgi->param('Trace') . " Tracer";  
         }  
     }  
     # Setup the tracing we've determined from all the stuff above.  
     TSetup($tracing, $dest);  
     # If we're a web script, trace the parameter and environment data.  
     if (defined $cgi) {  
         TraceParms($cgi);  
     }  
2734  }  }
2735    
 =head3 EmergencyFileName  
2736    
2737  C<< my $fileName = Tracer::EmergencyFileName($tkey); >>  =head2 Other Useful Methods
2738    
2739  Return the emergency tracing file name. This is the file that specifies  =head3 ParseParm
2740  the tracing information.  
2741        my $listValue = Tracer::ParseParm($string);
2742    
2743    Convert a parameter into a list reference. If the parameter is undefined,
2744    an undefined value will be returned. Otherwise, it will be parsed as a
2745    comma-separated list of values.
2746    
2747  =over 4  =over 4
2748    
2749  =item tkey  =item string
2750    
2751  Tracing key for the current program.  Incoming string.
2752    
2753  =item RETURN  =item RETURN
2754    
2755  Returns the name of the file to contain the emergency tracing information.  Returns a reference to a list of values, or C<undef> if the incoming value
2756    was undefined.
2757    
2758  =back  =back
2759    
2760  =cut  =cut
2761    
2762  sub EmergencyFileName {  sub ParseParm {
2763      # Get the parameters.      # Get the parameters.
2764      my ($tkey) = @_;      my ($string) = @_;
2765      # Compute the emergency tracing file name.      # Declare the return variable.
2766      return "$FIG_Config::temp/Emergency$tkey.txt";      my $retVal;
2767        # Check for data.
2768        if (defined $string) {
2769            # We have some, so split it into a list.
2770            $retVal = [ split /\s*,\s*/, $string];
2771        }
2772        # Return the result.
2773        return $retVal;
2774  }  }
2775    
2776  =head3 EmergencyFileTarget  =head3 Now
2777    
2778  C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>      my $string = Tracer::Now();
2779    
2780  Return the emergency tracing target file name. This is the file that receives  Return a displayable time stamp containing the local time. Whatever format this
2781  the tracing output for file-based tracing.  method produces must be parseable by L</ParseDate>.
2782    
2783    =cut
2784    
2785    sub Now {
2786        return DisplayTime(time);
2787    }
2788    
2789    =head3 DisplayTime
2790    
2791        my $string = Tracer::DisplayTime($time);
2792    
2793    Convert a time value to a displayable time stamp. Whatever format this
2794    method produces must be parseable by L</ParseDate>.
2795    
2796  =over 4  =over 4
2797    
2798  =item tkey  =item time
2799    
2800  Tracing key for the current program.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2801    
2802  =item RETURN  =item RETURN
2803    
2804  Returns the name of the file to contain the trace output.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2805    
2806  =back  =back
2807    
2808  =cut  =cut
2809    
2810  sub EmergencyFileTarget {  sub DisplayTime {
2811      # Get the parameters.      my ($time) = @_;
2812      my ($tkey) = @_;      my $retVal = "(n/a)";
2813      # Compute the emergency tracing file name.      if (defined $time) {
2814      return "$FIG_Config::temp/trace$tkey.log";          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2815            $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2816                      _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2817        }
2818        return $retVal;
2819  }  }
2820    
2821  =head3 EmergencyTracingDest  # Pad a number to 2 digits.
2822    sub _p2 {
2823  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>      my ($value) = @_;
2824        $value = "0$value" if ($value < 10);
2825        return $value;
2826    }
2827    
2828  This method converts an emergency tracing destination to a real  =head3 Escape
 tracing destination. The main difference is that if the  
 destination is C<FILE> or C<APPEND>, we convert it to file  
 output. If the destination is C<DUAL>, we convert it to file  
 and standard output.  
2829    
2830  =over 4      my $codedString = Tracer::Escape($realString);
2831    
2832  =item tkey  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2833    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2834    result is to reverse the effect of L</UnEscape>.
2835    
2836  Tracing key for this environment.  =over 4
2837    
2838  =item myDest  =item realString
2839    
2840  Destination from the emergency tracing file.  String to escape.
2841    
2842  =item RETURN  =item RETURN
2843    
2844  Returns a destination that can be passed into L</TSetup>.  Escaped equivalent of the real string.
2845    
2846  =back  =back
2847    
2848  =cut  =cut
2849    
2850  sub EmergencyTracingDest {  sub Escape {
2851      # Get the parameters.      # Get the parameter.
2852      my ($tkey, $myDest) = @_;      my ($realString) = @_;
2853      # Declare the return variable.      # Initialize the return variable.
2854      my $retVal;      my $retVal = "";
2855      # Process according to the destination value.      # Loop through the parameter string, looking for sequences to escape.
2856      if ($myDest eq 'FILE') {      while (length $realString > 0) {
2857          $retVal = ">" . EmergencyFileTarget($tkey);          # Look for the first sequence to escape.
2858      } elsif ($myDest eq 'APPEND') {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2859          $retVal = ">>" . EmergencyFileTarget($tkey);              # Here we found it. The text preceding the sequence is in $1. The sequence
2860      } elsif ($myDest eq 'DUAL') {              # itself is in $2. First, move the clear text to the return variable.
2861          $retVal = "+>" . EmergencyFileTarget($tkey);              $retVal .= $1;
2862                # Strip the processed section off the real string.
2863                $realString = substr $realString, (length $2) + (length $1);
2864                # Get the matched character.
2865                my $char = $2;
2866                # If we have a CR, we are done.
2867                if ($char ne "\r") {
2868                    # It's not a CR, so encode the escape sequence.
2869                    $char =~ tr/\t\n/tn/;
2870                    $retVal .= "\\" . $char;
2871                }
2872            } else {
2873                # Here there are no more escape sequences. The rest of the string is
2874                # transferred unmodified.
2875                $retVal .= $realString;
2876                $realString = "";
2877            }
2878      }      }
2879      # Return the result.      # Return the result.
2880      return $retVal;      return $retVal;
2881  }  }
2882    
2883  =head3 Emergency  =head3 UnEscape
2884    
2885  C<< Emergency($key, $hours, $dest, $level, @modules); >>      my $realString = Tracer::UnEscape($codedString);
2886    
2887  Turn on emergency tracing. This method is normally invoked over the web from  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2888  a debugging console, but it can also be called by the C<trace.pl> script.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2889  The caller specifies the duration of the emergency in hours, the desired tracing  be deleted.
 destination, the trace level, and a list of the trace modules to activate.  
 For the length of the duration, when a program in an environment with the  
 specified tracing key active invokes a Sprout CGI script, tracing will be  
 turned on automatically. See L</TSetup> for more about tracing setup and  
 L</ETracing> for more about emergency tracing.  
2890    
2891  =over 4  =over 4
2892    
2893  =item tkey  =item codedString
   
 The tracing key. This is used to identify the control file and the trace file.  
   
 =item hours  
   
 Number of hours to keep emergency tracing alive.  
   
 =item dest  
   
 Tracing destination. If no path information is specified for a file  
 destination, it is put in the FIG temporary directory.  
   
 =item level  
2894    
2895  Tracing level. A higher level means more trace messages.  String to un-escape.
2896    
2897  =item modules  =item RETURN
2898    
2899  A list of the tracing modules to activate.  Returns a copy of the original string with the escape sequences converted to their actual
2900    values.
2901    
2902  =back  =back
2903    
2904  =cut  =cut
2905    
2906  sub Emergency {  sub UnEscape {
2907      # Get the parameters.      # Get the parameter.
2908      my ($tkey, $hours, $dest, $level, @modules) = @_;      my ($codedString) = @_;
2909      # Create the emergency file.      # Initialize the return variable.
2910      my $specFile = EmergencyFileName($tkey);      my $retVal = "";
2911      my $outHandle = Open(undef, ">$specFile");      # Only proceed if the incoming string is nonempty.
2912      print $outHandle join("\n", $hours, $dest, $level, @modules, "");      if (defined $codedString) {
2913            # Loop through the parameter string, looking for escape sequences. We can't do
2914            # translating because it causes problems with the escaped slash. ("\\t" becomes
2915            # "\<tab>" no matter what we do.)
2916            while (length $codedString > 0) {
2917                # Look for the first escape sequence.
2918                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2919                    # Here we found it. The text preceding the sequence is in $1. The sequence
2920                    # itself is in $2. First, move the clear text to the return variable.
2921                    $retVal .= $1;
2922                    $codedString = substr $codedString, (2 + length $1);
2923                    # Get the escape value.
2924                    my $char = $2;
2925                    # If we have a "\r", we are done.
2926                    if ($char ne 'r') {
2927                        # Here it's not an 'r', so we convert it.
2928                        $char =~ tr/\\tn/\\\t\n/;
2929                        $retVal .= $char;
2930                    }
2931                } else {
2932                    # Here there are no more escape sequences. The rest of the string is
2933                    # transferred unmodified.
2934                    $retVal .= $codedString;
2935                    $codedString = "";
2936                }
2937            }
2938        }
2939        # Return the result.
2940        return $retVal;
2941  }  }
2942    
2943  =head3 EmergencyKey  =head3 Percent
2944    
2945  C<< my $tkey = EmergencyKey($parameter); >>      my $percent = Tracer::Percent($number, $base);
2946    
2947  Return the Key to be used for emergency tracing. This could be an IP address,  Returns the percent of the base represented by the given number. If the base
2948   a session ID, or a user name, depending on the environment.  is zero, returns zero.
2949    
2950  =over 4  =over 4
2951    
2952  =item parameter  =item number
2953    
2954  Parameter defining the method for finding the tracing key. If it is a scalar,  Percent numerator.
2955  then it is presumed to be the tracing key itself. If it is a CGI object, then  
2956  the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is  =item base
2957  taken from the C<TRACING> environment variable.  
2958    Percent base.
2959    
2960  =item RETURN  =item RETURN
2961    
2962  Returns the key to be used for labels in emergency tracing.  Returns the percentage of the base represented by the numerator.
2963    
2964  =back  =back
2965    
2966  =cut  =cut
2967    
2968  sub EmergencyKey {  sub Percent {
2969      # Get the parameters.      # Get the parameters.
2970      my ($parameter) = @_;      my ($number, $base) = @_;
2971      # Declare the return variable.      # Declare the return variable.
2972      my $retVal;      my $retVal = 0;
2973      # Determine the parameter type.      # Compute the percent.
2974      if (! defined $parameter) {      if ($base != 0) {
2975          # Here we're supposed to check the environment.          $retVal = $number * 100 / $base;
         $retVal = $ENV{TRACING};  
     } else {  
         my $ptype = ref $parameter;  
         if ($ptype eq 'CGI') {  
             # Here we were invoked from a web page. Look for a cookie.  
             $retVal = $parameter->cookie('IP');  
         } elsif (! $ptype) {  
             # Here the key was passed in.  
             $retVal = $parameter;  
         }  
     }  
     # If no luck finding a key, use the PID.  
     if (! defined $retVal) {  
         $retVal = $$;  
2976      }      }
2977      # Return the result.      # Return the result.
2978      return $retVal;      return $retVal;
2979  }  }
2980    
2981    =head3 Constrain
2982    
2983  =head3 TraceParms      my $constrained = Constrain($value, $min, $max);
   
 C<< Tracer::TraceParms($cgi); >>  
2984    
2985  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Modify a numeric value to bring it to a point in between a maximum and a minimum.
 at level CGI => 4.  
2986    
2987  =over 4  =over 4
2988    
2989  =item cgi  =item value
   
 CGI query object containing the parameters to trace.  
   
 =back  
   
 =cut  
   
 sub TraceParms {  
     # Get the parameters.  
     my ($cgi) = @_;  
     if (T(CGI => 3)) {  
         # Here we want to trace the parameter data.  
         my @names = $cgi->param;  
         for my $parmName (sort @names) {  
             # Note we skip the Trace parameters, which are for our use only.  
             if ($parmName ne 'Trace' && $parmName ne 'TF') {  
                 my @values = $cgi->param($parmName);  
                 Trace("CGI: $parmName = " . join(", ", @values));  
             }  
         }  
         # Display the request method.  
         my $method = $cgi->request_method();  
         Trace("Method: $method");  
     }  
     if (T(CGI => 4)) {  
         # Here we want the environment data too.  
         for my $envName (sort keys %ENV) {  
             Trace("ENV: $envName = $ENV{$envName}");  
         }  
     }  
 }  
   
 =head3 ScriptFinish  
   
 C<< ScriptFinish($webData, $varHash); >>  
   
 Output a web page at the end of a script. Either the string to be output or the  
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
   
 A typical standard script would loook like the following.  
   
     BEGIN {  
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
2990    
2991      my ($cgi, $varHash) = ScriptSetup();  Value to constrain.
     eval {  
         # ... get data from $cgi, put it in $varHash ...  
     };  
     if ($@) {  
         Trace("Script Error: $@") if T(0);  
     }  
     ScriptFinish("Html/MyTemplate.html", $varHash);  
2992    
2993  The idea here is that even if the script fails, you'll see trace messages and  =item min (optional)
 useful output.  
2994    
2995  =over 4  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
2996    
2997  =item webData  =item max (optional)
2998    
2999  A string containing either the full web page to be written to the output or the  Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3000    
3001  =item varHash (optional)  =item RETURN
3002    
3003  If specified, then a reference to a hash mapping variable names for a template  Returns the incoming value, constrained according to the other parameters.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3004    
3005  =back  =back
3006    
3007  =cut  =cut
3008    
3009  sub ScriptFinish {  sub Constrain {
3010      # Get the parameters.      # Get the parameters.
3011      my ($webData, $varHash) = @_;      my ($value, $min, $max) = @_;
3012      # Check for a template file situation.      # Declare the return variable.
3013      my $outputString;      my $retVal = $value;
3014      if (defined $varHash) {      # Apply the minimum constraint.
3015          # Here we have a template file. We need to determine the template type.      if (defined $min && $retVal < $min) {
3016          my $template;          $retVal = $min;
3017          if ($FIG_Config::template_url && $webData =~ /\.php$/) {      }
3018              $template = "$FIG_Config::template_url/$webData";      # Apply the maximum constraint.
3019          } else {      if (defined $max && $retVal > $max) {
3020              $template = "<<$webData";          $retVal = $max;
         }  
         $outputString = PageBuilder::Build($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 $actualDest.</p>\n";  
         } else {  
             # Here we have one of the special destinations.  
             $traceHtml = "<P>Tracing output type is $Destination.</p>\n";  
         }  
         substr $outputString, $pos, 0, $traceHtml;  
3021      }      }
3022      # Write the output string.      # Return the result.
3023      print $outputString;      return $retVal;
3024  }  }
3025    
3026  =head3 Insure  =head3 Min
3027    
3028  C<< Insure($dirName); >>      my $min = Min($value1, $value2, ... $valueN);
3029    
3030  Insure a directory is present.  Return the minimum argument. The arguments are treated as numbers.
3031    
3032  =over 4  =over 4
3033    
3034  =item dirName  =item $value1, $value2, ... $valueN
3035    
3036  Name of the directory to check. If it does not exist, it will be created.  List of numbers to compare.
3037    
3038    =item RETURN
3039    
3040    Returns the lowest number in the list.
3041    
3042  =back  =back
3043    
3044  =cut  =cut
3045    
3046  sub Insure {  sub Min {
3047      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
3048      if (! -d $dirName) {      my ($retVal, @values) = @_;
3049          Trace("Creating $dirName directory.") if T(File => 2);      # Loop through the remaining parameters, looking for the lowest.
3050          eval { mkpath $dirName; };      for my $value (@values) {
3051          if ($@) {          if ($value < $retVal) {
3052              Confess("Error creating $dirName: $@");              $retVal = $value;
3053          }          }
3054      }      }
3055        # Return the minimum found.
3056        return $retVal;
3057  }  }
3058    
3059  =head3 ChDir  =head3 Max
3060    
3061  C<< ChDir($dirName); >>      my $max = Max($value1, $value2, ... $valueN);
3062    
3063  Change to the specified directory.  Return the maximum argument. The arguments are treated as numbers.
3064    
3065  =over 4  =over 4
3066    
3067  =item dirName  =item $value1, $value2, ... $valueN
3068    
3069  Name of the directory to which we want to change.  List of numbers to compare.
3070    
3071    =item RETURN
3072    
3073    Returns the highest number in the list.
3074    
3075  =back  =back
3076    
3077  =cut  =cut
3078    
3079  sub ChDir {  sub Max {
3080      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
3081      if (! -d $dirName) {      my ($retVal, @values) = @_;
3082          Confess("Cannot change to directory $dirName: no such directory.");      # Loop through the remaining parameters, looking for the highest.
3083      } else {      for my $value (@values) {
3084          Trace("Changing to directory $dirName.") if T(File => 4);          if ($value > $retVal) {
3085          my $okFlag = chdir $dirName;              $retVal = $value;
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
3086          }          }
3087      }      }
3088        # Return the maximum found.
3089        return $retVal;
3090  }  }
3091    
3092  =head3 SendSMS  =head3 Strip
   
 C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>  
   
 Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  
 user name, password, and API ID for the relevant account in the hash reference variable  
 I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For  
 example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID  
 is C<2561022>, then the FIG_Config file must contain  
   
     $phone =  { user => 'BruceTheHumanPet',  
                 password => 'silly',  
                 api_id => '2561022' };  
   
 The original purpose of this method was to insure Bruce would be notified immediately when the  
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
   
 The message ID will be returned if successful, and C<undef> if an error occurs.  
3093    
3094  =over 4      my $string = Tracer::Strip($line);
3095    
3096  =item phoneNumber  Strip all line terminators off a string. This is necessary when dealing with files
3097    that may have been transferred back and forth several times among different
3098    operating environments.
3099    
3100  Phone number to receive the message, in international format. A United States phone number  =over 4
 would be prefixed by "1". A British phone number would be prefixed by "44".  
3101    
3102  =item msg  =item line
3103    
3104  Message to send to the specified phone.  Line of text to be stripped.
3105    
3106  =item RETURN  =item RETURN
3107    
3108  Returns the message ID if successful, and C<undef> if the message could not be sent.  The same line of text with all the line-ending characters chopped from the end.
3109    
3110  =back  =back
3111    
3112  =cut  =cut
3113    
3114  sub SendSMS {  sub Strip {
3115      # Get the parameters.      # Get a copy of the parameter string.
3116      my ($phoneNumber, $msg) = @_;      my ($string) = @_;
3117      # Declare the return variable. If we do not change it, C<undef> will be returned.      my $retVal = (defined $string ? $string : "");
3118      my $retVal;      # Strip the line terminator characters.
3119      # Only proceed if we have phone support.      $retVal =~ s/(\r|\n)+$//g;
     if (! defined $FIG_Config::phone) {  
         Trace("Phone support not present in FIG_Config.") if T(1);  
     } else {  
         # Get the phone data.  
         my $parms = $FIG_Config::phone;  
         # Get the Clickatell URL.  
         my $url = "http://api.clickatell.com/http/";  
         # Create the user agent.  
         my $ua = LWP::UserAgent->new;  
         # Request a Clickatell session.  
         my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},  
                                      password => $parms->{password},  
                                      api_id => $parms->{api_id},  
                                      to => $phoneNumber,  
                                      text => $msg});  
         # Check for an error.  
         if (! $resp->is_success) {  
             Trace("Alert failed.") if T(1);  
         } else {  
             # Get the message ID.  
             my $rstring = $resp->content;  
             if ($rstring =~ /^ID:\s+(.*)$/) {  
                 $retVal = $1;  
             } else {  
                 Trace("Phone attempt failed with $rstring") if T(1);  
             }  
         }  
     }  
3120      # Return the result.      # Return the result.
3121      return $retVal;      return $retVal;
3122  }  }
3123    
3124  =head3 CommaFormat  =head3 Pad
3125    
3126  C<< my $formatted = Tracer::CommaFormat($number); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3127    
3128  Insert commas into a number.  Pad a string to a specified length. The pad character will be a
3129    space, and the padding will be on the right side unless specified
3130    in the third parameter.
3131    
3132  =over 4  =over 4
3133    
3134  =item number  =item string
3135    
3136  A sequence of digits.  String to be padded.
3137    
3138    =item len
3139    
3140    Desired length of the padded string.
3141    
3142    =item left (optional)
3143    
3144    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3145    
3146    =item padChar (optional)
3147    
3148    Character to use for padding. The default is a space.
3149    
3150  =item RETURN  =item RETURN
3151    
3152  Returns the same digits with commas strategically inserted.  Returns a copy of the original string with the pad character added to the
3153    specified end so that it achieves the desired length.
3154    
3155  =back  =back
3156    
3157  =cut  =cut
3158    
3159  sub CommaFormat {  sub Pad {
3160      # Get the parameters.      # Get the parameters.
3161      my ($number) = @_;      my ($string, $len, $left, $padChar) = @_;
3162      # Pad the length up to a multiple of three.      # Compute the padding character.
3163      my $padded = "$number";      if (! defined $padChar) {
3164      $padded = " " . $padded while length($padded) % 3 != 0;          $padChar = " ";
3165      # This is a fancy PERL trick. The parentheses in the SPLIT pattern      }
3166      # cause the delimiters to be included in the output stream. The      # Compute the number of spaces needed.
3167      # GREP removes the empty strings in between the delimiters.      my $needed = $len - length $string;
3168      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));      # Copy the string into the return variable.
3169      # Clean out the spaces.      my $retVal = $string;
3170      $retVal =~ s/ //g;      # Only proceed if padding is needed.
3171        if ($needed > 0) {
3172            # Create the pad string.
3173            my $pad = $padChar x $needed;
3174            # Affix it to the return value.
3175            if ($left) {
3176                $retVal = $pad . $retVal;
3177            } else {
3178                $retVal .= $pad;
3179            }
3180        }
3181      # Return the result.      # Return the result.
3182      return $retVal;      return $retVal;
3183  }  }
 =head3 SetPermissions  
3184    
3185  C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  =head3 EOF
3186    
3187  Set the permissions for a directory and all the files and folders inside it.  This is a constant that is lexically greater than any useful string.
 In addition, the group ownership will be changed to the specified value.  
3188    
3189  This method is more vulnerable than most to permission and compatability  =cut
 problems, so it does internal error recovery.  
3190    
3191  =over 4  sub EOF {
3192        return "\xFF\xFF\xFF\xFF\xFF";
3193    }
3194    
3195  =item dirName  =head3 TICK
3196    
3197  Name of the directory to process.      my @results = TICK($commandString);
3198    
3199  =item group  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3200    dot-slash (C<./> will be removed. So, for example, if you were doing
3201    
3202  Name of the group to be assigned.      `./protein.cgi`
3203    
3204  =item mask  from inside a CGI script, it would work fine in Unix, but would issue an error message
3205    in Windows complaining that C<'.'> is not a valid command. If instead you code
3206    
3207  Permission mask. Bits that are C<1> in this mask will be ORed into the      TICK("./protein.cgi")
 permission bits of any file or directory that does not already have them  
 set to 1.  
3208    
3209  =item otherMasks  it will work correctly in both environments.
3210    
3211  Map of search patterns to permission masks. If a directory name matches  =over 4
 one of the patterns, that directory and all its members and subdirectories  
 will be assigned the new pattern. For example, the following would  
 assign 01664 to most files, but would use 01777 for directories named C<tmp>.  
3212    
3213      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  =item commandString
3214    
3215  The list is ordered, so the following would use 0777 for C<tmp1> and  The command string to pass to the system.
 0666 for C<tmp>, C<tmp2>, or C<tmp3>.  
3216    
3217      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  =item RETURN
                                                    '^tmp' => 0666);  
3218    
3219  Note that the pattern matches are all case-insensitive, and only directory  Returns the standard output from the specified command, as a list.
 names are matched, not file names.  
3220    
3221  =back  =back
3222    
3223  =cut  =cut
3224    #: Return Type @;
3225  sub SetPermissions {  sub TICK {
3226      # Get the parameters.      # Get the parameters.
3227      my ($dirName, $group, $mask, @otherMasks) = @_;      my ($commandString) = @_;
3228      # Set up for error recovery.      # Chop off the dot-slash if this is Windows.
3229      eval {      if ($FIG_Config::win_mode) {
3230          # Switch to the specified directory.          $commandString =~ s!^\./!!;
         ChDir($dirName);  
         # Get the group ID.  
         my $gid = getgrnam($group);  
         # Get the mask for tracing.  
         my $traceMask = sprintf("%04o", $mask) . "($mask)";  
         Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);  
         my $fixCount = 0;  
         my $lookCount = 0;  
         # @dirs will be a stack of directories to be processed.  
         my @dirs = (getcwd());  
         while (scalar(@dirs) > 0) {  
             # Get the current directory.  
             my $dir = pop @dirs;  
             # Check for a match to one of the specified directory names. To do  
             # that, we need to pull the individual part of the name off of the  
             # whole path.  
             my $simpleName = $dir;  
             if ($dir =~ m!/([^/]+)$!) {  
                 $simpleName = $1;  
             }  
             Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);  
             # Search for a match.  
             my $match = 0;  
             my $i;  
             for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {  
                 my $pattern = $otherMasks[$i];  
                 if ($simpleName =~ /$pattern/i) {  
                     $match = 1;  
                 }  
             }  
             # Check for a match. Note we use $i-1 because the loop added 2  
             # before terminating due to the match.  
             if ($match && $otherMasks[$i-1] != $mask) {  
                 # This directory matches one of the incoming patterns, and it's  
                 # a different mask, so we process it recursively with that mask.  
                 SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);  
             } else {  
                 # Here we can process normally. Get all of the non-hidden members.  
                 my @submems = OpenDir($dir, 1);  
                 for my $submem (@submems) {  
                     # Get the full name.  
                     my $thisMem = "$dir/$submem";  
                     Trace("Checking member $thisMem.") if T(4);  
                     $lookCount++;  
                     if ($lookCount % 1000 == 0) {  
                         Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);  
                     }  
                     # Fix the group.  
                     chown -1, $gid, $thisMem;  
                     # Insure this member is not a symlink.  
                     if (! -l $thisMem) {  
                         # Get its info.  
                         my $fileInfo = stat $thisMem;  
                         # Only proceed if we got the info. Otherwise, it's a hard link  
                         # and we want to skip it anyway.  
                         if ($fileInfo) {  
                             my $fileMode = $fileInfo->mode;  
                             if (($fileMode & $mask) != $mask) {  
                                 # Fix this member.  
                                 $fileMode |= $mask;  
                                 chmod $fileMode, $thisMem;  
                                 $fixCount++;  
                             }  
                             # If it's a subdirectory, stack it.  
                             if (-d $thisMem) {  
                                 push @dirs, $thisMem;  
                             }  
                         }  
                     }  
                 }  
             }  
3231          }          }
3232          Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);      # Activate the command and return the result.
3233      };      return `$commandString`;
     # Check for an error.  
     if ($@) {  
         Confess("SetPermissions error: $@");  
3234      }      }
3235    
3236    
3237    =head3 CommaFormat
3238    
3239        my $formatted = Tracer::CommaFormat($number);
3240    
3241    Insert commas into a number.
3242    
3243    =over 4
3244    
3245    =item number
3246    
3247    A sequence of digits.
3248    
3249    =item RETURN
3250    
3251    Returns the same digits with commas strategically inserted.
3252    
3253    =back
3254    
3255    =cut
3256    
3257    sub CommaFormat {
3258        # Get the parameters.
3259        my ($number) = @_;
3260        # Pad the length up to a multiple of three.
3261        my $padded = "$number";
3262        $padded = " " . $padded while length($padded) % 3 != 0;
3263        # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3264        # cause the delimiters to be included in the output stream. The
3265        # GREP removes the empty strings in between the delimiters.
3266        my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3267        # Clean out the spaces.
3268        $retVal =~ s/ //g;
3269        # Return the result.