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revision 1.86, Fri May 18 19:27:17 2007 UTC revision 1.112, Wed Oct 1 03:23:40 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 qw(:DEFAULT :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: $!";
496            # Lock the file.
497            flock TRACING, LOCK_EX;
498            print TRACING "$formatted\n";
499            close TRACING;
500            # If the Tee flag is on, echo it to the standard output.
501            if ($TeeFlag) {
502                print "$formatted\n";
503            }
504        }
505    }
506    
507  The parameters to this method are as follows.  =head3 T
508    
509  =over 4      my $switch = T($category, $traceLevel);
510    
511  =item categories      or
512    
513  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.  
514    
515  =item options  Return TRUE if the trace level is at or above a specified value and the specified category
516    is active, else FALSE. If no category is specified, the caller's package name is used.
517    
518  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).  
519    
520  =item parmHelp  =item category
521    
522  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
523  if the user specifies the C<-h> option.  used.
524    
525  =item argv  =item traceLevel
526    
527  List of command line parameters, including the option switches, which must  Relevant tracing level.
 precede the positional parameters and be prefixed by a hyphen.  
528    
529  =item RETURN  =item RETURN
530    
531  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.  
532    
533  =back  =back
534    
535  =cut  =cut
536    
537  sub StandardSetup {  sub T {
538        # Declare the return variable.
539        my $retVal = 0;
540        # Only proceed if tracing is turned on.
541        if ($Destination ne "NONE") {
542      # Get the parameters.      # Get the parameters.
543      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
544      # Get the default tracing key.          if (!defined $traceLevel) {
545      my $tkey = EmergencyKey();              # Here we have no category, so we need to get the calling package.
546      # Add the tracing options.              # The calling package is normally the first parameter. If it is
547      if (! exists $options->{trace}) {              # omitted, the first parameter will be the tracelevel. So, the
548          $options->{trace} = ['2', "tracing level (E for emergency tracing)"];              # first thing we do is shift the so-called category into the
549      }              # $traceLevel variable where it belongs.
550      $options->{sql} = [0, "turn on SQL tracing"];              $traceLevel = $category;
551      $options->{help} = [0, "display command-line options"];              my ($package, $fileName, $line) = caller;
552      $options->{user} = [$tkey, "tracing key"];              # If there is no calling package, we default to "main".
553      $options->{background} = [0, "spool standard and error output"];              if (!$package) {
554      # 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});  
555      } else {      } else {
556          # Here the tracing is controlled from the command line.                  my @cats = split /::/, $package;
557          my @cats = @{$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";  
558              }              }
             # 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";  
559              }              }
560            # Save the category name and level.
561            $LastCategory = $category;
562            $LastLevel = $traceLevel;
563            # Convert it to lower case before we hash it.
564            $category = lc $category;
565            # Validate the trace level.
566            if (ref $traceLevel) {
567                Confess("Bad trace level.");
568            } elsif (ref $TraceLevel) {
569                Confess("Bad trace config.");
570          }          }
571          # Now set up the tracing.          # Make the check. Note that level 0 shows even if the category is turned off.
572          TSetup("$traceLevel $cats", $traceMode);          $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
573      }      }
574      # Check for the "h" option. If it is specified, dump the command-line      # Return the computed result.
575      # 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] . ")";  
576              }              }
577              print "  $name $desc\n";  
578    =head3 QTrace
579    
580        my $data = QTrace($format);
581    
582    Return the queued trace data in the specified format.
583    
584    =over 4
585    
586    =item format
587    
588    C<html> to format the data as an HTML list, C<text> to format it as straight text.
589    
590    =back
591    
592    =cut
593    
594    sub QTrace {
595        # Get the parameter.
596        my ($format) = @_;
597        # Create the return variable.
598        my $retVal = "";
599        # Only proceed if there is an actual queue.
600        if (@Queue) {
601            # Process according to the format.
602            if ($format =~ m/^HTML$/i) {
603                # Convert the queue into an HTML list.
604                $retVal = "<ul>\n";
605                for my $line (@Queue) {
606                    my $escapedLine = CGI::escapeHTML($line);
607                    $retVal .= "<li>$escapedLine</li>\n";
608          }          }
609          exit(0);              $retVal .= "</ul>\n";
610            } elsif ($format =~ m/^TEXT$/i) {
611                # Convert the queue into a list of text lines.
612                $retVal = join("\n", @Queue) . "\n";
613      }      }
614      # Trace the options, if applicable.          # Clear the queue.
615      if (T(3)) {          @Queue = ();
         my @parms = grep { $retOptions->{$_} } keys %{$retOptions};  
         Trace("Selected options: " . join(", ", sort @parms) . ".");  
616      }      }
617      # Return the parsed parameters.      # Return the formatted list.
618      return ($retOptions, @retParameters);      return $retVal;
619  }  }
620    
621  =head3 Setups  =head3 Confess
622    
623  C<< my $count = Tracer::Setups(); >>      Confess($message);
624    
625  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
626    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
627    So, for example
628    
629  This method allows for the creation of conditional tracing setups where, for example, we      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
630  may want to set up tracing if nobody else has done it before us.  
631    Will abort the program with a stack trace if the value of C<$recNum> is negative.
632    
633    =over 4
634    
635    =item message
636    
637    Message to include in the trace.
638    
639    =back
640    
641  =cut  =cut
642    
643  sub Setups {  sub Confess {
644      return $SetupCount;      # Get the parameters.
645        my ($message) = @_;
646        # Set up the category and level.
647        $LastCategory = "(confess)";
648        $LastLevel = 0;
649        if (! defined($FIG_Config::no_tool_hdr)) {
650            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
651            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
652            # Only proceed if the tool header file is actually present.
653            if (-f $toolHeaderFile) {
654                my $fh;
655                if (open $fh, "<$toolHeaderFile") {
656                    my @lines = <$fh>;
657                    Trace("Tool header has " . scalar(@lines) . " lines.");
658                }
659            }
660        }
661        # Trace the call stack.
662        Cluck($message);
663        # Abort the program.
664        croak(">>> $message");
665  }  }
666    
667  =head3 Open  =head3 SaveCGI
   
 C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  
668    
669  Open a file.      Tracer::SaveCGI($cgi);
670    
671  The I<$fileSpec> is essentially the second argument of the PERL C<open>  This method saves the CGI object but does not activate emergency tracing.
672  function. The mode is specified using Unix-like shell information. So, for  It is used to allow L</Warn> to work in situations where emergency
673  example,  tracing is contra-indicated (e.g. the wiki).
674    
675      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =over 4
676    
677  would open for output appended to the specified file, and  =item cgi
678    
679      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  Active CGI query object.
680    
681  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.  
682    
683      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =cut
684    
685  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  sub SaveCGI {
686  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a      $SavedCGI = $_[0];
687  failed open will throw an exception and the third parameter will be used to construct  }
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
688    
689      Could not open "/usr/spool/news/twitlog"  =head3 Warn
690    
691  Note that the mode characters are automatically cleaned from the file name.      Warn($message, @options);
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
692    
693      Could not open "/usr/spool/news/twitlog": file not found.  This method traces an important message. If an RSS feed is configured
694    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
695    then the message will be echoed to the feed. In general, a tracing
696    destination of C<WARN> indicates that the caller is running as a web
697    service in a production environment; however, this is not a requirement.
698    
699  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
700  corresponds to the C++ C<errno> value.  is not C<WARN>, simply specify the C<Feed> tracing module. This can be
701    configured automatically when L</StandardSetup> is used.
702    
703      Could not open "/usr/spool/news/twitlog": 6.  The L</Cluck> method calls this one for its final message. Since
704    L</Confess> calls L</Cluck>, this means that any error which is caught
705    and confessed will put something in the feed. This insures that someone
706    will be alerted relatively quickly when a failure occurs.
707    
708  =over 4  =over 4
709    
710  =item fileHandle  =item message
711    
712  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.  
713    
714  =item fileSpec  =item options
715    
716  File name and mode, as per the PERL C<open> function.  A list containing zero or more options.
717    
718  =item message (optional)  =back
719    
720  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>.  
721    
722  =item RETURN  =over 4
723    
724  Returns the name of the file handle assigned to the file, or C<undef> if the  =item noStack
725  open failed.  
726    If specified, then the stack trace is not included in the output.
727    
728  =back  =back
729    
730  =cut  =cut
731    
732  sub Open {  sub Warn {
733      # Get the parameters.      # Get the parameters.
734      my ($fileHandle, $fileSpec, $message) = @_;      my $message = shift @_;
735      # Attempt to open the file.      my %options = map { $_ => 1 } @_;
736      my $rv = open $fileHandle, $fileSpec;      # Save $@;
737      # If the open failed, generate an error message.      my $savedError = $@;
738      if (! $rv) {      # Trace the message.
739          # Save the system error message.      Trace($message);
740          my $sysMessage = $!;      # This will contain the lock handle. If it's defined, it means we need to unlock.
741          # See if we need a default message.      my $lock;
742          if (!$message) {      # Check for feed forcing.
743              # Clean any obvious mode characters and leading spaces from the      my $forceFeed = exists $Categories{feed};
744              # filename.      # An error here would be disastrous. Note that if debug mode is specified,
745              my ($fileName) = FindNamePart($fileSpec);      # we do this stuff even in a test environment.
746              $message = "Could not open \"$fileName\"";      eval {
747            # Do we need to put this in the RSS feed?
748            if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
749                # Probably. We need to check first, however, to see if it's from an
750                # ignored IP. For non-CGI situations, we default the IP to the self-referent.
751                my $key = "127.0.0.1";
752                if (defined $SavedCGI) {
753                    # Get the IP address.
754                    $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
755                }
756                # Is the IP address in the ignore list?
757                my $found = scalar(grep { $_ eq $key } @FIG_Config::error_ignore_ips);
758                if (! $found) {
759                    # No. We're good. We now need to compute the date, the link, and the title.
760                    # First, the date, in a very specific format.
761                    my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
762                        (tz_local_offset() / 30);
763                    # Environment data goes in here. We start with the date.
764                    my $environment = "$date.  ";
765                    # If we need to recap the message (because it's too long to be a title), we'll
766                    # put it in here.
767                    my $recap;
768                    # Copy the message and remove excess space.
769                    my $title = $message;
770                    $title =~ s/\s+/ /gs;
771                    # If it's too long, we have to split it up.
772                    if (length $title > 60) {
773                        # Put the full message in the environment string.
774                        $recap = $title;
775                        # Excerpt it as the title.
776                        $title = substr($title, 0, 50) . "...";
777                    }
778                    # If we have a CGI object, then this is a web error. Otherwise, it's
779                    # command-line.
780                    if (defined $SavedCGI) {
781                        # We're in a web service. The environment is the user's IP, and the link
782                        # is the URL that got us here.
783                        $environment .= "Event Reported at IP address $key process $$.";
784                        my $url = $SavedCGI->self_url();
785                        # We need the user agent string and (if available) the referrer.
786                        # The referrer will be the link.
787                        $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
788                        if ($ENV{HTTP_REFERER}) {
789                            my $link = $ENV{HTTP_REFERER};
790                            $environment .= " referred from <a href=\"$link\">$link</a>.";
791                        } else {
792                            $environment .= " referrer unknown.";
793                        }
794                        # Close off the sentence with the original link.
795                        $environment .= " URL of event is <a href=\"$url\">$url</a>.";
796                    } else {
797                        # No CGI object, so we're a command-line tool. Use the tracing
798                        # key and the PID as the user identifier, and add the command.
799                        my $key = EmergencyKey();
800                        $environment .= "Event Reported by $key process $$.";
801                        if ($CommandLine) {
802                            # We're in a StandardSetup script, so we have the real command line.
803                            $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
804                        } elsif ($ENV{_}) {
805                            # We're in a BASH script, so the command has been stored in the _ variable.
806                            $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
807                        }
808                    }
809                    # Build a GUID. We use the current time, the title, and the process ID,
810                    # then digest the result.
811                    my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
812                    # Finally, the description. This is a stack trace plus various environmental stuff.
813                    # The trace is optional.
814                    my $stackTrace;
815                    if ($options{noStack}) {
816                        $stackTrace = "";
817                    } else {
818                        my @trace = LongMess();
819                        # Only proceed if we got something back.
820                        if (scalar(@trace) > 0) {
821                            $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
822                            $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
823                        }
824                    }
825                    # We got the stack trace. Now it's time to put it all together.
826                    # We have a goofy thing here in that we need to HTML-escape some sections of the description
827                    # twice. They will be escaped once here, and then once when written by XML::Simple. They are
828                    # unescaped once when processed by the RSS reader, and stuff in the description is treated as
829                    # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
830                    # our <br>s and <pre>s are used to format the description.
831                    $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
832                    my $description = "$recap$environment  $stackTrace";
833                    # Okay, we have all the pieces. Create a hash of the new event.
834                    my $newItem = { title => $title,
835                                    description => $description,
836                                    category => $LastCategory,
837                                    pubDate => $date,
838                                    guid => $guid,
839                                  };
840                    # We need XML capability for this.
841                    require XML::Simple;
842                    # The RSS document goes in here.
843                    my $rss;
844                    # Get the name of the RSS file. It's in the FIG temporary directory.
845                    my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
846                    # Open the config file and lock it.
847                    $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
848                    flock $lock, LOCK_EX;
849                    # Does it exist?
850                    if (-s $fileName) {
851                        # Slurp it in.
852                        $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
853                    } else {
854                        my $size = -s $fileName;
855                        # Create an empty channel.
856                        $rss = {
857                            channel => {
858                                title => 'NMPDR Warning Feed',
859                                link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
860                                description => "Important messages regarding the status of the NMPDR.",
861                                generator => "NMPDR Trace Facility",
862                                docs => "http://blogs.law.harvard.edu/tech/rss",
863                                item => []
864                            },
865                        };
866          }          }
867          # Terminate with an error using the supplied message and the                  # Get the channel object.
868          # error message from the file system.                  my $channel = $rss->{channel};
869          Confess("$message: $!");                  # Update the last-build date.
870                    $channel->{lastBuildDate} = $date;
871                    # Get the item array.
872                    my $items = $channel->{item};
873                    # Insure it has only 100 entries.
874                    while (scalar @{$items} > 100) {
875                        pop @{$items};
876                    }
877                    # Add our new item at the front.
878                    unshift @{$items}, $newItem;
879                    # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
880                    # the requirements for those.
881                    my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
882                    # Here we put in the root and declaration. The problem is that the root has to have the version attribute
883                    # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
884                    $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
885                    # We don't use Open here because we can't afford an error.
886                    if (open XMLOUT, ">$fileName") {
887                        print XMLOUT $xml;
888                        close XMLOUT;
889      }      }
890      # Return the file handle.              }
891      return $fileHandle;          }
892        };
893        if ($@) {
894            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
895            # (which is a good thing).
896            my $error = $@;
897            Trace("Feed Error: $error") if T(Feed => 0);
898        }
899        # Be sure to unlock.
900        if ($lock) {
901            flock $lock, LOCK_UN;
902            undef $lock;
903        }
904        # Restore the error message.
905        $@ = $savedError;
906  }  }
907    
 =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  
908    
 If the method cannot find a file name using its normal methods, it will return the  
 whole incoming string.  
909    
 =over 4  
910    
911  =item fileSpec  =head3 Assert
912    
913  File specification string from which the file name is to be extracted.      Assert($condition1, $condition2, ... $conditionN);
914    
915  =item RETURN  Return TRUE if all the conditions are true. This method can be used in conjunction with
916    the OR operator and the L</Confess> method as a debugging assert.
917    So, for example
918    
919  Returns a three-element list. The first element contains the file name portion of      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
 the specified string, or the whole string if a file name cannot be found via normal  
 methods. The second element contains the start position of the file name portion and  
 the third element contains the length.  
920    
921  =back  Will abort the program with a stack trace if the value of C<$recNum> is negative.
922    
923  =cut  =cut
924  #: Return Type $;  sub Assert {
925  sub FindNamePart {      my $retVal = 1;
926      # Get the parameters.      LOOP: for my $condition (@_) {
927      my ($fileSpec) = @_;          if (! $condition) {
928      # Default to the whole input string.              $retVal = 0;
929      my ($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) - $len;  
930      }      }
931      # Return the result.      }
932      return ($retVal, $pos, $len);      return $retVal;
933  }  }
934    
935  =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  
936    
937      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");      Cluck($message);
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
938    
939  Similarly, the following code  Trace the call stack. Note that for best results, you should qualify the call with a
940    trace condition. For example,
941    
942      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);      Cluck("Starting record parse.") if T(3);
943    
944  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  will only trace the stack if the trace level for the package is 3 or more.
 automatically returns an empty list if the directory fails to open.  
945    
946  =over 4  =over 4
947    
948  =item dirName  =item message
949    
950  Name of the directory to open.  Message to include in the trace.
951    
952  =item filtered  =back
953    
954  TRUE if files whose names begin with a period (C<.>) should be automatically removed  =cut
 from the list, else FALSE.  
955    
956  =item flag  sub Cluck {
957        # Get the parameters.
958        my ($message) = @_;
959        # Trace what's happening.
960        Trace("Stack trace for event: $message");
961        # Get the stack trace.
962        my @trace = LongMess();
963        # Convert the trace to a series of messages.
964        for my $line (@trace) {
965            # Replace the tab at the beginning with spaces.
966            $line =~ s/^\t/    /;
967            # Trace the line.
968            Trace($line);
969        }
970        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
971        Warn($message);
972    }
973    
974  TRUE if a failure to open is okay, else FALSE  =head3 LongMess
975    
976  =back      my @lines = Tracer::LongMess();
977    
978    Return a stack trace with all tracing methods removed. The return will be in the form of a list
979    of message strings.
980    
981  =cut  =cut
982  #: Return Type @;  
983  sub OpenDir {  sub LongMess {
     # Get the parameters.  
     my ($dirName, $filtered, $flag) = @_;  
984      # Declare the return variable.      # Declare the return variable.
985      my @retVal = ();      my @retVal = ();
986      # Open the directory.      my $confession = longmess("");
987      if (opendir(my $dirHandle, $dirName)) {      for my $line (split /\s*\n/, $confession) {
988          # The directory opened successfully. Get the appropriate list according to the          unless ($line =~ /Tracer\.pm/) {
989          # strictures of the filter parameter.              # Here we have a line worth keeping. Push it onto the result list.
990          if ($filtered) {              push @retVal, $line;
             @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;  
         } else {  
             @retVal = readdir $dirHandle;  
991          }          }
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
992      }      }
993      # Return the result.      # Return the result.
994      return @retVal;      return @retVal;
995  }  }
996    
997  =head3 SetLevel  =head3 ETracing
998    
999  C<< Tracer::SetLevel($newLevel); >>      ETracing($parameter);
1000    
1001  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
1002    on automatically for any program that calls this method. The emergency
1003    tracing parameters are stored in a a file identified by a tracing key.
1004    If this method is called with a CGI object, then the tracing key is
1005    taken from a cookie. If it is called with no parameters, then the tracing
1006    key is taken from an environment variable. If it is called with a string,
1007    the tracing key is that string.
1008    
1009  =over 4  =over 4
1010    
1011  =item newLevel  =item parameter
1012    
1013  Proposed new trace level.  A parameter from which the tracing key is computed. If it is a scalar,
1014    that scalar is used as the tracing key. If it is a CGI object, the
1015    tracing key is taken from the C<IP> cookie. If it is omitted, the
1016    tracing key is taken from the C<TRACING> environment variable. If it
1017    is a CGI object and emergency tracing is not on, the C<Trace> and
1018    C<TF> parameters will be used to determine the type of tracing.
1019    
1020  =back  =back
1021    
1022  =cut  =cut
1023    
1024  sub SetLevel {  sub ETracing {
1025      $TraceLevel = $_[0];      # Get the parameter.
1026        my ($parameter) = @_;
1027        # Check for CGI mode.
1028        if (defined $parameter && ref $parameter eq 'CGI') {
1029            $SavedCGI = $parameter;
1030        } else {
1031            $SavedCGI = undef;
1032        }
1033        # Default to no tracing except errors.
1034        my ($tracing, $dest) = ("0", "WARN");
1035        # Check for emergency tracing.
1036        my $tkey = EmergencyKey($parameter);
1037        my $emergencyFile = EmergencyFileName($tkey);
1038        if (-e $emergencyFile) {
1039            # We have the file. Read in the data.
1040            my @tracing = GetFile($emergencyFile);
1041            # Pull off the time limit.
1042            my $expire = shift @tracing;
1043            # Convert it to seconds.
1044            $expire *= 3600;
1045            # Check the file data.
1046            my $stat = stat($emergencyFile);
1047            my ($now) = gettimeofday;
1048            if ($now - $stat->mtime > $expire) {
1049                # Delete the expired file.
1050                unlink $emergencyFile;
1051            } else {
1052                # Emergency tracing is on. Pull off the destination and
1053                # the trace level;
1054                $dest = shift @tracing;
1055                my $level = shift @tracing;
1056                # Convert the destination to a real tracing destination.
1057                # temp directory.
1058                $dest = EmergencyTracingDest($tkey, $dest);
1059                # Insure Tracer is specified.
1060                my %moduleHash = map { $_ => 1 } @tracing;
1061                $moduleHash{Tracer} = 1;
1062                # Set the trace parameter.
1063                $tracing = join(" ", $level, sort keys %moduleHash);
1064            }
1065        } elsif (defined $SavedCGI) {
1066            # There's no emergency tracing, but we have a CGI object, so check
1067            # for tracing from the form parameters.
1068            if ($SavedCGI->param('Trace')) {
1069                # Here the user has requested tracing via a form.
1070                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1071                $tracing = $SavedCGI->param('Trace') . " Tracer";
1072            }
1073        }
1074        # Setup the tracing we've determined from all the stuff above.
1075        TSetup($tracing, $dest);
1076        # Check to see if we're a web script.
1077        if (defined $SavedCGI) {
1078            # Yes we are. Trace the form and environment data.
1079            TraceParms($SavedCGI);
1080            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1081            # emitted by the script in its raw form.
1082            if (T(Raw => 3)) {
1083                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1084  }  }
   
 =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;  
1085  }  }
   
 # Pad a number to 2 digits.  
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
1086  }  }
1087    
1088  =head3 ParseTraceDate  =head3 EmergencyFileName
1089    
1090  C<< my $time = Tracer::ParseTraceDate($dateString); >>      my $fileName = Tracer::EmergencyFileName($tkey);
1091    
1092  Convert a date from the trace file into a PERL timestamp.  Return the emergency tracing file name. This is the file that specifies
1093    the tracing information.
1094    
1095  =over 4  =over 4
1096    
1097  =item dateString  =item tkey
1098    
1099  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.  
1100    
1101  =item RETURN  =item RETURN
1102    
1103  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.  
1104    
1105  =back  =back
1106    
1107  =cut  =cut
1108    
1109  sub ParseTraceDate {  sub EmergencyFileName {
1110      # Get the parameters.      # Get the parameters.
1111      my ($dateString) = @_;      my ($tkey) = @_;
1112      # Declare the return variable.      # Compute the emergency tracing file name.
1113      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 $retVal;  
1114  }  }
1115    
1116  =head3 LogErrors  =head3 EmergencyFileTarget
1117    
1118  C<< Tracer::LogErrors($fileName); >>      my $fileName = Tracer::EmergencyFileTarget($tkey);
1119    
1120  Route the standard error output to a log file.  Return the emergency tracing target file name. This is the file that receives
1121    the tracing output for file-based tracing.
1122    
1123  =over 4  =over 4
1124    
1125  =item fileName  =item tkey
1126    
1127  Name of the file to receive the error output.  Tracing key for the current program.
1128    
1129    =item RETURN
1130    
1131    Returns the name of the file to contain the trace output.
1132    
1133  =back  =back
1134    
1135  =cut  =cut
1136    
1137  sub LogErrors {  sub EmergencyFileTarget {
1138      # Get the file name.      # Get the parameters.
1139      my ($fileName) = @_;      my ($tkey) = @_;
1140      # Open the file as the standard error output.      # Compute the emergency tracing file name.
1141      open STDERR, '>', $fileName;      return "$FIG_Config::temp/trace$tkey.log";
1142  }  }
1143    
1144  =head3 ReadOptions  =head3 EmergencyTracingDest
1145    
1146  C<< my %options = Tracer::ReadOptions($fileName); >>      my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1147    
1148  Read a set of options from a file. Each option is encoded in a line of text that has the  This method converts an emergency tracing destination to a real
1149  format  tracing destination. The main difference is that if the
1150    destination is C<FILE> or C<APPEND>, we convert it to file
1151    output. If the destination is C<DUAL>, we convert it to file
1152    and standard output.
1153    
1154  I<optionName>C<=>I<optionValue>C<; >I<comment>  =over 4
1155    
1156  The option name must consist entirely of letters, digits, and the punctuation characters  =item tkey
 C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  
 character is a semi-colon will be ignored. The return hash will map each option name to  
 the corresponding option value.  
1157    
1158  =over 4  Tracing key for this environment.
1159    
1160  =item fileName  =item myDest
1161    
1162  Name of the file containing the option data.  Destination from the emergency tracing file.
1163    
1164  =item RETURN  =item RETURN
1165    
1166  Returns a hash mapping the option names specified in the file to their corresponding option  Returns a destination that can be passed into L</TSetup>.
 value.  
1167    
1168  =back  =back
1169    
1170  =cut  =cut
1171    
1172  sub ReadOptions {  sub EmergencyTracingDest {
1173      # Get the parameters.      # Get the parameters.
1174      my ($fileName) = @_;      my ($tkey, $myDest) = @_;
1175      # Open the file.      # Declare the return variable.
1176      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");      my $retVal = $myDest;
1177      # Count the number of records read.      # Process according to the destination value.
1178      my ($records, $comments) = 0;      if ($myDest eq 'FILE') {
1179      # Create the return hash.          $retVal = ">" . EmergencyFileTarget($tkey);
1180      my %retVal = ();      } elsif ($myDest eq 'APPEND') {
1181      # Loop through the file, accumulating key-value pairs.          $retVal = ">>" . EmergencyFileTarget($tkey);
1182      while (my $line = <CONFIGFILE>) {      } elsif ($myDest eq 'DUAL') {
1183          # Denote we've read a line.          $retVal = "+>" . EmergencyFileTarget($tkey);
1184          $records++;      } elsif ($myDest eq 'WARN') {
1185          # 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);  
         }  
1186      }      }
1187      # Return the hash created.      # Return the result.
1188      return %retVal;      return $retVal;
1189  }  }
1190    
1191  =head3 GetOptions  =head3 Emergency
   
 C<< Tracer::GetOptions(\%defaults, \%options); >>  
1192    
1193  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.  
1194    
1195  Consider the following example.  Turn on emergency tracing. This method is normally invoked over the web from
1196    a debugging console, but it can also be called by the C<trace.pl> script.
1197    The caller specifies the duration of the emergency in hours, the desired tracing
1198    destination, the trace level, and a list of the trace modules to activate.
1199    For the length of the duration, when a program in an environment with the
1200    specified tracing key active invokes a Sprout CGI script, tracing will be
1201    turned on automatically. See L</TSetup> for more about tracing setup and
1202    L</ETracing> for more about emergency tracing.
1203    
1204  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  =over 4
1205    
1206  In this example, the variable B<$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<$options> is defined as  
1207    
1208  C<< {databaseType => 'Oracle'} >>  The tracing key. This is used to identify the control file and the trace file.
1209    
1210  an error will occur because the B<databaseType> option does not exist.  =item hours
1211    
1212  =over 4  Number of hours to keep emergency tracing alive.
1213    
1214  =item defaults  =item dest
1215    
1216  Table of default option values.  Tracing destination. If no path information is specified for a file
1217    destination, it is put in the FIG temporary directory.
1218    
1219  =item options  =item level
1220    
1221  Table of overrides, if any.  Tracing level. A higher level means more trace messages.
1222    
1223  =item RETURN  =item modules
1224    
1225  Returns a reference to the default table passed in as the first parameter.  A list of the tracing modules to activate.
1226    
1227  =back  =back
1228    
1229  =cut  =cut
1230    
1231  sub GetOptions {  sub Emergency {
1232      # Get the parameters.      # Get the parameters.
1233      my ($defaults, $options) = @_;      my ($tkey, $hours, $dest, $level, @modules) = @_;
1234      # Check for overrides.      # Create the emergency file.
1235      if ($options) {      my $specFile = EmergencyFileName($tkey);
1236          # Loop through the overrides.      my $outHandle = Open(undef, ">$specFile");
1237          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;  
1238  }  }
1239    
1240  =head3 MergeOptions  =head3 EmergencyKey
1241    
1242  C<< Tracer::MergeOptions(\%table, \%defaults); >>      my $tkey = EmergencyKey($parameter);
1243    
1244  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,
1245  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.  
1246    
1247  =over 4  =over 4
1248    
1249  =item table  =item parameter
1250    
1251  Hash table to be updated with the default values.  Parameter defining the method for finding the tracing key. If it is a scalar,
1252    then it is presumed to be the tracing key itself. If it is a CGI object, then
1253    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1254    taken from the C<TRACING> environment variable.
1255    
1256  =item defaults  =item RETURN
1257    
1258  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.
1259    
1260  =back  =back
1261    
1262  =cut  =cut
1263    
1264  sub MergeOptions {  sub EmergencyKey {
1265      # Get the parameters.      # Get the parameters.
1266      my ($table, $defaults) = @_;      my ($parameter) = @_;
1267      # Loop through the defaults.      # Declare the return variable.
1268      while (my ($key, $value) = each %{$defaults}) {      my $retVal;
1269          if (!exists $table->{$key}) {      # Determine the parameter type.
1270              $table->{$key} = $value;      if (! defined $parameter) {
1271            # Here we're supposed to check the environment. If that fails, we
1272            # get the effective login ID.
1273            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1274        } else {
1275            my $ptype = ref $parameter;
1276            if ($ptype eq 'CGI') {
1277                # Here we were invoked from a web page. Look for a cookie.
1278                $retVal = $parameter->cookie('IP');
1279            } elsif (! $ptype) {
1280                # Here the key was passed in.
1281                $retVal = $parameter;
1282            }
1283          }          }
1284        # If no luck finding a key, use the PID.
1285        if (! defined $retVal) {
1286            $retVal = $$;
1287      }      }
1288        # Return the result.
1289        return $retVal;
1290  }  }
1291    
 =head3 Trace  
1292    
1293  C<< Trace($message); >>  =head3 TraceParms
1294    
1295  Write a trace message to the target location specified in L</TSetup>. If there has not been      Tracer::TraceParms($cgi);
1296  any prior call to B<TSetup>.  
1297    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1298    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1299    
1300  =over 4  =over 4
1301    
1302  =item message  =item cgi
1303    
1304  Message to write.  CGI query object containing the parameters to trace.
1305    
1306  =back  =back
1307    
1308  =cut  =cut
1309    
1310  sub Trace {  sub TraceParms {
1311      # Get the parameters.      # Get the parameters.
1312      my ($message) = @_;      my ($cgi) = @_;
1313      # Get the timestamp.      if (T(CGI => 2)) {
1314      my $timeStamp = Now();          # Here we trace the GET-style URL for the script.
1315      # Format the message. Note we strip off any line terminators at the end.          Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1316      my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);      }
1317      # Process according to the destination.      if (T(CGI => 3)) {
1318      if ($Destination eq "TEXT") {          # Here we want to trace the parameter data.
1319          # Write the message to the standard output.          my @names = $cgi->param;
1320          print "$formatted\n";          for my $parmName (sort @names) {
1321      } elsif ($Destination eq "ERROR") {              # Note we skip the Trace parameters, which are for our use only.
1322          # Write the message to the error output.              if ($parmName ne 'Trace' && $parmName ne 'TF') {
1323          print STDERR "$formatted\n";                  my @values = $cgi->param($parmName);
1324      } elsif ($Destination eq "QUEUE") {                  Trace("[CGI] $parmName = " . join(", ", @values));
1325          # Push the message into the queue.              }
1326          push @Queue, "$formatted";          }
1327      } elsif ($Destination eq "HTML") {          # Display the request method.
1328          # Convert the message to HTML and write it to the standard output.          my $method = $cgi->request_method();
1329          my $escapedMessage = CGI::escapeHTML($message);          Trace("Method: $method");
1330          print "<p>$formatted</p>\n";      }
1331      } elsif ($Destination eq "WARN") {      if (T(CGI => 4)) {
1332         # Emit the message as a warning.          # Here we want the environment data too.
1333         warn $message;          for my $envName (sort keys %ENV) {
1334      } 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";  
1335          }          }
1336      }      }
1337  }  }
1338    
1339  =head3 T  =head3 TraceImages
1340    
1341  C<< my $switch = T($category, $traceLevel); >>      Tracer::TraceImages($htmlString);
1342    
1343      or  Trace information about all of an html document's images. The tracing
1344    will be for type "IMG" at level 3. The image's source string
1345    will be displayed. This is generally either the URL of the image or
1346    raw data for the image itself. If the source is too long, only the first 300
1347    characters will be shown at trace level 3. The entire source will be shown,
1348    however, at trace level 4. This method is not very smart, and might catch
1349    Javascript code, but it is still useful when debugging the arcane
1350    behavior of images in multiple browser environments.
1351    
1352  C<< my $switch = T($traceLevel); >>  =over 4
1353    
1354  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.  
1355    
1356  =over 4  HTML text for an outgoing web page.
1357    
1358  =item category  =back
1359    
1360  Category to which the message belongs. If not specified, the caller's package name is  =cut
 used.  
1361    
1362  =item traceLevel  sub TraceImages {
1363        # Only proceed if we're at the proper trace level.
1364        if (T(IMG => 3)) {
1365            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1366            # into a variable called "$htmlString". This is because we expect html strings to be
1367            # long, and don't want to copy them any more than we have to.
1368            Trace(length($_[0]) . " characters in web page.");
1369            # Loop through the HTML, culling image tags.
1370            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1371                # Extract the source string and determine whether or not it's too long.
1372                my $srcString = $1;
1373                my $pos = pos($_[0]) - length($srcString);
1374                my $excess = length($srcString) - 300;
1375                # We'll put the display string in here.
1376                my $srcDisplay = $srcString;
1377                # If it's a data string, split it at the comma.
1378                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1379                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1380                # a long string, however, we only show the first 300 characters.
1381                if ($excess > 0 && ! T(IMG => 4)) {
1382                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1383                }
1384                # Output the trace message.
1385                Trace("Image tag at position $pos:\n$srcDisplay");
1386            }
1387        }
1388    }
1389    
1390  Relevant tracing level.  =head2 Command-Line Utility Methods
1391    
1392  =item RETURN  =head3 SendSMS
1393    
1394  TRUE if a message at the specified trace level would appear in the trace, else FALSE.      my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1395    
1396  =back  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1397    user name, password, and API ID for the relevant account in the hash reference variable
1398    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1399    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1400    is C<2561022>, then the FIG_Config file must contain
1401    
1402  =cut      $phone =  { user => 'BruceTheHumanPet',
1403                    password => 'silly',
1404                    api_id => '2561022' };
1405    
1406  sub T {  The original purpose of this method was to insure Bruce would be notified immediately when the
1407      # Declare the return variable.  Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1408      my $retVal = 0;  when you call this method.
1409      # Only proceed if tracing is turned on.  
1410      if ($Destination ne "NONE") {  The message ID will be returned if successful, and C<undef> if an error occurs.
1411    
1412    =over 4
1413    
1414    =item phoneNumber
1415    
1416    Phone number to receive the message, in international format. A United States phone number
1417    would be prefixed by "1". A British phone number would be prefixed by "44".
1418    
1419    =item msg
1420    
1421    Message to send to the specified phone.
1422    
1423    =item RETURN
1424    
1425    Returns the message ID if successful, and C<undef> if the message could not be sent.
1426    
1427    =back
1428    
1429    =cut
1430    
1431    sub SendSMS {
1432          # Get the parameters.          # Get the parameters.
1433          my ($category, $traceLevel) = @_;      my ($phoneNumber, $msg) = @_;
1434          if (!defined $traceLevel) {      # Declare the return variable. If we do not change it, C<undef> will be returned.
1435              # Here we have no category, so we need to get the calling package.      my $retVal;
1436              # The calling package is normally the first parameter. If it is      # Only proceed if we have phone support.
1437              # omitted, the first parameter will be the tracelevel. So, the      if (! defined $FIG_Config::phone) {
1438              # first thing we do is shift the so-called category into the          Trace("Phone support not present in FIG_Config.") if T(1);
1439              # $traceLevel variable where it belongs.      } else {
1440              $traceLevel = $category;          # Get the phone data.
1441              my ($package, $fileName, $line) = caller;          my $parms = $FIG_Config::phone;
1442              # If there is no calling package, we default to "main".          # Get the Clickatell URL.
1443              if (!$package) {          my $url = "http://api.clickatell.com/http/";
1444                  $category = "main";          # Create the user agent.
1445            my $ua = LWP::UserAgent->new;
1446            # Request a Clickatell session.
1447            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1448                                         password => $parms->{password},
1449                                         api_id => $parms->{api_id},
1450                                         to => $phoneNumber,
1451                                         text => $msg});
1452            # Check for an error.
1453            if (! $resp->is_success) {
1454                Trace("Alert failed.") if T(1);
1455            } else {
1456                # Get the message ID.
1457                my $rstring = $resp->content;
1458                if ($rstring =~ /^ID:\s+(.*)$/) {
1459                    $retVal = $1;
1460                } else {
1461                    Trace("Phone attempt failed with $rstring") if T(1);
1462                }
1463            }
1464        }
1465        # Return the result.
1466        return $retVal;
1467    }
1468    
1469    =head3 StandardSetup
1470    
1471        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1472    
1473    This method performs standard command-line parsing and tracing setup. The return
1474    values are a hash of the command-line options and a list of the positional
1475    parameters. Tracing is automatically set up and the command-line options are
1476    validated.
1477    
1478    This is a complex method that does a lot of grunt work. The parameters can
1479    be more easily understood, however, once they are examined individually.
1480    
1481    The I<categories> parameter is the most obtuse. It is a reference to a list of
1482    special-purpose tracing categories. Most tracing categories are PERL package
1483    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1484    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1485    
1486        ["Sprout", "SproutLoad", "ERDB"]
1487    
1488    This would cause trace messages in the specified three packages to appear in
1489    the output. There are two special tracing categories that are automatically
1490    handled by this method. In other words, if you used L</TSetup> you would need
1491    to include these categories manually, but if you use this method they are turned
1492    on automatically.
1493    
1494    =over 4
1495    
1496    =item SQL
1497    
1498    Traces SQL commands and activity.
1499    
1500    =item Tracer
1501    
1502    Traces error messages and call stacks.
1503    
1504    =back
1505    
1506    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1507    The trace level is specified using the C<-trace> command-line option. For example,
1508    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1509    all tracing at level 3.
1510    
1511        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1512    
1513    Standard tracing is output to the standard output and echoed to the file
1514    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1515    process ID. You can also specify the C<user> parameter to put a user ID
1516    instead of a process ID in the trace file name. So, for example
1517    
1518    The default trace level is 2. To get all messages, specify a trace level of 4.
1519    For a genome-by-genome update, use 3.
1520    
1521        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1522    
1523    would send the trace output to C<traceBruce.log> in the temporary directory.
1524    
1525    The I<options> parameter is a reference to a hash containing the command-line
1526    options, their default values, and an explanation of what they mean. Command-line
1527    options may be in the form of switches or keywords. In the case of a switch, the
1528    option value is 1 if it is specified and 0 if it is not specified. In the case
1529    of a keyword, the value is separated from the option name by an equal sign. You
1530    can see this last in the command-line example above.
1531    
1532    You can specify a different default trace level by setting C<$options->{trace}>
1533    prior to calling this method.
1534    
1535    An example at this point would help. Consider, for example, the command-line utility
1536    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1537    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1538    the following code.
1539    
1540        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1541                            { safe => [0, "use database transactions"],
1542                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1543                              start => [' ', "start with this genome"],
1544                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1545                            "<command> <transactionDirectory> <IDfile>",
1546                          @ARGV);
1547    
1548    
1549    The call to C<ParseCommand> specifies the default values for the options and
1550    stores the actual options in a hash that is returned as C<$options>. The
1551    positional parameters are returned in C<@parameters>.
1552    
1553    The following is a sample command line for C<TransactFeatures>.
1554    
1555        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1556    
1557    Single and double hyphens are equivalent. So, you could also code the
1558    above command as
1559    
1560        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1561    
1562    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1563    parameters, and would find themselves in I<@parameters> after executing the
1564    above code fragment. The tracing would be set to level 2, and the categories
1565    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1566    and C<DocUtils> was included because it came in within the first parameter
1567    to this method. The I<$options> hash would be
1568    
1569        { trace => 2, sql => 0, safe => 0,
1570          noAlias => 1, start => ' ', tblFiles => 0 }
1571    
1572    Use of C<StandardSetup> in this way provides a simple way of performing
1573    standard tracing setup and command-line parsing. Note that the caller is
1574    not even aware of the command-line switches C<-trace> and C<-sql>, which
1575    are used by this method to control the tracing. If additional tracing features
1576    need to be added in the future, they can be processed by this method without
1577    upsetting the command-line utilities.
1578    
1579    If the C<background> option is specified on the command line, then the
1580    standard and error outputs will be directed to files in the temporary
1581    directory, using the same suffix as the trace file. So, if the command
1582    line specified
1583    
1584        -user=Bruce -background
1585    
1586    then the trace output would go to C<traceBruce.log>, the standard output to
1587    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1588    simplify starting a command in the background.
1589    
1590    The user name is also used as the tracing key for L</Emergency Tracing>.
1591    Specifying a value of C<E> for the trace level causes emergency tracing to
1592    be used instead of custom tracing. If the user name is not specified,
1593    the tracing key is taken from the C<Tracing> environment variable. If there
1594    is no value for that variable, the tracing key will be computed from the active
1595    login ID.
1596    
1597    Since the default situation in StandardSetup is to trace to the standard
1598    output, errors that occur in command-line scripts will not generate
1599    RSS events. To force the events, use the C<warn> option.
1600    
1601        TransactFeatures -background -warn register ../xacts IDs.tbl
1602    
1603    Finally, if the special option C<-help> is specified, the option
1604    names will be traced at level 0 and the program will exit without processing.
1605    This provides a limited help capability. For example, if the user enters
1606    
1607        TransactFeatures -help
1608    
1609    he would see the following output.
1610    
1611        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1612            -trace    tracing level (default E)
1613            -sql      trace SQL commands
1614            -safe     use database transactions
1615            -noAlias  do not expect aliases in CHANGE transactions
1616            -start    start with this genome
1617            -tblFiles output TBL files containing the corrected IDs
1618            -forked   do not erase the trace file before tracing
1619    
1620    The caller has the option of modifying the tracing scheme by placing a value
1621    for C<trace> in the incoming options hash. The default value can be overridden,
1622    or the tracing to the standard output can be turned off by suffixing a minus
1623    sign to the trace level. So, for example,
1624    
1625        { trace => [0, "tracing level (default 0)"],
1626           ...
1627    
1628    would set the default trace level to 0 instead of E, while
1629    
1630        { trace => ["2-", "tracing level (default 2)"],
1631           ...
1632    
1633    would set the default to 2, but trace only to the log file, not to the
1634    standard output.
1635    
1636    The parameters to this method are as follows.
1637    
1638    =over 4
1639    
1640    =item categories
1641    
1642    Reference to a list of tracing category names. These should be names of
1643    packages whose internal workings will need to be debugged to get the
1644    command working.
1645    
1646    =item options
1647    
1648    Reference to a hash containing the legal options for the current command mapped
1649    to their default values and descriptions. The user can override the defaults
1650    by specifying the options as command-line switches prefixed by a hyphen.
1651    Tracing-related options may be added to this hash. If the C<-h> option is
1652    specified on the command line, the option descriptions will be used to
1653    explain the options. To turn off tracing to the standard output, add a
1654    minus sign to the value for C<trace> (see above).
1655    
1656    =item parmHelp
1657    
1658    A string that vaguely describes the positional parameters. This is used
1659    if the user specifies the C<-h> option.
1660    
1661    =item argv
1662    
1663    List of command line parameters, including the option switches, which must
1664    precede the positional parameters and be prefixed by a hyphen.
1665    
1666    =item RETURN
1667    
1668    Returns a list. The first element of the list is the reference to a hash that
1669    maps the command-line option switches to their values. These will either be the
1670    default values or overrides specified on the command line. The remaining
1671    elements of the list are the position parameters, in order.
1672    
1673    =back
1674    
1675    =cut
1676    
1677    sub StandardSetup {
1678        # Get the parameters.
1679        my ($categories, $options, $parmHelp, @argv) = @_;
1680        # Get the default tracing key.
1681        my $tkey = EmergencyKey();
1682        # Save the command line.
1683        $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1684        # Add the tracing options.
1685        if (! exists $options->{trace}) {
1686            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1687        }
1688        if (! exists $options->{forked}) {
1689            $options->{forked} = [0, "keep old trace file"];
1690        }
1691        $options->{sql} = [0, "turn on SQL tracing"];
1692        $options->{help} = [0, "display command-line options"];
1693        $options->{user} = [$tkey, "tracing key"];
1694        $options->{background} = [0, "spool standard and error output"];
1695        $options->{warn} = [0, "send errors to RSS feed"];
1696        # Create a parsing hash from the options hash. The parsing hash
1697        # contains the default values rather than the default value
1698        # and the description. While we're at it, we'll memorize the
1699        # length of the longest option name.
1700        my $longestName = 0;
1701        my %parseOptions = ();
1702        for my $key (keys %{$options}) {
1703            if (length $key > $longestName) {
1704                $longestName = length $key;
1705            }
1706            $parseOptions{$key} = $options->{$key}->[0];
1707        }
1708        # Parse the command line.
1709        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1710        # Get the logfile suffix.
1711        my $suffix = $retOptions->{user};
1712        # Check for background mode.
1713        if ($retOptions->{background}) {
1714            my $outFileName = "$FIG_Config::temp/out$suffix$$.log";
1715            my $errFileName = "$FIG_Config::temp/err$suffix$$.log";
1716            open STDOUT, ">$outFileName";
1717            open STDERR, ">$errFileName";
1718            # Check for phone support. If we have phone support and a phone number,
1719            # we want to turn it on.
1720            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1721                $retOptions->{phone} = $ENV{PHONE};
1722            }
1723        }
1724        # Now we want to set up tracing. First, we need to know if the user
1725        # wants emergency tracing.
1726        if ($retOptions->{trace} eq 'E') {
1727            ETracing($retOptions->{user});
1728        } else {
1729            # Here the tracing is controlled from the command line.
1730            my @cats = @{$categories};
1731            if ($retOptions->{sql}) {
1732                push @cats, "SQL";
1733            }
1734            if ($retOptions->{warn}) {
1735                push @cats, "Feed";
1736            }
1737            # Add the default categories.
1738            push @cats, "Tracer";
1739            # Next, we create the category string by joining the categories.
1740            my $cats = join(" ", @cats);
1741            # Check to determine whether or not the caller wants to turn off tracing
1742            # to the standard output.
1743            my $traceLevel = $retOptions->{trace};
1744            my $textOKFlag = 1;
1745            if ($traceLevel =~ /^(.)-/) {
1746                $traceLevel = $1;
1747                $textOKFlag = 0;
1748            }
1749            # Now we set up the trace mode.
1750            my $traceMode;
1751            # Verify that we can open a file in the FIG temporary directory.
1752            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1753            my $traceFileSpec = ($retOptions->{forked} ? ">>$traceFileName" : ">$traceFileName");
1754            if (open TESTTRACE, "$traceFileSpec") {
1755                # Here we can trace to a file.
1756                $traceMode = ">>$traceFileName";
1757                if ($textOKFlag) {
1758                    # Echo to standard output if the text-OK flag is set.
1759                    $traceMode = "+$traceMode";
1760                }
1761                # Close the test file.
1762                close TESTTRACE;
1763            } else {
1764                # Here we can't trace to a file. Complain about this.
1765                warn "Could not open trace file $traceFileName: $!\n";
1766                # We trace to the standard output if it's
1767                # okay, and the error log otherwise.
1768                if ($textOKFlag) {
1769                    $traceMode = "TEXT";
1770              } else {              } else {
1771                  $category = $package;                  $traceMode = "WARN";
1772              }              }
1773          }          }
1774          # Save the category name.          # Now set up the tracing.
1775          $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.");  
1776          }          }
1777          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));      # Check for the "help" option. If it is specified, dump the command-line
1778        # options and exit the program.
1779        if ($retOptions->{help}) {
1780            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1781            print "$1 [options] $parmHelp\n";
1782            for my $key (sort keys %{$options}) {
1783                my $name = Pad($key, $longestName, 0, ' ');
1784                my $desc = $options->{$key}->[1];
1785                if ($options->{$key}->[0]) {
1786                    $desc .= " (default " . $options->{$key}->[0] . ")";
1787      }      }
1788      # Return the computed result.              print "  $name $desc\n";
1789      return $retVal;          }
1790            exit(0);
1791        }
1792        # Trace the options, if applicable.
1793        if (T(3)) {
1794            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1795            Trace("Selected options: " . join(", ", sort @parms) . ".");
1796        }
1797        # Return the parsed parameters.
1798        return ($retOptions, @retParameters);
1799  }  }
1800    
1801  =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<$options> will be  
1802    
1803  C<< { errors => 0, logFile => 'error.log' } >>      my %options = Tracer::ReadOptions($fileName);
1804    
1805  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
1806    format
1807    
1808  C<< apple orange rutabaga >>  I<optionName>C<=>I<optionValue>C<; >I<comment>
1809    
1810  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
1811  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
1812    character is a semi-colon will be ignored. The return hash will map each option name to
1813    the corresponding option value.
1814    
1815  =over 4  =over 4
1816    
1817  =item optionTable  =item fileName
   
 Table of default options.  
   
 =item inputList  
1818    
1819  List of words on the command line.  Name of the file containing the option data.
1820    
1821  =item RETURN  =item RETURN
1822    
1823  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
1824    value.
1825    
1826  =back  =back
1827    
1828  =cut  =cut
1829    
1830  sub ParseCommand {  sub ReadOptions {
1831      # Get the parameters.      # Get the parameters.
1832      my ($optionTable, @inputList) = @_;      my ($fileName) = @_;
1833      # Process any options in the input list.      # Open the file.
1834      my %overrides = ();      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1835      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {      # Count the number of records read.
1836          # Get the current option.      my ($records, $comments) = 0;
1837          my $arg = shift @inputList;      # Create the return hash.
1838          # Pull out the option name.      my %retVal = ();
1839          $arg =~ /^--?([^=]*)/g;      # Loop through the file, accumulating key-value pairs.
1840          my $name = $1;      while (my $line = <CONFIGFILE>) {
1841          # Check for an option value.          # Denote we've read a line.
1842          if ($arg =~ /\G=(.*)$/g) {          $records++;
1843              # Here we have a value for the option.          # Determine the line type.
1844              $overrides{$name} = UnEscape($1);          if ($line =~ /^\s*[\n\r]/) {
1845                # A blank line is a comment.
1846                $comments++;
1847            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1848                # Here we have an option assignment.
1849                retVal{$1} = $2;
1850            } elsif ($line =~ /^\s*;/) {
1851                # Here we have a text comment.
1852                $comments++;
1853          } else {          } else {
1854              # Here there is no value, so we use 1.              # Here we have an invalid line.
1855              $overrides{$name} = 1;              Trace("Invalid option statement in record $records.") if T(0);
         }  
1856      }      }
     # Merge the options into the defaults.  
     GetOptions($optionTable, \%overrides);  
     # Translate the remaining parameters.  
     my @retVal = ();  
     for my $inputParm (@inputList) {  
         push @retVal, UnEscape($inputParm);  
1857      }      }
1858      # Return the results.      # Return the hash created.
1859      return ($optionTable, @retVal);      return %retVal;
1860  }  }
1861    
1862  =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  
1863    
1864  String to escape.      Tracer::GetOptions(\%defaults, \%options);
1865    
1866  =item RETURN  Merge a specified set of options into a table of defaults. This method takes two hash references
1867    as input and uses the data from the second to update the first. If the second does not exist,
1868    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1869    exist in the first.
1870    
1871  Escaped equivalent of the real string.  Consider the following example.
1872    
1873  =back      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1874    
1875  =cut  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1876    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1877    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1878    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1879    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1880    
1881  sub Escape {      {databaseType => 'Oracle'}
     # Get the parameter.  
     my ($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;  
 }  
1882    
1883  =head3 UnEscape  an error will occur because the B<databaseType> option does not exist.
1884    
1885  C<< my $realString = Tracer::UnEscape($codedString); >>  =over 4
1886    
1887  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.  
1888    
1889  =over 4  Table of default option values.
1890    
1891  =item codedString  =item options
1892    
1893  String to un-escape.  Table of overrides, if any.
1894    
1895  =item RETURN  =item RETURN
1896    
1897  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.  
1898    
1899  =back  =back
1900    
1901  =cut  =cut
1902    
1903  sub UnEscape {  sub GetOptions {
1904      # Get the parameter.      # Get the parameters.
1905      my ($codedString) = @_;      my ($defaults, $options) = @_;
1906      # Initialize the return variable.      # Check for overrides.
1907      my $retVal = "";      if ($options) {
1908      # Only proceed if the incoming string is nonempty.          # Loop through the overrides.
1909      if (defined $codedString) {          while (my ($option, $setting) = each %{$options}) {
1910          # Loop through the parameter string, looking for escape sequences. We can't do              # Insure this override exists.
1911          # translating because it causes problems with the escaped slash. ("\\t" becomes              if (!exists $defaults->{$option}) {
1912          # "\<tab>" no matter what we do.)                  croak "Unrecognized option $option encountered.";
1913          while (length $codedString > 0) {              } else {
1914              # Look for the first escape sequence.                  # Apply the override.
1915              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {                  $defaults->{$option} = $setting;
                 # Here we found it. The text preceding the sequence is in $1. The sequence  
                 # itself is in $2. First, move the clear text to the return variable.  
                 $retVal .= $1;  
                 $codedString = substr $codedString, (2 + length $1);  
                 # Get the escape value.  
                 my $char = $2;  
                 # If we have a "\r", we are done.  
                 if ($char ne 'r') {  
                     # Here it's not an 'r', so we convert it.  
                     $char =~ tr/\\tn/\\\t\n/;  
                     $retVal .= $char;  
                 }  
             } else {  
                 # Here there are no more escape sequences. The rest of the string is  
                 # transferred unmodified.  
                 $retVal .= $codedString;  
                 $codedString = "";  
1916              }              }
1917          }          }
1918      }      }
1919      # Return the result.      # Return the merged table.
1920      return $retVal;      return $defaults;
1921  }  }
1922    
1923  =head3 ParseRecord  =head3 MergeOptions
1924    
1925  C<< my @fields = Tracer::ParseRecord($line); >>      Tracer::MergeOptions(\%table, \%defaults);
1926    
1927  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
1928  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
1929  These will automatically be converted.  pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1930    checking and no return value.
1931    
1932  =over 4  =over 4
1933    
1934  =item line  =item table
1935    
1936  Line of data containing the tab-delimited fields.  Hash table to be updated with the default values.
1937    
1938  =item RETURN  =item defaults
1939    
1940  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.
1941    
1942  =back  =back
1943    
1944  =cut  =cut
1945    
1946  sub ParseRecord {  sub MergeOptions {
1947      # Get the parameter.      # Get the parameters.
1948      my ($line) = @_;      my ($table, $defaults) = @_;
1949      # Remove the trailing new-line, if any.      # Loop through the defaults.
1950      chomp $line;      while (my ($key, $value) = each %{$defaults}) {
1951      # Split the line read into pieces using the tab character.          if (!exists $table->{$key}) {
1952      my @retVal = split /\t/, $line;              $table->{$key} = $value;
1953      # 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;  
1954      }      }
     # Return the result.  
     return @retVal;  
1955  }  }
1956    
1957  =head3 Merge  =head3 UnparseOptions
1958    
1959  C<< my @mergedList = Tracer::Merge(@inputList); >>      my $optionString = Tracer::UnparseOptions(\%options);
1960    
1961  Sort a list of strings and remove duplicates.  Convert an option hash into a command-line string. This will not
1962    necessarily be the same text that came in, but it will nonetheless
1963    produce the same ultimate result when parsed by L</StandardSetup>.
1964    
1965  =over 4  =over 4
1966    
1967  =item inputList  =item options
1968    
1969  List of scalars to sort and merge.  Reference to a hash of options to convert into an option string.
1970    
1971  =item RETURN  =item RETURN
1972    
1973  Returns a list containing the same elements sorted in ascending order with duplicates  Returns a string that will parse to the same set of options when
1974  removed.  parsed by L</StandardSetup>.
1975    
1976  =back  =back
1977    
1978  =cut  =cut
1979    
1980  sub Merge {  sub UnparseOptions {
1981      # Get the input list in sort order.      # Get the parameters.
1982      my @inputList = sort @_;      my ($options) = @_;
1983      # Only proceed if the list has at least two elements.      # The option segments will be put in here.
1984      if (@inputList > 1) {      my @retVal = ();
1985          # Now we want to move through the list splicing out duplicates.      # Loop through the options.
1986          my $i = 0;      for my $key (keys %$options) {
1987          while ($i < @inputList) {          # Get the option value.
1988              # Get the current entry.          my $value = $options->{$key};
1989              my $thisEntry = $inputList[$i];          # Only use it if it's nonempty.
1990              # Find out how many elements duplicate the current entry.          if (defined $value && $value ne "") {
1991              my $j = $i + 1;              my $segment = "--$key=$value";
1992              my $dup1 = $i + 1;              # Quote it if necessary.
1993              while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };              if ($segment =~ /[ |<>*]/) {
1994              # If the number is nonzero, splice out the duplicates found.                  $segment = '"' . $segment . '"';
             if ($j > $dup1) {  
                 splice @inputList, $dup1, $j - $dup1;  
1995              }              }
1996              # Now the element at position $dup1 is different from the element before it              # Add it to the return list.
1997              # at position $i. We push $i forward one position and start again.              push @retVal, $segment;
             $i++;  
1998          }          }
1999      }      }
2000      # Return the merged list.      # Return the result.
2001      return @inputList;      return join(" ", @retVal);
2002  }  }
2003    
2004  =head3 Percent  =head3 ParseCommand
2005    
2006  C<< my $percent = Tracer::Percent($number, $base); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2007    
2008  Returns the percent of the base represented by the given number. If the base  Parse a command line consisting of a list of parameters. The initial parameters may be option
2009  is zero, returns zero.  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2010    off and merged into a table of default options. The remainder of the command line is
2011    returned as a list of positional arguments. For example, consider the following invocation.
2012    
2013        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2014    
2015    In this case, the list @words will be treated as a command line and there are two options available,
2016    B<errors> and B<logFile>. If @words has the following format
2017    
2018        -logFile=error.log apple orange rutabaga
2019    
2020    then at the end of the invocation, C<$options> will be
2021    
2022        { errors => 0, logFile => 'error.log' }
2023    
2024    and C<@arguments> will contain
2025    
2026        apple orange rutabaga
2027    
2028    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2029    support for quote characters. Options can be specified with single or double hyphens.
2030    
2031  =over 4  =over 4
2032    
2033  =item number  =item optionTable
2034    
2035  Percent numerator.  Table of default options.
2036    
2037  =item base  =item inputList
2038    
2039  Percent base.  List of words on the command line.
2040    
2041  =item RETURN  =item RETURN
2042    
2043  Returns the percentage of the base represented by the numerator.  Returns a reference to the option table and a list of the positional arguments.
2044    
2045  =back  =back
2046    
2047  =cut  =cut
2048    
2049  sub Percent {  sub ParseCommand {
2050      # Get the parameters.      # Get the parameters.
2051      my ($number, $base) = @_;      my ($optionTable, @inputList) = @_;
2052      # Declare the return variable.      # Process any options in the input list.
2053      my $retVal = 0;      my %overrides = ();
2054      # Compute the percent.      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2055      if ($base != 0) {          # Get the current option.
2056          $retVal = $number * 100 / $base;          my $arg = shift @inputList;
2057            # Pull out the option name.
2058            $arg =~ /^--?([^=]*)/g;
2059            my $name = $1;
2060            # Check for an option value.
2061            if ($arg =~ /\G=(.*)$/g) {
2062                # Here we have a value for the option.
2063                $overrides{$name} = UnEscape($1);
2064            } else {
2065                # Here there is no value, so we use 1.
2066                $overrides{$name} = 1;
2067      }      }
2068      # Return the result.      }
2069      return $retVal;      # Merge the options into the defaults.
2070        GetOptions($optionTable, \%overrides);
2071        # Translate the remaining parameters.
2072        my @retVal = ();
2073        for my $inputParm (@inputList) {
2074            push @retVal, UnEscape($inputParm);
2075        }
2076        # Return the results.
2077        return ($optionTable, @retVal);
2078  }  }
2079    
2080    
2081    =head2 File Utility Methods
2082    
2083  =head3 GetFile  =head3 GetFile
2084    
2085  C<< my @fileContents = Tracer::GetFile($fileName); >>      my @fileContents = Tracer::GetFile($fileName);
2086    
2087      or      or
2088    
2089  C<< my $fileContents = Tracer::GetFile($fileName); >>      my $fileContents = Tracer::GetFile($fileName);
2090    
2091  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
2092  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 2136 
2136    
2137  =head3 PutFile  =head3 PutFile
2138    
2139  C<< Tracer::PutFile($fileName, \@lines); >>      Tracer::PutFile($fileName, \@lines);
2140    
2141  Write out a file from a list of lines of text.  Write out a file from a list of lines of text.
2142    
# Line 1704  Line 2179 
2179      close $handle;      close $handle;
2180  }  }
2181    
2182  =head3 QTrace  =head3 ParseRecord
2183    
2184  C<< my $data = QTrace($format); >>      my @fields = Tracer::ParseRecord($line);
2185    
2186  Return the queued trace data in the specified format.  Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2187    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2188    These will automatically be converted.
2189    
2190  =over 4  =over 4
2191    
2192  =item format  =item line
2193    
2194  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Line of data containing the tab-delimited fields.
2195    
2196    =item RETURN
2197    
2198    Returns a list of the fields found in the data line.
2199    
2200  =back  =back
2201    
2202  =cut  =cut
2203    
2204  sub QTrace {  sub ParseRecord {
2205      # Get the parameter.      # Get the parameter.
2206      my ($format) = @_;      my ($line) = @_;
2207      # Create the return variable.      # Remove the trailing new-line, if any.
2208      my $retVal = "";      chomp $line;
2209      # Only proceed if there is an actual queue.      # Split the line read into pieces using the tab character.
2210      if (@Queue) {      my @retVal = split /\t/, $line;
2211          # Process according to the format.      # Trim and fix the escapes in each piece.
2212          if ($format =~ m/^HTML$/i) {      for my $value (@retVal) {
2213              # Convert the queue into an HTML list.          # Trim leading whitespace.
2214              $retVal = "<ul>\n";          $value =~ s/^\s+//;
2215              for my $line (@Queue) {          # Trim trailing whitespace.
2216                  my $escapedLine = CGI::escapeHTML($line);          $value =~ s/\s+$//;
2217                  $retVal .= "<li>$escapedLine</li>\n";          # Delete the carriage returns.
2218            $value =~ s/\r//g;
2219            # Convert the escapes into their real values.
2220            $value =~ s/\\t/"\t"/ge;
2221            $value =~ s/\\n/"\n"/ge;
2222              }              }
2223              $retVal .= "</ul>\n";      # Return the result.
2224          } elsif ($format =~ m/^TEXT$/i) {      return @retVal;
             # Convert the queue into a list of text lines.  
             $retVal = join("\n", @Queue) . "\n";  
2225          }          }
2226          # Clear the queue.  
2227          @Queue = ();  =head3 Merge
2228    
2229        my @mergedList = Tracer::Merge(@inputList);
2230    
2231    Sort a list of strings and remove duplicates.
2232    
2233    =over 4
2234    
2235    =item inputList
2236    
2237    List of scalars to sort and merge.
2238    
2239    =item RETURN
2240    
2241    Returns a list containing the same elements sorted in ascending order with duplicates
2242    removed.
2243    
2244    =back
2245    
2246    =cut
2247    
2248    sub Merge {
2249        # Get the input list in sort order.
2250        my @inputList = sort @_;
2251        # Only proceed if the list has at least two elements.
2252        if (@inputList > 1) {
2253            # Now we want to move through the list splicing out duplicates.
2254            my $i = 0;
2255            while ($i < @inputList) {
2256                # Get the current entry.
2257                my $thisEntry = $inputList[$i];
2258                # Find out how many elements duplicate the current entry.
2259                my $j = $i + 1;
2260                my $dup1 = $i + 1;
2261                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2262                # If the number is nonzero, splice out the duplicates found.
2263                if ($j > $dup1) {
2264                    splice @inputList, $dup1, $j - $dup1;
2265      }      }
2266      # Return the formatted list.              # Now the element at position $dup1 is different from the element before it
2267      return $retVal;              # at position $i. We push $i forward one position and start again.
2268                $i++;
2269            }
2270        }
2271        # Return the merged list.
2272        return @inputList;
2273  }  }
2274    
2275  =head3 Confess  =head3 Open
   
 C<< Confess($message); >>  
2276    
2277  Trace the call stack and abort the program with the specified message. When used with      my $handle = Open($fileHandle, $fileSpec, $message);
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
2278    
2279  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  Open a file.
2280    
2281  Will abort the program with a stack trace if the value of C<$recNum> is negative.  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2282    function. The mode is specified using Unix-like shell information. So, for
2283    example,
2284    
2285  =over 4      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2286    
2287  =item message  would open for output appended to the specified file, and
2288    
2289  Message to include in the trace.      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2290    
2291  =back  would open a pipe that sorts the records written and removes duplicates. Note
2292    the use of file handle syntax in the Open call. To use anonymous file handles,
2293    code as follows.
2294    
2295  =cut      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2296    
2297  sub Confess {  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2298      # Get the parameters.  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2299      my ($message) = @_;  failed open will throw an exception and the third parameter will be used to construct
2300      # Trace the call stack.  an error message. If the parameter is omitted, a standard message is constructed
2301      Cluck($message);  using the file spec.
     # Abort the program.  
     croak(">>> $message");  
 }  
2302    
2303  =head3 Assert      Could not open "/usr/spool/news/twitlog"
2304    
2305  C<< Assert($condition1, $condition2, ... $conditionN); >>  Note that the mode characters are automatically cleaned from the file name.
2306    The actual error message from the file system will be captured and appended to the
2307    message in any case.
2308    
2309  Return TRUE if all the conditions are true. This method can be used in conjunction with      Could not open "/usr/spool/news/twitlog": file not found.
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
2310    
2311  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  In some versions of PERL the only error message we get is a number, which
2312    corresponds to the C++ C<errno> value.
2313    
2314  Will abort the program with a stack trace if the value of C<$recNum> is negative.      Could not open "/usr/spool/news/twitlog": 6.
2315    
2316  =cut  =over 4
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
2317    
2318  =head3 Cluck  =item fileHandle
2319    
2320  C<< Cluck($message); >>  File handle. If this parameter is C<undef>, a file handle will be generated
2321    and returned as the value of this method.
2322    
2323  Trace the call stack. Note that for best results, you should qualify the call with a  =item fileSpec
 trace condition. For example,  
2324    
2325  C<< Cluck("Starting record parse.") if T(3); >>  File name and mode, as per the PERL C<open> function.
2326    
2327  will only trace the stack if the trace level for the package is 3 or more.  =item message (optional)
2328    
2329  =over 4  Error message to use if the open fails. If omitted, a standard error message
2330    will be generated. In either case, the error information from the file system
2331    is appended to the message. To specify a conditional open that does not throw
2332    an error if it fails, use C<0>.
2333    
2334  =item message  =item RETURN
2335    
2336  Message to include in the trace.  Returns the name of the file handle assigned to the file, or C<undef> if the
2337    open failed.
2338    
2339  =back  =back
2340    
2341  =cut  =cut
2342    
2343  sub Cluck {  sub Open {
2344      # Get the parameters.      # Get the parameters.
2345      my ($message) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2346      # Trace what's happening.      # Attempt to open the file.
2347      Trace("Stack trace for event: $message");      my $rv = open $fileHandle, $fileSpec;
2348      my $confession = longmess($message);      # If the open failed, generate an error message.
2349      # Convert the confession to a series of trace messages. Note we skip any      if (! $rv) {
2350      # messages relating to calls into Tracer.          # Save the system error message.
2351      for my $line (split /\s*\n/, $confession) {          my $sysMessage = $!;
2352          Trace($line) if ($line !~ /Tracer\.pm/);          # See if we need a default message.
2353            if (!$message) {
2354                # Clean any obvious mode characters and leading spaces from the
2355                # filename.
2356                my ($fileName) = FindNamePart($fileSpec);
2357                $message = "Could not open \"$fileName\"";
2358            }
2359            # Terminate with an error using the supplied message and the
2360            # error message from the file system.
2361            Confess("$message: $!");
2362      }      }
2363        # Return the file handle.
2364        return $fileHandle;
2365  }  }
2366    
2367  =head3 Min  =head3 FindNamePart
2368    
2369  C<< my $min = Min($value1, $value2, ... $valueN); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2370    
2371  Return the minimum argument. The arguments are treated as numbers.  Extract the portion of a file specification that contains the file name.
2372    
2373    A file specification is the string passed to an C<open> call. It specifies the file
2374    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2375    method assumes that the file name is whatever follows the first angle bracket
2376    sequence.  So, for example, in the following strings the file name is
2377    C</usr/fig/myfile.txt>.
2378    
2379        >>/usr/fig/myfile.txt
2380        </usr/fig/myfile.txt
2381        | sort -u > /usr/fig/myfile.txt
2382    
2383    If the method cannot find a file name using its normal methods, it will return the
2384    whole incoming string.
2385    
2386  =over 4  =over 4
2387    
2388  =item $value1, $value2, ... $valueN  =item fileSpec
2389    
2390  List of numbers to compare.  File specification string from which the file name is to be extracted.
2391    
2392  =item RETURN  =item RETURN
2393    
2394  Returns the lowest number in the list.  Returns a three-element list. The first element contains the file name portion of
2395    the specified string, or the whole string if a file name cannot be found via normal
2396    methods. The second element contains the start position of the file name portion and
2397    the third element contains the length.
2398    
2399  =back  =back
2400    
2401  =cut  =cut
2402    #: Return Type $;
2403  sub Min {  sub FindNamePart {
2404      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2405      my ($retVal, @values) = @_;      my ($fileSpec) = @_;
2406      # Loop through the remaining parameters, looking for the lowest.      # Default to the whole input string.
2407      for my $value (@values) {      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2408          if ($value < $retVal) {      # Parse out the file name if we can.
2409              $retVal = $value;      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2410          }          $retVal = $2;
2411            $len = length $retVal;
2412            $pos = (length $fileSpec) - (length $3) - $len;
2413      }      }
2414      # Return the minimum found.      # Return the result.
2415      return $retVal;      return ($retVal, $pos, $len);
2416  }  }
2417    
2418  =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.  
2419    
2420  =item RETURN      my @files = OpenDir($dirName, $filtered, $flag);
2421    
2422  Returns the highest number in the list.  Open a directory and return all the file names. This function essentially performs
2423    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2424    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2425    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2426    filtered out of the return list. If the directory does not open and I<$flag> is not
2427    set, an exception is thrown. So, for example,
2428    
2429  =back      my @files = OpenDir("/Volumes/fig/contigs", 1);
2430    
2431  =cut  is effectively the same as
2432    
2433  sub Max {      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2434      # 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;  
 }  
2435    
2436  =head3 AddToListMap  Similarly, the following code
2437    
2438  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2439    
2440  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2441  is created for the key. Otherwise, the new value is pushed onto the list.  automatically returns an empty list if the directory fails to open.
2442    
2443  =over 4  =over 4
2444    
2445  =item hash  =item dirName
2446    
2447  Reference to the target hash.  Name of the directory to open.
2448    
2449  =item key  =item filtered
2450    
2451  Key for which the value is to be added.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2452    from the list, else FALSE.
2453    
2454  =item value1, value2, ... valueN  =item flag
2455    
2456  List of values to add to the key's value list.  TRUE if a failure to open is okay, else FALSE
2457    
2458  =back  =back
2459    
2460  =cut  =cut
2461    #: Return Type @;
2462  sub AddToListMap {  sub OpenDir {
2463      # Get the parameters.      # Get the parameters.
2464      my ($hash, $key, @values) = @_;      my ($dirName, $filtered, $flag) = @_;
2465      # Process according to whether or not the key already has a value.      # Declare the return variable.
2466      if (! exists $hash->{$key}) {      my @retVal = ();
2467          $hash->{$key} = [@values];      # Open the directory.
2468        if (opendir(my $dirHandle, $dirName)) {
2469            # The directory opened successfully. Get the appropriate list according to the
2470            # strictures of the filter parameter.
2471            if ($filtered) {
2472                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2473      } else {      } else {
2474          push @{$hash->{$key}}, @values;              @retVal = readdir $dirHandle;
2475            }
2476        } elsif (! $flag) {
2477            # Here the directory would not open and it's considered an error.
2478            Confess("Could not open directory $dirName.");
2479      }      }
2480        # Return the result.
2481        return @retVal;
2482  }  }
2483    
 =head3 DebugMode  
2484    
2485  C<< if (Tracer::DebugMode) { ...code... } >>  =head3 Insure
2486    
2487        Insure($dirName, $chmod);
2488    
2489    Insure a directory is present.
2490    
2491    =over 4
2492    
2493    =item dirName
2494    
2495    Name of the directory to check. If it does not exist, it will be created.
2496    
2497    =item chmod (optional)
2498    
2499  Return TRUE if debug mode has been turned on, else abort.  Security privileges to be given to the directory if it is created.
2500    
2501  Certain CGI scripts are too dangerous to exist in the production  =back
 environment. This method provides a simple way to prevent them  
 from working unless they are explicitly turned on by creating a password  
 cookie via the B<SetPassword> script.  If debugging mode  
 is not turned on, an error will occur.  
2502    
2503  =cut  =cut
2504    
2505  sub DebugMode {  sub Insure {
2506      # Declare the return variable.      my ($dirName, $chmod) = @_;
2507      my $retVal = 0;      if (! -d $dirName) {
2508      # Check the debug configuration.          Trace("Creating $dirName directory.") if T(2);
2509      my $password = CGI::cookie("DebugMode");          eval {
2510      my $encrypted = Digest::MD5::md5_hex($password);              mkpath $dirName;
2511      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {              # If we have permissions specified, set them here.
2512          $retVal = 1;              if (defined($chmod)) {
2513      } else {                  chmod $chmod, $dirName;
2514          # Here debug mode is off, so we generate an error.              }
2515          Confess("Cannot use this facility without logging in.");          };
2516            if ($@) {
2517                Confess("Error creating $dirName: $@");
2518            }
2519      }      }
     # Return the determination indicator.  
     return $retVal;  
2520  }  }
2521    
2522  =head3 Strip  =head3 ChDir
   
 C<< my $string = Tracer::Strip($line); >>  
   
 Strip all line terminators off a string. This is necessary when dealing with files  
 that may have been transferred back and forth several times among different  
 operating environments.  
2523    
2524  =over 4      ChDir($dirName);
2525    
2526  =item line  Change to the specified directory.
2527    
2528  Line of text to be stripped.  =over 4
2529    
2530  =item RETURN  =item dirName
2531    
2532  The same line of text with all the line-ending characters chopped from the end.  Name of the directory to which we want to change.
2533    
2534  =back  =back
2535    
2536  =cut  =cut
2537    
2538  sub Strip {  sub ChDir {
2539      # Get a copy of the parameter string.      my ($dirName) = @_;
2540      my ($string) = @_;      if (! -d $dirName) {
2541      my $retVal = (defined $string ? $string : "");          Confess("Cannot change to directory $dirName: no such directory.");
2542      # Strip the line terminator characters.      } else {
2543      $retVal =~ s/(\r|\n)+$//g;          Trace("Changing to directory $dirName.") if T(File => 4);
2544      # Return the result.          my $okFlag = chdir $dirName;
2545      return $retVal;          if (! $okFlag) {
2546                Confess("Error switching to directory $dirName.");
2547            }
2548        }
2549  }  }
2550    
2551  =head3 Pad  =head3 SetPermissions
2552    
2553  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2554    
2555  Pad a string to a specified length. The pad character will be a  Set the permissions for a directory and all the files and folders inside it.
2556  space, and the padding will be on the right side unless specified  In addition, the group ownership will be changed to the specified value.
2557  in the third parameter.  
2558    This method is more vulnerable than most to permission and compatability
2559    problems, so it does internal error recovery.
2560    
2561  =over 4  =over 4
2562    
2563  =item string  =item dirName
2564    
2565  String to be padded.  Name of the directory to process.
2566    
2567  =item len  =item group
2568    
2569  Desired length of the padded string.  Name of the group to be assigned.
2570    
2571  =item left (optional)  =item mask
2572    
2573  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  Permission mask. Bits that are C<1> in this mask will be ORed into the
2574    permission bits of any file or directory that does not already have them
2575    set to 1.
2576    
2577  =item padChar (optional)  =item otherMasks
2578    
2579  Character to use for padding. The default is a space.  Map of search patterns to permission masks. If a directory name matches
2580    one of the patterns, that directory and all its members and subdirectories
2581    will be assigned the new pattern. For example, the following would
2582    assign 0664 to most files, but would use 0777 for directories named C<tmp>.
2583    
2584  =item RETURN      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2585    
2586  Returns a copy of the original string with the pad character added to the  The list is ordered, so the following would use 0777 for C<tmp1> and
2587  specified end so that it achieves the desired length.  0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2588    
2589        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2590                                                       '^tmp' => 0666);
2591    
2592    Note that the pattern matches are all case-insensitive, and only directory
2593    names are matched, not file names.
2594    
2595  =back  =back
2596    
2597  =cut  =cut
2598    
2599  sub Pad {  sub SetPermissions {
2600      # Get the parameters.      # Get the parameters.
2601      my ($string, $len, $left, $padChar) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2602      # Compute the padding character.      # Set up for error recovery.
2603      if (! defined $padChar) {      eval {
2604          $padChar = " ";          # Switch to the specified directory.
2605            ChDir($dirName);
2606            # Get the group ID.
2607            my $gid = getgrnam($group);
2608            # Get the mask for tracing.
2609            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2610            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2611            my $fixCount = 0;
2612            my $lookCount = 0;
2613            # @dirs will be a stack of directories to be processed.
2614            my @dirs = (getcwd());
2615            while (scalar(@dirs) > 0) {
2616                # Get the current directory.
2617                my $dir = pop @dirs;
2618                # Check for a match to one of the specified directory names. To do
2619                # that, we need to pull the individual part of the name off of the
2620                # whole path.
2621                my $simpleName = $dir;
2622                if ($dir =~ m!/([^/]+)$!) {
2623                    $simpleName = $1;
2624      }      }
2625      # Compute the number of spaces needed.              Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2626      my $needed = $len - length $string;              # Search for a match.
2627      # Copy the string into the return variable.              my $match = 0;
2628      my $retVal = $string;              my $i;
2629      # Only proceed if padding is needed.              for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2630      if ($needed > 0) {                  my $pattern = $otherMasks[$i];
2631          # Create the pad string.                  if ($simpleName =~ /$pattern/i) {
2632          my $pad = $padChar x $needed;                      $match = 1;
2633          # Affix it to the return value.                  }
2634          if ($left) {              }
2635              $retVal = $pad . $retVal;              # Find out if we have a match. Note we use $i-1 because the loop added 2
2636                # before terminating due to the match.
2637                if ($match && $otherMasks[$i-1] != $mask) {
2638                    # This directory matches one of the incoming patterns, and it's
2639                    # a different mask, so we process it recursively with that mask.
2640                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2641          } else {          } else {
2642              $retVal .= $pad;                  # Here we can process normally. Get all of the non-hidden members.
2643                    my @submems = OpenDir($dir, 1);
2644                    for my $submem (@submems) {
2645                        # Get the full name.
2646                        my $thisMem = "$dir/$submem";
2647                        Trace("Checking member $thisMem.") if T(4);
2648                        $lookCount++;
2649                        if ($lookCount % 1000 == 0) {
2650                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2651          }          }
2652                        # Fix the group.
2653                        chown -1, $gid, $thisMem;
2654                        # Insure this member is not a symlink.
2655                        if (! -l $thisMem) {
2656                            # Get its info.
2657                            my $fileInfo = stat $thisMem;
2658                            # Only proceed if we got the info. Otherwise, it's a hard link
2659                            # and we want to skip it anyway.
2660                            if ($fileInfo) {
2661                                my $fileMode = $fileInfo->mode;
2662                                if (($fileMode & $mask) != $mask) {
2663                                    # Fix this member.
2664                                    $fileMode |= $mask;
2665                                    chmod $fileMode, $thisMem;
2666                                    $fixCount++;
2667      }      }
2668      # Return the result.                              # If it's a subdirectory, stack it.
2669      return $retVal;                              if (-d $thisMem) {
2670                                    push @dirs, $thisMem;
2671                                }
2672                            }
2673                        }
2674                    }
2675                }
2676            }
2677            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2678        };
2679        # Check for an error.
2680        if ($@) {
2681            Confess("SetPermissions error: $@");
2682  }  }
   
 =head3 EOF  
   
 This is a constant that is lexically greater than any useful string.  
   
 =cut  
   
 sub EOF {  
     return "\xFF\xFF\xFF\xFF\xFF";  
2683  }  }
2684    
2685  =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  
2686    
2687      TICK("./protein.cgi")      my @data = Tracer::GetLine($handle);
2688    
2689  it will work correctly in both environments.  Read a line of data from a tab-delimited file.
2690    
2691  =over 4  =over 4
2692    
2693  =item commandString  =item handle
2694    
2695  The command string to pass to the system.  Open file handle from which to read.
2696    
2697  =item RETURN  =item RETURN
2698    
2699  Returns the standard output from the specified command, as a list.  Returns a list of the fields in the record read. The fields are presumed to be
2700    tab-delimited. If we are at the end of the file, then an empty list will be
2701    returned. If an empty line is read, a single list item consisting of a null
2702    string will be returned.
2703    
2704  =back  =back
2705    
2706  =cut  =cut
2707  #: Return Type @;  
2708  sub TICK {  sub GetLine {
2709      # Get the parameters.      # Get the parameters.
2710      my ($commandString) = @_;      my ($handle) = @_;
2711      # Chop off the dot-slash if this is Windows.      # Declare the return variable.
2712      if ($FIG_Config::win_mode) {      my @retVal = ();
2713          $commandString =~ s!^\./!!;      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2714        # Read from the file.
2715        my $line = <$handle>;
2716        # Only proceed if we found something.
2717        if (defined $line) {
2718            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2719            # upload control and have a nonstandard EOL combination.
2720            $line =~ s/(\r|\n)+$//;
2721            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2722            if (T(File => 4)) {
2723                my $escapedLine = $line;
2724                $escapedLine =~ s/\n/\\n/g;
2725                $escapedLine =~ s/\r/\\r/g;
2726                $escapedLine =~ s/\t/\\t/g;
2727                Trace("Line read: -->$escapedLine<--");
2728      }      }
2729      # Activate the command and return the result.          # If the line is empty, return a single empty string; otherwise, parse
2730      return `$commandString`;          # it into fields.
2731            if ($line eq "") {
2732                push @retVal, "";
2733            } else {
2734                push @retVal, split /\t/,$line;
2735            }
2736        } else {
2737            # Trace the reason the read failed.
2738            Trace("End of file: $!") if T(File => 3);
2739        }
2740        # Return the result.
2741        return @retVal;
2742  }  }
2743    
2744  =head3 ScriptSetup  =head3 PutLine
   
 C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  
2745    
2746  Perform standard tracing and debugging setup for scripts. The value returned is      Tracer::PutLine($handle, \@fields, $eol);
 the CGI object followed by a pre-built variable hash. At the end of the script,  
 the client should call L</ScriptFinish> to output the web page.  
2747    
2748  This method calls L</ETracing> to configure tracing, which allows the tracing  Write a line of data to a tab-delimited file. The specified field values will be
2749  to be configured via the emergency tracing form on the debugging control panel.  output in tab-separated form, with a trailing new-line.
 Tracing will then be turned on automatically for all programs that use the L</ETracing>  
 method, which includes every program that uses this method or L</StandardSetup>.  
2750    
2751  =over 4  =over 4
2752    
2753  =item noTrace (optional)  =item handle
2754    
2755  If specified, tracing will be suppressed. This is useful if the script wants to set up  Output file handle.
2756  tracing manually.  
2757    =item fields
2758    
2759    List of field values.
2760    
2761  =item RETURN  =item eol (optional)
2762    
2763  Returns a two-element list consisting of a CGI query object and a variable hash for  End-of-line character (default is "\n").
 the output page.  
2764    
2765  =back  =back
2766    
2767  =cut  =cut
2768    
2769  sub ScriptSetup {  sub PutLine {
2770      # Get the parameters.      # Get the parameters.
2771      my ($noTrace) = @_;      my ($handle, $fields, $eol) = @_;
2772      # Get the CGI query object.      # Write the data.
2773      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, $varHash);  
2774  }  }
2775    
 =head3 ETracing  
2776    
2777  C<< ETracing($parameter); >>  =head3 PrintLine
2778    
2779  Set up emergency tracing. Emergency tracing is tracing that is turned      Tracer::PrintLine($line);
2780  on automatically for any program that calls this method. The emergency  
2781  tracing parameters are stored in a a file identified by a tracing key.  Print a line of text with a trailing new-line.
 If this method is called with a CGI object, then the tracing key is  
 taken from a cookie. If it is called with no parameters, then the tracing  
 key is taken from an environment variable. If it is called with a string,  
 the tracing key is that string.  
2782    
2783  =over 4  =over 4
2784    
2785  =item parameter  =item line
2786    
2787  A parameter from which the tracing key is computed. If it is a scalar,  Line of text to print.
 that scalar is used as the tracing key. If it is a CGI object, the  
 tracing key is taken from the C<IP> cookie. If it is omitted, the  
 tracing key is taken from the C<TRACING> environment variable. If it  
 is a CGI object and emergency tracing is not on, the C<Trace> and  
 C<TF> parameters will be used to determine the type of tracing.  
2788    
2789  =back  =back
2790    
2791  =cut  =cut
2792    
2793  sub ETracing {  sub PrintLine {
2794      # Get the parameter.      # Get the parameters.
2795      my ($parameter) = @_;      my ($line) = @_;
2796      # Check for CGI mode.      # Print the line.
2797      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);  
     }  
2798  }  }
2799    
 =head3 EmergencyFileName  
2800    
2801  C<< my $fileName = Tracer::EmergencyFileName($tkey); >>  =head2 Other Useful Methods
2802    
2803  Return the emergency tracing file name. This is the file that specifies  =head3 ParseParm
2804  the tracing information.  
2805        my $listValue = Tracer::ParseParm($string);
2806    
2807    Convert a parameter into a list reference. If the parameter is undefined,
2808    an undefined value will be returned. Otherwise, it will be parsed as a
2809    comma-separated list of values.
2810    
2811  =over 4  =over 4
2812    
2813  =item tkey  =item string
2814    
2815  Tracing key for the current program.  Incoming string.
2816    
2817  =item RETURN  =item RETURN
2818    
2819  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
2820    was undefined.
2821    
2822  =back  =back
2823    
2824  =cut  =cut
2825    
2826  sub EmergencyFileName {  sub ParseParm {
2827      # Get the parameters.      # Get the parameters.
2828      my ($tkey) = @_;      my ($string) = @_;
2829      # Compute the emergency tracing file name.      # Declare the return variable.
2830      return "$FIG_Config::temp/Emergency$tkey.txt";      my $retVal;
2831        # Check for data.
2832        if (defined $string) {
2833            # We have some, so split it into a list.
2834            $retVal = [ split /\s*,\s*/, $string];
2835        }
2836        # Return the result.
2837        return $retVal;
2838  }  }
2839    
2840  =head3 EmergencyFileTarget  =head3 Now
2841    
2842  C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>      my $string = Tracer::Now();
2843    
2844  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
2845  the tracing output for file-based tracing.  method produces must be parseable by L</ParseDate>.
2846    
2847    =cut
2848    
2849    sub Now {
2850        return DisplayTime(time);
2851    }
2852    
2853    =head3 DisplayTime
2854    
2855        my $string = Tracer::DisplayTime($time);
2856    
2857    Convert a time value to a displayable time stamp. Whatever format this
2858    method produces must be parseable by L</ParseDate>.
2859    
2860  =over 4  =over 4
2861    
2862  =item tkey  =item time
2863    
2864  Tracing key for the current program.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2865    
2866  =item RETURN  =item RETURN
2867    
2868  Returns the name of the file to contain the trace output.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2869    
2870  =back  =back
2871    
2872  =cut  =cut
2873    
2874  sub EmergencyFileTarget {  sub DisplayTime {
2875      # Get the parameters.      my ($time) = @_;
2876      my ($tkey) = @_;      my $retVal = "(n/a)";
2877      # Compute the emergency tracing file name.      if (defined $time) {
2878      return "$FIG_Config::temp/trace$tkey.log";          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2879            $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2880                      _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2881        }
2882        return $retVal;
2883  }  }
2884    
2885  =head3 EmergencyTracingDest  # Pad a number to 2 digits.
2886    sub _p2 {
2887  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>      my ($value) = @_;
2888        $value = "0$value" if ($value < 10);
2889        return $value;
2890    }
2891    
2892  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.  
2893    
2894  =over 4      my $codedString = Tracer::Escape($realString);
2895    
2896  =item tkey  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2897    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2898    result is to reverse the effect of L</UnEscape>.
2899    
2900  Tracing key for this environment.  =over 4
2901    
2902  =item myDest  =item realString
2903    
2904  Destination from the emergency tracing file.  String to escape.
2905    
2906  =item RETURN  =item RETURN
2907    
2908  Returns a destination that can be passed into L</TSetup>.  Escaped equivalent of the real string.
2909    
2910  =back  =back
2911    
2912  =cut  =cut
2913    
2914  sub EmergencyTracingDest {  sub Escape {
2915      # Get the parameters.      # Get the parameter.
2916      my ($tkey, $myDest) = @_;      my ($realString) = @_;
2917      # Declare the return variable.      # Initialize the return variable.
2918      my $retVal = $myDest;      my $retVal = "";
2919      # Process according to the destination value.      # Loop through the parameter string, looking for sequences to escape.
2920      if ($myDest eq 'FILE') {      while (length $realString > 0) {
2921          $retVal = ">" . EmergencyFileTarget($tkey);          # Look for the first sequence to escape.
2922      } elsif ($myDest eq 'APPEND') {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2923          $retVal = ">>" . EmergencyFileTarget($tkey);              # Here we found it. The text preceding the sequence is in $1. The sequence
2924      } elsif ($myDest eq 'DUAL') {              # itself is in $2. First, move the clear text to the return variable.
2925          $retVal = "+>" . EmergencyFileTarget($tkey);              $retVal .= $1;
2926                # Strip the processed section off the real string.
2927                $realString = substr $realString, (length $2) + (length $1);
2928                # Get the matched character.
2929                my $char = $2;
2930                # If we have a CR, we are done.
2931                if ($char ne "\r") {
2932                    # It's not a CR, so encode the escape sequence.
2933                    $char =~ tr/\t\n/tn/;
2934                    $retVal .= "\\" . $char;
2935                }
2936            } else {
2937                # Here there are no more escape sequences. The rest of the string is
2938                # transferred unmodified.
2939                $retVal .= $realString;
2940                $realString = "";
2941            }
2942      }      }
2943      # Return the result.      # Return the result.
2944      return $retVal;      return $retVal;
2945  }  }
2946    
2947  =head3 Emergency  =head3 UnEscape
2948    
2949  C<< Emergency($key, $hours, $dest, $level, @modules); >>      my $realString = Tracer::UnEscape($codedString);
2950    
2951  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
2952  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
2953  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.  
2954    
2955  =over 4  =over 4
2956    
2957  =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  
2958    
2959  Tracing level. A higher level means more trace messages.  String to un-escape.
2960    
2961  =item modules  =item RETURN
2962    
2963  A list of the tracing modules to activate.  Returns a copy of the original string with the escape sequences converted to their actual
2964    values.
2965    
2966  =back  =back
2967    
2968  =cut  =cut
2969    
2970  sub Emergency {  sub UnEscape {
2971      # Get the parameters.      # Get the parameter.
2972      my ($tkey, $hours, $dest, $level, @modules) = @_;      my ($codedString) = @_;
2973      # Create the emergency file.      # Initialize the return variable.
2974      my $specFile = EmergencyFileName($tkey);      my $retVal = "";
2975      my $outHandle = Open(undef, ">$specFile");      # Only proceed if the incoming string is nonempty.
2976      print $outHandle join("\n", $hours, $dest, $level, @modules, "");      if (defined $codedString) {
2977            # Loop through the parameter string, looking for escape sequences. We can't do
2978            # translating because it causes problems with the escaped slash. ("\\t" becomes
2979            # "\<tab>" no matter what we do.)
2980            while (length $codedString > 0) {
2981                # Look for the first escape sequence.
2982                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2983                    # Here we found it. The text preceding the sequence is in $1. The sequence
2984                    # itself is in $2. First, move the clear text to the return variable.
2985                    $retVal .= $1;
2986                    $codedString = substr $codedString, (2 + length $1);
2987                    # Get the escape value.
2988                    my $char = $2;
2989                    # If we have a "\r", we are done.
2990                    if ($char ne 'r') {
2991                        # Here it's not an 'r', so we convert it.
2992                        $char =~ tr/\\tn/\\\t\n/;
2993                        $retVal .= $char;
2994  }  }
   
 =head3 EmergencyKey  
   
 C<< my $tkey = EmergencyKey($parameter); >>  
   
 Return the Key to be used for emergency tracing. This could be an IP address,  
  a session ID, or a user name, depending on the environment.  
   
 =over 4  
   
 =item parameter  
   
 Parameter defining the method for finding the tracing key. If it is a scalar,  
 then it is presumed to be the tracing key itself. If it is a CGI object, then  
 the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is  
 taken from the C<TRACING> environment variable.  
   
 =item RETURN  
   
 Returns the key to be used for labels in emergency tracing.  
   
 =back  
   
 =cut  
   
 sub EmergencyKey {  
     # Get the parameters.  
     my ($parameter) = @_;  
     # Declare the return variable.  
     my $retVal;  
     # Determine the parameter type.  
     if (! defined $parameter) {  
         # Here we're supposed to check the environment.  
         $retVal = $ENV{TRACING};  
2995      } else {      } else {
2996          my $ptype = ref $parameter;                  # Here there are no more escape sequences. The rest of the string is
2997          if ($ptype eq 'CGI') {                  # transferred unmodified.
2998              # Here we were invoked from a web page. Look for a cookie.                  $retVal .= $codedString;
2999              $retVal = $parameter->cookie('IP');                  $codedString = "";
         } elsif (! $ptype) {  
             # Here the key was passed in.  
             $retVal = $parameter;  
3000          }          }
3001      }      }
     # If no luck finding a key, use the PID.  
     if (! defined $retVal) {  
         $retVal = $$;  
3002      }      }
3003      # Return the result.      # Return the result.
3004      return $retVal;      return $retVal;
3005  }  }
3006    
3007    =head3 Percent
3008    
3009  =head3 TraceParms      my $percent = Tracer::Percent($number, $base);
   
 C<< Tracer::TraceParms($cgi); >>  
3010    
3011  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Returns the percent of the base represented by the given number. If the base
3012  at level CGI => 4.  is zero, returns zero.
3013    
3014  =over 4  =over 4
3015    
3016  =item cgi  =item number
3017    
3018  CGI query object containing the parameters to trace.  Percent numerator.
3019    
3020    =item base
3021    
3022    Percent base.
3023    
3024    =item RETURN
3025    
3026    Returns the percentage of the base represented by the numerator.
3027    
3028  =back  =back
3029    
3030  =cut  =cut
3031    
3032  sub TraceParms {  sub Percent {
3033      # Get the parameters.      # Get the parameters.
3034      my ($cgi) = @_;      my ($number, $base) = @_;
3035      if (T(CGI => 3)) {      # Declare the return variable.
3036          # Here we want to trace the parameter data.      my $retVal = 0;
3037          my @names = $cgi->param;      # Compute the percent.
3038          for my $parmName (sort @names) {      if ($base != 0) {
3039              # Note we skip the Trace parameters, which are for our use only.          $retVal = $number * 100 / $base;
             if ($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}");  
         }  
3040      }      }
3041        # Return the result.
3042        return $retVal;
3043  }  }
3044    
3045  =head3 ScriptFinish  =head3 Constrain
3046    
3047  C<< ScriptFinish($webData, $varHash); >>      my $constrained = Constrain($value, $min, $max);
3048    
3049  Output a web page at the end of a script. Either the string to be output or the  Modify a numeric value to bring it to a point in between a maximum and a minimum.
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
3050    
3051  A typical standard script would loook like the following.  =over 4
3052    
3053      BEGIN {  =item value
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
3054    
3055      my ($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", $varHash);  
3056    
3057  The idea here is that even if the script fails, you'll see trace messages and  =item min (optional)
 useful output.  
3058    
3059  =over 4  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3060    
3061  =item webData  =item max (optional)
3062    
3063  A string containing either the full web page to be written to the output or the  Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3064    
3065  =item varHash (optional)  =item RETURN
3066    
3067  If specified, then a reference to a hash mapping variable names for a template  Returns the incoming value, constrained according to the other parameters.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3068    
3069  =back  =back
3070    
3071  =cut  =cut
3072    
3073  sub ScriptFinish {  sub Constrain {
3074      # Get the parameters.      # Get the parameters.
3075      my ($webData, $varHash) = @_;      my ($value, $min, $max) = @_;
3076      # Check for a template file situation.      # Declare the return variable.
3077      my $outputString;      my $retVal = $value;
3078      if (defined $varHash) {      # Apply the minimum constraint.
3079          # Here we have a template file. We need to determine the template type.      if (defined $min && $retVal < $min) {
3080          my $template;          $retVal = $min;
3081          if ($FIG_Config::template_url && $webData =~ /\.php$/) {      }
3082              $template = "$FIG_Config::template_url/$webData";      # Apply the maximum constraint.
3083          } else {      if (defined $max && $retVal > $max) {
3084              $template = "<<$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;  
3085      }      }
3086      # Write the output string.      # Return the result.
3087      print $outputString;      return $retVal;
3088  }  }
3089    
3090  =head3 Insure  =head3 Min
3091    
3092  C<< Insure($dirName); >>      my $min = Min($value1, $value2, ... $valueN);
3093    
3094  Insure a directory is present.  Return the minimum argument. The arguments are treated as numbers.
3095    
3096  =over 4  =over 4
3097    
3098  =item dirName  =item $value1, $value2, ... $valueN
3099    
3100  Name of the directory to check. If it does not exist, it will be created.  List of numbers to compare.
3101    
3102    =item RETURN
3103    
3104    Returns the lowest number in the list.
3105    
3106  =back  =back
3107    
3108  =cut  =cut
3109    
3110  sub Insure {  sub Min {
3111      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
3112      if (! -d $dirName) {      my ($retVal, @values) = @_;
3113          Trace("Creating $dirName directory.") if T(File => 2);      # Loop through the remaining parameters, looking for the lowest.
3114          eval { mkpath $dirName; };      for my $value (@values) {
3115          if ($@) {          if ($value < $retVal) {
3116              Confess("Error creating $dirName: $@");              $retVal = $value;
3117          }          }
3118      }      }
3119        # Return the minimum found.
3120        return $retVal;
3121  }  }
3122    
3123  =head3 ChDir  =head3 Max
3124    
3125  C<< ChDir($dirName); >>      my $max = Max($value1, $value2, ... $valueN);
3126    
3127  Change to the specified directory.  Return the maximum argument. The arguments are treated as numbers.
3128    
3129  =over 4  =over 4
3130    
3131  =item dirName  =item $value1, $value2, ... $valueN
3132    
3133  Name of the directory to which we want to change.  List of numbers to compare.
3134    
3135    =item RETURN
3136    
3137    Returns the highest number in the list.
3138    
3139  =back  =back
3140    
3141  =cut  =cut
3142    
3143  sub ChDir {  sub Max {
3144      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
3145      if (! -d $dirName) {      my ($retVal, @values) = @_;
3146          Confess("Cannot change to directory $dirName: no such directory.");      # Loop through the remaining parameters, looking for the highest.
3147      } else {      for my $value (@values) {
3148          Trace("Changing to directory $dirName.") if T(File => 4);          if ($value > $retVal) {
3149          my $okFlag = chdir $dirName;              $retVal = $value;
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
3150          }          }
3151      }      }
3152        # Return the maximum found.
3153        return $retVal;
3154  }  }
3155    
3156  =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.  
3157    
3158  =over 4      my $string = Tracer::Strip($line);
3159    
3160  =item phoneNumber  Strip all line terminators off a string. This is necessary when dealing with files
3161    that may have been transferred back and forth several times among different
3162    operating environments.
3163    
3164  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".  
3165    
3166  =item msg  =item line
3167    
3168  Message to send to the specified phone.  Line of text to be stripped.
3169    
3170  =item RETURN  =item RETURN
3171    
3172  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.
3173    
3174  =back  =back
3175    
3176  =cut  =cut
3177    
3178  sub SendSMS {  sub Strip {
3179      # Get the parameters.      # Get a copy of the parameter string.
3180      my ($phoneNumber, $msg) = @_;      my ($string) = @_;
3181      # Declare the return variable. If we do not change it, C<undef> will be returned.      my $retVal = (defined $string ? $string : "");
3182      my $retVal;      # Strip the line terminator characters.
3183      # 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);  
             }  
         }  
     }  
3184      # Return the result.      # Return the result.
3185      return $retVal;      return $retVal;
3186  }  }
3187    
3188  =head3 CommaFormat  =head3 Pad
3189    
3190  C<< my $formatted = Tracer::CommaFormat($number); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3191    
3192  Insert commas into a number.  Pad a string to a specified length. The pad character will be a
3193    space, and the padding will be on the right side unless specified
3194    in the third parameter.
3195    
3196  =over 4  =over 4
3197    
3198  =item number  =item string
3199    
3200  A sequence of digits.  String to be padded.
3201    
3202    =item len
3203    
3204    Desired length of the padded string.
3205    
3206    =item left (optional)
3207    
3208    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3209    
3210    =item padChar (optional)
3211    
3212    Character to use for padding. The default is a space.
3213    
3214  =item RETURN  =item RETURN
3215    
3216  Returns the same digits with commas strategically inserted.  Returns a copy of the original string with the pad character added to the
3217    specified end so that it achieves the desired length.
3218    
3219  =back  =back
3220    
3221  =cut  =cut
3222    
3223  sub CommaFormat {  sub Pad {
3224      # Get the parameters.      # Get the parameters.
3225      my ($number) = @_;      my ($string, $len, $left, $padChar) = @_;
3226      # Pad the length up to a multiple of three.      # Compute the padding character.
3227      my $padded = "$number";      if (! defined $padChar) {
3228      $padded = " " . $padded while length($padded) % 3 != 0;          $padChar = " ";
3229      # This is a fancy PERL trick. The parentheses in the SPLIT pattern      }
3230      # cause the delimiters to be included in the output stream. The      # Compute the number of spaces needed.
3231      # GREP removes the empty strings in between the delimiters.      my $needed = $len - length $string;
3232      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));      # Copy the string into the return variable.
3233      # Clean out the spaces.      my $retVal = $string;
3234      $retVal =~ s/ //g;      # Only proceed if padding is needed.
3235        if ($needed > 0) {
3236            # Create the pad string.
3237            my $pad = $padChar x $needed;
3238            # Affix it to the return value.
3239            if ($left) {
3240                $retVal = $pad . $retVal;
3241            } else {
3242                $retVal .= $pad;
3243            }
3244        }
3245      # Return the result.      # Return the result.
3246      return $retVal;      return $retVal;
3247  }  }
 =head3 SetPermissions  
3248    
3249  C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  =head3 EOF
3250    
3251  Set the permissions for a directory and all the files and folders inside it.  This is a constant that is lexically greater than any useful string.
 In addition, the group ownership will be changed to the specified value.  
3252    
3253  This method is more vulnerable than most to permission and compatability  =cut
 problems, so it does internal error recovery.  
3254    
3255  =over 4  sub EOF {
3256        return "\xFF\xFF\xFF\xFF\xFF";
3257    }
3258    
3259  =item dirName  =head3 TICK
3260    
3261  Name of the directory to process.      my @results = TICK($commandString);
3262    
3263  =item group  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3264    dot-slash (C<./> will be removed. So, for example, if you were doing
3265    
3266  Name of the group to be assigned.      `./protein.cgi`
3267    
3268  =item mask  from inside a CGI script, it would work fine in Unix, but would issue an error message
3269    in Windows complaining that C<'.'> is not a valid command. If instead you code
3270    
3271  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.  
3272    
3273  =item otherMasks  it will work correctly in both environments.
3274    
3275  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>.  
3276    
3277      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  =item commandString
3278