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revision 1.86, Fri May 18 19:27:17 2007 UTC revision 1.101, Thu May 8 18:03:10 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    
42    
43  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
44    
# Line 159  Line 163 
163    
164  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
165  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
166  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
167  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
168  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
169  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
170  the tracing in your environment without stepping on other users.  the tracing in your environment without stepping on other users.
# Line 183  Line 187 
187    
188  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
189  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
190  using the L</StandardScript> or L</StandardSetup> methods, emergency tracing  using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
191  will be configured automatically.  will be configured automatically.
192    
 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.  
   
193  =cut  =cut
194    
195  # Declare the configuration variables.  # Declare the configuration variables.
196    
197  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
198  my $TeeFlag = 0;            # TRUE if output is going to a file and to the  my $TeeFlag = 0;            # TRUE if output is going to a file and to the
199                              # standard output                              # standard output
200  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
201                              # hash of active category names                              # hash of active category names
202    my @LevelNames = qw(error warn notice info detail);
203  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
204                              # messages                              # messages
205  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
206  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
207    my $LastLevel = 0;          # level of the last test call
208  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
209  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
210    my $SavedCGI;               # CGI object passed to ETracing
211    umask 2;                    # Fix the damn umask so everything is group-writable.
212    
213    =head2 Tracing Methods
214    
215    =head3 Setups
216    
217        my $count = Tracer::Setups();
218    
219    Return the number of times L</TSetup> has been called.
220    
221    This method allows for the creation of conditional tracing setups where, for example, we
222    may want to set up tracing if nobody else has done it before us.
223    
224    =cut
225    
226  =head2 Public Methods  sub Setups {
227        return $SetupCount;
228    }
229    
230  =head3 TSetup  =head3 TSetup
231    
232  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
233    
234  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
235  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 350  Line 279 
279          }          }
280      }      }
281      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
282      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
283      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
284        # the standard output (tee mode).
285      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
286          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
287              $TeeFlag = 1;              $TeeFlag = 1;
288              $target = substr($target, 1);              $target = substr($target, 1);
289          }          }
290          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
291                # We need to initialize the file (which clears it).
292              open TRACEFILE, $target;              open TRACEFILE, $target;
293              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
294              close TRACEFILE;              close TRACEFILE;
295                # Set to append mode now that the file has been cleared.
296              $Destination = ">$target";              $Destination = ">$target";
297          } else {          } else {
298              $Destination = $target;              $Destination = $target;
# Line 372  Line 304 
304      $SetupCount++;      $SetupCount++;
305  }  }
306    
307  =head3 StandardSetup  =head3 SetLevel
308    
309  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
310    
311  This method performs standard command-line parsing and tracing setup. The return  Modify the trace level. A higher trace level will cause more messages to appear.
 values are a hash of the command-line options and a list of the positional  
 parameters. Tracing is automatically set up and the command-line options are  
 validated.  
312    
313  This is a complex method that does a lot of grunt work. The parameters can  =over 4
 be more easily understood, however, once they are examined individually.  
314    
315  The I<categories> parameter is the most obtuse. It is a reference to a list of  =item newLevel
 special-purpose tracing categories. Most tracing categories are PERL package  
 names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,  
 B<ERDB>, and B<SproutLoad> packages, you would specify the categories  
316    
317      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
318    
319  This would cause trace messages in the specified three packages to appear in  =back
 the output. There are 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  =cut
322    
323  =item SQL  sub SetLevel {
324        $TraceLevel = $_[0];
325    }
326    
327  Traces SQL commands and activity.  =head3 ParseDate
328    
329  =item Tracer      my $time = Tracer::ParseDate($dateString);
330    
331  Traces error messages and call stacks.  Convert a date into a PERL time number. This method expects a date-like string
332    and parses it into a number. The string must be vaguely date-like or it will
333    return an undefined value. Our requirement is that a month and day be
334    present and that three pieces of the date string (time of day, month and day,
335    year) be separated by likely delimiters, such as spaces, commas, and such-like.
336    
337  =back  If a time of day is present, it must be in military time with two digits for
338    everything but the hour.
339    
340  C<SQL> is only turned on if the C<-sql> option is specified in the command line.  The year must be exactly four digits.
 The trace level is specified using the C<-trace> command-line option. For example,  
 the following command line for C<TransactFeatures> turns on SQL tracing and runs  
 all tracing at level 3.  
341    
342      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  Additional stuff can be in the string. We presume it's time zones or weekdays or something
343    equally innocuous. This means, however, that a sufficiently long sentence with date-like
344    parts in it may be interpreted as a date. Hopefully this will not be a problem.
345    
346  Standard tracing is output to the standard output and echoed to the file  It should be guaranteed that this method will parse the output of the L</Now> function.
 C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the  
 process ID. You can also specify the C<user> parameter to put a user ID  
 instead of a process ID in the trace file name. So, for example  
347    
348  The default trace level is 2. To get all messages, specify a trace level of 4.  The parameters are as follows.
 For a genome-by-genome update, use 3.  
349    
350      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  =over 4
351    
352  would send the trace output to C<traceBruce.log> in the temporary directory.  =item dateString
353    
354  The I<options> parameter is a reference to a hash containing the command-line  The date string to convert.
 options, their default values, and an explanation of what they mean. Command-line  
 options may be in the form of switches or keywords. In the case of a switch, the  
 option value is 1 if it is specified and 0 if it is not specified. In the case  
 of a keyword, the value is separated from the option name by an equal sign. You  
 can see this last in the command-line example above.  
355    
356  You can specify a different default trace level by setting C<$options->{trace}>  =item RETURN
 prior to calling this method.  
357    
358  An example at this point would help. Consider, for example, the command-line utility  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
359  C<TransactFeatures>. It accepts a list of positional parameters plus the options  the date string is invalid. A valid date string must contain a month and day.
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
360    
361      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  =back
                         { safe => [0, "use database transactions"],  
                           noAlias => [0, "do not expect aliases in CHANGE transactions"],  
                           start => [' ', "start with this genome"],  
                           tblFiles => [0, "output TBL files containing the corrected IDs"] },  
                         "<command> <transactionDirectory> <IDfile>",  
                       @ARGV);  
362    
363    =cut
364    
365  The call to C<ParseCommand> specifies the default values for the options and  # Universal month conversion table.
366  stores the actual options in a hash that is returned as C<$options>. The  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
367  positional parameters are returned in C<@parameters>.                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
368                                Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
369                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
370                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
371                                Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
372                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
373                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
374                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
375                                Oct =>  9, October  =>   9, '10' =>  9,
376                                Nov => 10, November =>  10, '11' => 10,
377                                Dec => 11, December =>  11, '12' => 11
378                            };
379    
380  The following is a sample command line for C<TransactFeatures>.  sub ParseDate {
381        # Get the parameters.
382        my ($dateString) = @_;
383        # Declare the return variable.
384        my $retVal;
385        # Find the month and day of month. There are two ways that can happen. We check for the
386        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
387        # won't be fooled into thinking the month is Sunday.
388        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
389            my ($mon, $mday) = (MONTHS->{$1}, $2);
390            # Insist that the month and day are valid.
391            if (defined($mon) && $2 >= 1 && $2 <= 31) {
392                # Find the time.
393                my ($hour, $min, $sec) = (0, 0, 0);
394                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
395                    ($hour, $min, $sec) = ($1, $2, $3);
396                }
397                # Find the year.
398                my $year;
399                if ($dateString =~ /\b(\d{4})\b/) {
400                    $year = $1;
401                } else {
402                    # Get the default year, which is this one. Note we must convert it to
403                    # the four-digit value expected by "timelocal".
404                    (undef, undef, undef, undef, undef, $year) = localtime();
405                    $year += 1900;
406                }
407                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
408            }
409        }
410        # Return the result.
411        return $retVal;
412    }
413    
414      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  =head3 LogErrors
415    
416  Single and double hyphens are equivalent. So, you could also code the      Tracer::LogErrors($fileName);
 above command as  
417    
418      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl  Route the standard error output to a log file.
419    
420  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  =over 4
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<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<$options> hash would be  
421    
422      { trace => 2, sql => 0, safe => 0,  =item fileName
       noAlias => 1, start => ' ', tblFiles => 0 }  
423    
424  Use of C<StandardSetup> in this way provides a simple way of performing  Name of the file to receive the error output.
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
425    
426  If the C<background> option is specified on the command line, then the  =back
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
427    
428      -user=Bruce -background  =cut
429    
430  then the trace output would go to C<traceBruce.log>, the standard output to  sub LogErrors {
431  C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to      # Get the file name.
432  simplify starting a command in the background.      my ($fileName) = @_;
433        # Open the file as the standard error output.
434        open STDERR, '>', $fileName;
435    }
436    
437  The user name is also used as the tracing key for L</Emergency Tracing>.  =head3 Trace
 Specifying a value of C<E> for the trace level causes emergency tracing to  
 be used instead of custom tracing. If the user name is not specified,  
 the tracing key is taken from the C<Tracing> environment variable. If there  
 is no value for that variable, the tracing key will be computed from the PID.  
438    
439  Finally, if the special option C<-help> is specified, the option      Trace($message);
 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  Write a trace message to the target location specified in L</TSetup>. If there has not been
442    any prior call to B<TSetup>.
443    
444  he would see the following output.  =over 4
445    
446      TransactFeatures [options] <command> <transactionDirectory> <IDfile>  =item message
         -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  Message to write.
 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)"],  =back
        ...  
451    
452  would set the default trace level to 0 instead of E, while  =cut
453    
454      { trace => ["2-", "tracing level (default 2)"],  sub Trace {
455         ...      # Get the parameters.
456        my ($message) = @_;
457        # Strip off any line terminators at the end of the message. We will add
458        # new-line stuff ourselves.
459        my $stripped = Strip($message);
460        # Compute the caller information.
461        my ($callPackage, $callFile, $callLine) = caller();
462        my $callFileTitle = basename($callFile);
463        # Check the caller.
464        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
465        # Get the timestamp.
466        my $timeStamp = Now();
467        # Build the prefix.
468        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
469        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
470        # Format the message.
471        my $formatted = "$prefix $stripped";
472        # Process according to the destination.
473        if ($Destination eq "TEXT") {
474            # Write the message to the standard output.
475            print "$formatted\n";
476        } elsif ($Destination eq "ERROR") {
477            # Write the message to the error output. Here, we want our prefix fields.
478            print STDERR "$formatted\n";
479        } elsif ($Destination eq "WARN") {
480            # Emit the message to the standard error output. It is presumed that the
481            # error logger will add its own prefix fields, the notable exception being
482            # the caller info.
483            print STDERR "$callerInfo$stripped\n";
484        } elsif ($Destination eq "QUEUE") {
485            # Push the message into the queue.
486            push @Queue, "$formatted";
487        } elsif ($Destination eq "HTML") {
488            # Convert the message to HTML and write it to the standard output.
489            my $escapedMessage = CGI::escapeHTML($stripped);
490            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
491        } elsif ($Destination =~ m/^>>/) {
492            # Write the trace message to an output file.
493            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
494            print TRACING "$formatted\n";
495            close TRACING;
496            # If the Tee flag is on, echo it to the standard output.
497            if ($TeeFlag) {
498                print "$formatted\n";
499            }
500        }
501    }
502    
503  would set the default to 2, but trace only to the log file, not to the  =head3 T
 standard output.  
504    
505  The parameters to this method are as follows.      my $switch = T($category, $traceLevel);
506    
507  =over 4      or
508    
509  =item categories      my $switch = T($traceLevel);
510    
511  Reference to a list of tracing category names. These should be names of  Return TRUE if the trace level is at or above a specified value and the specified category
512  packages whose internal workings will need to be debugged to get the  is active, else FALSE. If no category is specified, the caller's package name is used.
 command working.  
513    
514  =item options  =over 4
515    
516  Reference to a hash containing the legal options for the current command mapped  =item category
 to their default values and descriptions. The user can override the defaults  
 by specifying the options as command-line switches prefixed by a hyphen.  
 Tracing-related options may be added to this hash. If the C<-h> option is  
 specified on the command line, the option descriptions will be used to  
 explain the options. To turn off tracing to the standard output, add a  
 minus sign to the value for C<trace> (see above).  
517    
518  =item parmHelp  Category to which the message belongs. If not specified, the caller's package name is
519    used.
 A string that vaguely describes the positional parameters. This is used  
 if the user specifies the C<-h> option.  
520    
521  =item argv  =item traceLevel
522    
523  List of command line parameters, including the option switches, which must  Relevant tracing level.
 precede the positional parameters and be prefixed by a hyphen.  
524    
525  =item RETURN  =item RETURN
526    
527  Returns a list. The first element of the list is the reference to a hash that  TRUE if a message at the specified trace level would appear in the trace, else FALSE.
 maps the command-line option switches to their values. These will either be the  
 default values or overrides specified on the command line. The remaining  
 elements of the list are the position parameters, in order.  
528    
529  =back  =back
530    
531  =cut  =cut
532    
533  sub StandardSetup {  sub T {
534        # Declare the return variable.
535        my $retVal = 0;
536        # Only proceed if tracing is turned on.
537        if ($Destination ne "NONE") {
538      # Get the parameters.      # Get the parameters.
539      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
540      # Get the default tracing key.          if (!defined $traceLevel) {
541      my $tkey = EmergencyKey();              # Here we have no category, so we need to get the calling package.
542      # Add the tracing options.              # The calling package is normally the first parameter. If it is
543      if (! exists $options->{trace}) {              # omitted, the first parameter will be the tracelevel. So, the
544          $options->{trace} = ['2', "tracing level (E for emergency tracing)"];              # first thing we do is shift the so-called category into the
545      }              # $traceLevel variable where it belongs.
546      $options->{sql} = [0, "turn on SQL tracing"];              $traceLevel = $category;
547      $options->{help} = [0, "display command-line options"];              my ($package, $fileName, $line) = caller;
548      $options->{user} = [$tkey, "tracing key"];              # If there is no calling package, we default to "main".
549      $options->{background} = [0, "spool standard and error output"];              if (!$package) {
550      # 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($retOptions->{user});  
     } else {  
         # Here the tracing is controlled from the command line.  
         my @cats = @{$categories};  
         if ($retOptions->{sql}) {  
             push @cats, "SQL";  
         }  
         # Add the default categories.  
         push @cats, "Tracer";  
         # Next, we create the category string by joining the categories.  
         my $cats = join(" ", @cats);  
         # Check to determine whether or not the caller wants to turn off tracing  
         # to the standard output.  
         my $traceLevel = $retOptions->{trace};  
         my $textOKFlag = 1;  
         if ($traceLevel =~ /^(.)-/) {  
             $traceLevel = $1;  
             $textOKFlag = 0;  
         }  
         # Now we set up the trace mode.  
         my $traceMode;  
         # Verify that we can open a file in the FIG temporary directory.  
         my $traceFileName = "$FIG_Config::temp/trace$suffix.log";  
         if (open TESTTRACE, ">$traceFileName") {  
             # Here we can trace to a file.  
             $traceMode = ">$traceFileName";  
             if ($textOKFlag) {  
                 # Echo to standard output if the text-OK flag is set.  
                 $traceMode = "+$traceMode";  
             }  
             # Close the test file.  
             close TESTTRACE;  
         } else {  
             # Here we can't trace to a file. We trace to the standard output if it's  
             # okay, and the error log otherwise.  
             if ($textOKFlag) {  
                 $traceMode = "TEXT";  
551              } else {              } else {
552                  $traceMode = "WARN";                  my @cats = split /::/, $package;
553              }                  $category = $cats[$#cats];
         }  
         # Now set up the tracing.  
         TSetup("$traceLevel $cats", $traceMode);  
     }  
     # Check for the "h" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($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] . ")";  
554              }              }
             print "  $name $desc\n";  
555          }          }
556          exit(0);          # Save the category name and level.
557            $LastCategory = $category;
558            $LastLevel = $traceLevel;
559            # Convert it to lower case before we hash it.
560            $category = lc $category;
561            # Validate the trace level.
562            if (ref $traceLevel) {
563                Confess("Bad trace level.");
564            } elsif (ref $TraceLevel) {
565                Confess("Bad trace config.");
566      }      }
567      # Trace the options, if applicable.          # Make the check. Note that level 0 shows even if the category is turned off.
568      if (T(3)) {          $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
         my @parms = grep { $retOptions->{$_} } keys %{$retOptions};  
         Trace("Selected options: " . join(", ", sort @parms) . ".");  
569      }      }
570      # Return the parsed parameters.      # Return the computed result.
571      return ($retOptions, @retParameters);      return $retVal;
572  }  }
573    
574  =head3 Setups  =head3 QTrace
575    
576  C<< my $count = Tracer::Setups(); >>      my $data = QTrace($format);
577    
578  Return the number of times L</TSetup> has been called.  Return the queued trace data in the specified format.
579    
580  This method allows for the creation of conditional tracing setups where, for example, we  =over 4
581  may want to set up tracing if nobody else has done it before us.  
582    =item format
583    
584    C<html> to format the data as an HTML list, C<text> to format it as straight text.
585    
586    =back
587    
588  =cut  =cut
589    
590  sub Setups {  sub QTrace {
591      return $SetupCount;      # Get the parameter.
592        my ($format) = @_;
593        # Create the return variable.
594        my $retVal = "";
595        # Only proceed if there is an actual queue.
596        if (@Queue) {
597            # Process according to the format.
598            if ($format =~ m/^HTML$/i) {
599                # Convert the queue into an HTML list.
600                $retVal = "<ul>\n";
601                for my $line (@Queue) {
602                    my $escapedLine = CGI::escapeHTML($line);
603                    $retVal .= "<li>$escapedLine</li>\n";
604                }
605                $retVal .= "</ul>\n";
606            } elsif ($format =~ m/^TEXT$/i) {
607                # Convert the queue into a list of text lines.
608                $retVal = join("\n", @Queue) . "\n";
609            }
610            # Clear the queue.
611            @Queue = ();
612        }
613        # Return the formatted list.
614        return $retVal;
615  }  }
616    
617  =head3 Open  =head3 Confess
   
 C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  
618    
619  Open a file.      Confess($message);
620    
621  The I<$fileSpec> is essentially the second argument of the PERL C<open>  Trace the call stack and abort the program with the specified message. When used with
622  function. The mode is specified using Unix-like shell information. So, for  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
623  example,  So, for example
624    
625      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
626    
627  would open for output appended to the specified file, and  Will abort the program with a stack trace if the value of C<$recNum> is negative.
628    
629      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  =over 4
630    
631  would open a pipe that sorts the records written and removes duplicates. Note  =item message
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
632    
633      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  Message to include in the trace.
634    
635  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  =back
 the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a  
 failed open will throw an exception and the third parameter will be used to construct  
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
636    
637      Could not open "/usr/spool/news/twitlog"  =cut
638    
639  Note that the mode characters are automatically cleaned from the file name.  sub Confess {
640  The actual error message from the file system will be captured and appended to the      # Get the parameters.
641  message in any case.      my ($message) = @_;
642        # Set up the category and level.
643        $LastCategory = "(confess)";
644        $LastLevel = 0;
645        if (! defined($FIG_Config::no_tool_hdr)) {
646            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
647            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
648            # Only proceed if the tool header file is actually present.
649            if (-f $toolHeaderFile) {
650                my $fh;
651                if (open $fh, "<$toolHeaderFile") {
652                    my @lines = <$fh>;
653                    Trace("Tool header has " . scalar(@lines) . " lines.");
654                }
655            }
656        }
657        # Trace the call stack.
658        Cluck($message);
659        # Abort the program.
660        croak(">>> $message");
661    }
662    
663      Could not open "/usr/spool/news/twitlog": file not found.  =head3 Warn
664    
665  In some versions of PERL the only error message we get is a number, which      Warn($message);
 corresponds to the C++ C<errno> value.  
666    
667      Could not open "/usr/spool/news/twitlog": 6.  This method traces an important message. If an RSS feed is configured
668    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
669    then the message will be echoed to the feed. In general, a tracing
670    destination of C<WARN> indicates that the caller is running as a web
671    service in a production environment; however, this is not a requirement.
672    
673    The L</Cluck> method calls this one for its final message. Since
674    L</Confess> calls L</Cluck>, this means that any error which is caught
675    and confessed will put something in the feed. This insures that someone
676    will be alerted relatively quickly when a failure occurs.
677    
678  =over 4  =over 4
679    
680  =item fileHandle  =item message
681    
682  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.  
683    
684  =item fileSpec  =back
685    
686  File name and mode, as per the PERL C<open> function.  =cut
687    
688  =item message (optional)  sub Warn {
689        # Get the parameters.
690        my ($message) = @_;
691        # Trace the message.
692        Trace($message);
693        # An error here would be disastrous. Note, however, that we aren't too worried
694        # about losing events. The error log is always available for the occasions where
695        # we mess up.
696        eval {
697            # Do we need to put this in the RSS feed?
698            if ($FIG_Config::error_feed && $Destination eq 'WARN') {
699                # Yes. We now need to compute the date, the link, and the title.
700                # First, the date, in a very specific format.
701                my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
702                    (tz_local_offset() / 30);
703                # Environment data goes in here.
704                my $environment;
705                # HTML-escape the message and remove excess space.
706                my $title = CGI::escapeHTML($message);
707                $title =~ s/\s+/ /gs;
708                # Compute the title from the message. If it's too long, we have to
709                # split it up.
710                if (length $title > 60) {
711                    $title = substr($title, 0, 50) . "...";
712                }
713                # We'll put the link in here.
714                my $link;
715                # If we have a CGI object, then this is a web error. Otherwise, it's
716                # command-line.
717                if (defined $SavedCGI) {
718                    # We're in a web service. The environment is the user's IP, and the link
719                    # is the URL that got us here.
720                    my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
721                    $environment = "Event Reported at IP address $key.";
722                    $link = $SavedCGI->url(-full => 1, -query => 1);
723                    # We need the user agent string and (if available) the referrer.
724                    $environment .= "User Agent $ENV{HTTP_USER_AGENT}";
725                    if ($ENV{HTTP_REFERER}) {
726                        $environment .= " referred from $ENV{HTTP_REFERER}"
727                    }
728                    # Close off the sentence.
729                    $environment .= ". ";
730                } else {
731                    # No CGI object, so we're a command-line tool. Use the tracing
732                    # key and the PID as the user identifier, and add the command.
733                    my $key = EmergencyKey();
734                    $environment = "Event Reported by $key Process $$. Command $ENV{_}.";
735                    # Set the link to the development NMPDR. There is really no good
736                    # choice here.
737                    $link = "http://$FIG_Config::dev_server";
738                }
739                # Build a GUID. We use the current time, the title, and the process ID,
740                # then digest the result.
741                my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
742                # Finally, the description. This is a stack trace plus various environmental stuff.
743                # We have a goofy thing here in that we need to HTML-escape some sections of the description
744                # twice. They will be unescaped once when processed by the RSS reader. First, the stack
745                # trace.
746                my $stackTrace = "";
747                my @trace = LongMess();
748                # Only proceed if we got something back.
749                if (scalar(@trace) > 0) {
750                    $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
751                    $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
752                }
753                my $basicDescription = CGI::escapeHTML($message) . "<br /><br />" .
754                        CGI::escapeHTML($environment) . $stackTrace;
755                # Okay, we have all the pieces. Create a hash of the new event.
756                my $newItem = { title => $title,
757                                description => CGI::escapeHTML($basicDescription),
758                                link => $link,
759                                category => $LastCategory,
760                                pubDate => $date,
761                                guid => $guid,
762                               };
763                # We need XML capability for this.
764                require XML::Simple;
765                # The RSS document goes in here.
766                my $rss;
767                # Get the name of the RSS file. It's in the FIG temporary directory.
768                my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
769                # Does it exist?
770                if (-s $fileName) {
771                    # Slurp it in.
772                    $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
773                } else {
774                    my $size = -s $fileName;
775                    # Create an empty channel.
776                    $rss = {
777                        channel => {
778                            title => 'NMPDR Warning Feed',
779                            link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
780                            description => "Important messages regarding the status of the NMPDR.",
781                            generator => "NMPDR Trace Facility",
782                            docs => "http://blogs.law.harvard.edu/tech/rss",
783                            item => []
784                        },
785                    };
786                }
787                # Get the channel object.
788                my $channel = $rss->{channel};
789                # Update the last-build date.
790                $channel->{lastBuildDate} = $date;
791                # Get the item array.
792                my $items = $channel->{item};
793                # Insure it has only 100 entries.
794                while (scalar @{$items} > 100) {
795                    pop @{$items};
796                }
797                # Add our new item at the front.
798                unshift @{$items}, $newItem;
799                # Replace the file.
800                my $xml = XML::Simple::XMLout($rss, NoAttr => 1, RootName => 'rss version="2.0"', XmlDecl => '<?xml version="1.0" encoding="utf-8"?>',
801                                              NoEscape => 1);
802                # We don't use Open here because we can't afford an error.
803                if (open XMLOUT, ">$fileName") {
804                    print XMLOUT $xml;
805                    close XMLOUT;
806                }
807            }
808        };
809        # There's no "if ($@)" here, because putting an error message in the log
810        # saying that we missed putting an error message in the feed of messages
811        # in the log is not going to help anybody.
812    }
813    
814  Error message to use if the open fails. If omitted, a standard error message  =head3 Assert
 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>.  
815    
816  =item RETURN      Assert($condition1, $condition2, ... $conditionN);
817    
818  Returns the name of the file handle assigned to the file, or C<undef> if the  Return TRUE if all the conditions are true. This method can be used in conjunction with
819  open failed.  the OR operator and the L</Confess> method as a debugging assert.
820    So, for example
821    
822  =back      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
823    
824    Will abort the program with a stack trace if the value of C<$recNum> is negative.
825    
826    =cut
827    sub Assert {
828        my $retVal = 1;
829        LOOP: for my $condition (@_) {
830            if (! $condition) {
831                $retVal = 0;
832                last LOOP;
833            }
834        }
835        return $retVal;
836    }
837    
838    =head3 Cluck
839    
840        Cluck($message);
841    
842    Trace the call stack. Note that for best results, you should qualify the call with a
843    trace condition. For example,
844    
845        Cluck("Starting record parse.") if T(3);
846    
847    will only trace the stack if the trace level for the package is 3 or more.
848    
849    =over 4
850    
851    =item message
852    
853    Message to include in the trace.
854    
855    =back
856    
857    =cut
858    
859    sub Cluck {
860        # Get the parameters.
861        my ($message) = @_;
862        # Trace what's happening.
863        Trace("Stack trace for event: $message");
864        # Get the stack trace.
865        my @trace = LongMess();
866        # Convert the trace to a series of messages.
867        for my $line (@trace) {
868            # Replace the tab at the beginning with spaces.
869            $line =~ s/^\t/    /;
870            # Trace the line.
871            Trace($line);
872        }
873        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
874        Warn($message);
875    }
876    
877    =head3 LongMess
878    
879        my @lines = Tracer::LongMess();
880    
881    Return a stack trace with all tracing methods removed. The return will be in the form of a list
882    of message strings.
883    
884    =cut
885    
886    sub LongMess {
887        # Declare the return variable.
888        my @retVal = ();
889        my $confession = longmess("");
890        for my $line (split /\s*\n/, $confession) {
891            unless ($line =~ /Tracer\.pm/) {
892                # Here we have a line worth keeping. Push it onto the result list.
893                push @retVal, $line;
894            }
895        }
896        # Return the result.
897        return @retVal;
898    }
899    
900    =head3 ScriptSetup (deprecated)
901    
902        my ($cgi, $varHash) = ScriptSetup($noTrace);
903    
904    Perform standard tracing and debugging setup for scripts. The value returned is
905    the CGI object followed by a pre-built variable hash. At the end of the script,
906    the client should call L</ScriptFinish> to output the web page.
907    
908    This method calls L</ETracing> to configure tracing, which allows the tracing
909    to be configured via the emergency tracing form on the debugging control panel.
910    Tracing will then be turned on automatically for all programs that use the L</ETracing>
911    method, which includes every program that uses this method or L</StandardSetup>.
912    
913    =over 4
914    
915    =item noTrace (optional)
916    
917    If specified, tracing will be suppressed. This is useful if the script wants to set up
918    tracing manually.
919    
920    =item RETURN
921    
922    Returns a two-element list consisting of a CGI query object and a variable hash for
923    the output page.
924    
925    =back
926    
927    =cut
928    
929    sub ScriptSetup {
930        # Get the parameters.
931        my ($noTrace) = @_;
932        # Get the CGI query object.
933        my $cgi = CGI->new();
934        # Set up tracing if it's not suppressed.
935        ETracing($cgi) unless $noTrace;
936        # Create the variable hash.
937        my $varHash = { results => '' };
938        # Return the query object and variable hash.
939        return ($cgi, $varHash);
940    }
941    
942    =head3 ETracing
943    
944        ETracing($parameter);
945    
946    Set up emergency tracing. Emergency tracing is tracing that is turned
947    on automatically for any program that calls this method. The emergency
948    tracing parameters are stored in a a file identified by a tracing key.
949    If this method is called with a CGI object, then the tracing key is
950    taken from a cookie. If it is called with no parameters, then the tracing
951    key is taken from an environment variable. If it is called with a string,
952    the tracing key is that string.
953    
954    =over 4
955    
956    =item parameter
957    
958    A parameter from which the tracing key is computed. If it is a scalar,
959    that scalar is used as the tracing key. If it is a CGI object, the
960    tracing key is taken from the C<IP> cookie. If it is omitted, the
961    tracing key is taken from the C<TRACING> environment variable. If it
962    is a CGI object and emergency tracing is not on, the C<Trace> and
963    C<TF> parameters will be used to determine the type of tracing.
964    
965    =back
966    
967    =cut
968    
969    sub ETracing {
970        # Get the parameter.
971        my ($parameter) = @_;
972        # Check for CGI mode.
973        if (defined $parameter && ref $parameter eq 'CGI') {
974            $SavedCGI = $parameter;
975        } else {
976            $SavedCGI = undef;
977        }
978        # Default to no tracing except errors.
979        my ($tracing, $dest) = ("0", "WARN");
980        # Check for emergency tracing.
981        my $tkey = EmergencyKey($parameter);
982        my $emergencyFile = EmergencyFileName($tkey);
983        if (-e $emergencyFile) {
984            # We have the file. Read in the data.
985            my @tracing = GetFile($emergencyFile);
986            # Pull off the time limit.
987            my $expire = shift @tracing;
988            # Convert it to seconds.
989            $expire *= 3600;
990            # Check the file data.
991            my $stat = stat($emergencyFile);
992            my ($now) = gettimeofday;
993            if ($now - $stat->mtime > $expire) {
994                # Delete the expired file.
995                unlink $emergencyFile;
996            } else {
997                # Emergency tracing is on. Pull off the destination and
998                # the trace level;
999                $dest = shift @tracing;
1000                my $level = shift @tracing;
1001                # Convert the destination to a real tracing destination.
1002                # temp directory.
1003                $dest = EmergencyTracingDest($tkey, $dest);
1004                # Insure Tracer is specified.
1005                my %moduleHash = map { $_ => 1 } @tracing;
1006                $moduleHash{Tracer} = 1;
1007                # Set the trace parameter.
1008                $tracing = join(" ", $level, sort keys %moduleHash);
1009            }
1010        } elsif (defined $SavedCGI) {
1011            # There's no emergency tracing, but we have a CGI object, so check
1012            # for tracing from the form parameters.
1013            if ($SavedCGI->param('Trace')) {
1014                # Here the user has requested tracing via a form.
1015                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1016                $tracing = $SavedCGI->param('Trace') . " Tracer";
1017            }
1018        }
1019        # Setup the tracing we've determined from all the stuff above.
1020        TSetup($tracing, $dest);
1021        # Check to see if we're a web script.
1022        if (defined $SavedCGI) {
1023            # Yes we are. Trace the form and environment data.
1024            TraceParms($SavedCGI);
1025            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1026            # emitted by the script in its raw form.
1027            if (T(Raw => 3)) {
1028                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1029            }
1030        }
1031    }
1032    
1033    =head3 EmergencyFileName
1034    
1035        my $fileName = Tracer::EmergencyFileName($tkey);
1036    
1037    Return the emergency tracing file name. This is the file that specifies
1038    the tracing information.
1039    
1040    =over 4
1041    
1042    =item tkey
1043    
1044    Tracing key for the current program.
1045    
1046    =item RETURN
1047    
1048    Returns the name of the file to contain the emergency tracing information.
1049    
1050    =back
1051    
1052    =cut
1053    
1054    sub EmergencyFileName {
1055        # Get the parameters.
1056        my ($tkey) = @_;
1057        # Compute the emergency tracing file name.
1058        return "$FIG_Config::temp/Emergency$tkey.txt";
1059    }
1060    
1061    =head3 EmergencyFileTarget
1062    
1063        my $fileName = Tracer::EmergencyFileTarget($tkey);
1064    
1065    Return the emergency tracing target file name. This is the file that receives
1066    the tracing output for file-based tracing.
1067    
1068    =over 4
1069    
1070    =item tkey
1071    
1072    Tracing key for the current program.
1073    
1074    =item RETURN
1075    
1076    Returns the name of the file to contain the trace output.
1077    
1078    =back
1079    
1080    =cut
1081    
1082    sub EmergencyFileTarget {
1083        # Get the parameters.
1084        my ($tkey) = @_;
1085        # Compute the emergency tracing file name.
1086        return "$FIG_Config::temp/trace$tkey.log";
1087    }
1088    
1089    =head3 EmergencyTracingDest
1090    
1091        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1092    
1093    This method converts an emergency tracing destination to a real
1094    tracing destination. The main difference is that if the
1095    destination is C<FILE> or C<APPEND>, we convert it to file
1096    output. If the destination is C<DUAL>, we convert it to file
1097    and standard output.
1098    
1099    =over 4
1100    
1101    =item tkey
1102    
1103    Tracing key for this environment.
1104    
1105    =item myDest
1106    
1107    Destination from the emergency tracing file.
1108    
1109    =item RETURN
1110    
1111    Returns a destination that can be passed into L</TSetup>.
1112    
1113    =back
1114    
1115    =cut
1116    
1117    sub EmergencyTracingDest {
1118        # Get the parameters.
1119        my ($tkey, $myDest) = @_;
1120        # Declare the return variable.
1121        my $retVal = $myDest;
1122        # Process according to the destination value.
1123        if ($myDest eq 'FILE') {
1124            $retVal = ">" . EmergencyFileTarget($tkey);
1125        } elsif ($myDest eq 'APPEND') {
1126            $retVal = ">>" . EmergencyFileTarget($tkey);
1127        } elsif ($myDest eq 'DUAL') {
1128            $retVal = "+>" . EmergencyFileTarget($tkey);
1129        } elsif ($myDest eq 'WARN') {
1130            $retVal = "WARN";
1131        }
1132        # Return the result.
1133        return $retVal;
1134    }
1135    
1136    =head3 Emergency
1137    
1138        Emergency($key, $hours, $dest, $level, @modules);
1139    
1140    Turn on emergency tracing. This method is normally invoked over the web from
1141    a debugging console, but it can also be called by the C<trace.pl> script.
1142    The caller specifies the duration of the emergency in hours, the desired tracing
1143    destination, the trace level, and a list of the trace modules to activate.
1144    For the length of the duration, when a program in an environment with the
1145    specified tracing key active invokes a Sprout CGI script, tracing will be
1146    turned on automatically. See L</TSetup> for more about tracing setup and
1147    L</ETracing> for more about emergency tracing.
1148    
1149    =over 4
1150    
1151    =item tkey
1152    
1153    The tracing key. This is used to identify the control file and the trace file.
1154    
1155    =item hours
1156    
1157    Number of hours to keep emergency tracing alive.
1158    
1159    =item dest
1160    
1161    Tracing destination. If no path information is specified for a file
1162    destination, it is put in the FIG temporary directory.
1163    
1164    =item level
1165    
1166    Tracing level. A higher level means more trace messages.
1167    
1168    =item modules
1169    
1170    A list of the tracing modules to activate.
1171    
1172    =back
1173    
1174    =cut
1175    
1176    sub Emergency {
1177        # Get the parameters.
1178        my ($tkey, $hours, $dest, $level, @modules) = @_;
1179        # Create the emergency file.
1180        my $specFile = EmergencyFileName($tkey);
1181        my $outHandle = Open(undef, ">$specFile");
1182        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1183    }
1184    
1185    =head3 EmergencyKey
1186    
1187        my $tkey = EmergencyKey($parameter);
1188    
1189    Return the Key to be used for emergency tracing. This could be an IP address,
1190     a session ID, or a user name, depending on the environment.
1191    
1192    =over 4
1193    
1194    =item parameter
1195    
1196    Parameter defining the method for finding the tracing key. If it is a scalar,
1197    then it is presumed to be the tracing key itself. If it is a CGI object, then
1198    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1199    taken from the C<TRACING> environment variable.
1200    
1201    =item RETURN
1202    
1203    Returns the key to be used for labels in emergency tracing.
1204    
1205    =back
1206    
1207  =cut  =cut
1208    
1209  sub Open {  sub EmergencyKey {
1210      # Get the parameters.      # Get the parameters.
1211      my ($fileHandle, $fileSpec, $message) = @_;      my ($parameter) = @_;
1212      # Attempt to open the file.      # Declare the return variable.
1213      my $rv = open $fileHandle, $fileSpec;      my $retVal;
1214      # If the open failed, generate an error message.      # Determine the parameter type.
1215      if (! $rv) {      if (! defined $parameter) {
1216          # Save the system error message.          # Here we're supposed to check the environment. If that fails, we
1217          my $sysMessage = $!;          # get the effective login ID.
1218          # See if we need a default message.          $retVal = $ENV{TRACING} || scalar getpwuid($<);
1219          if (!$message) {      } else {
1220              # Clean any obvious mode characters and leading spaces from the          my $ptype = ref $parameter;
1221              # filename.          if ($ptype eq 'CGI') {
1222              my ($fileName) = FindNamePart($fileSpec);              # Here we were invoked from a web page. Look for a cookie.
1223              $message = "Could not open \"$fileName\"";              $retVal = $parameter->cookie('IP');
1224            } elsif (! $ptype) {
1225                # Here the key was passed in.
1226                $retVal = $parameter;
1227            }
1228        }
1229        # If no luck finding a key, use the PID.
1230        if (! defined $retVal) {
1231            $retVal = $$;
1232        }
1233        # Return the result.
1234        return $retVal;
1235    }
1236    
1237    
1238    =head3 TraceParms
1239    
1240        Tracer::TraceParms($cgi);
1241    
1242    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1243    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1244    
1245    =over 4
1246    
1247    =item cgi
1248    
1249    CGI query object containing the parameters to trace.
1250    
1251    =back
1252    
1253    =cut
1254    
1255    sub TraceParms {
1256        # Get the parameters.
1257        my ($cgi) = @_;
1258        if (T(CGI => 2)) {
1259            # Here we trace the GET-style URL for the script.
1260            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1261        }
1262        if (T(CGI => 3)) {
1263            # Here we want to trace the parameter data.
1264            my @names = $cgi->param;
1265            for my $parmName (sort @names) {
1266                # Note we skip the Trace parameters, which are for our use only.
1267                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1268                    my @values = $cgi->param($parmName);
1269                    Trace("[CGI] $parmName = " . join(", ", @values));
1270                }
1271            }
1272            # Display the request method.
1273            my $method = $cgi->request_method();
1274            Trace("Method: $method");
1275        }
1276        if (T(CGI => 4)) {
1277            # Here we want the environment data too.
1278            for my $envName (sort keys %ENV) {
1279                Trace("[ENV] $envName = $ENV{$envName}");
1280            }
1281        }
1282    }
1283    
1284    =head3 TraceImages
1285    
1286        Tracer::TraceImages($htmlString);
1287    
1288    Trace information about all of an html document's images. The tracing
1289    will be for type "IMG" at level 3. The image's source string
1290    will be displayed. This is generally either the URL of the image or
1291    raw data for the image itself. If the source is too long, only the first 300
1292    characters will be shown at trace level 3. The entire source will be shown,
1293    however, at trace level 4. This method is not very smart, and might catch
1294    Javascript code, but it is still useful when debugging the arcane
1295    behavior of images in multiple browser environments.
1296    
1297    =over 4
1298    
1299    =item htmlString
1300    
1301    HTML text for an outgoing web page.
1302    
1303    =back
1304    
1305    =cut
1306    
1307    sub TraceImages {
1308        # Only proceed if we're at the proper trace level.
1309        if (T(IMG => 3)) {
1310            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1311            # into a variable called "$htmlString". This is because we expect html strings to be
1312            # long, and don't want to copy them any more than we have to.
1313            Trace(length($_[0]) . " characters in web page.");
1314            # Loop through the HTML, culling image tags.
1315            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1316                # Extract the source string and determine whether or not it's too long.
1317                my $srcString = $1;
1318                my $pos = pos($_[0]) - length($srcString);
1319                my $excess = length($srcString) - 300;
1320                # We'll put the display string in here.
1321                my $srcDisplay = $srcString;
1322                # If it's a data string, split it at the comma.
1323                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1324                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1325                # a long string, however, we only show the first 300 characters.
1326                if ($excess > 0 && ! T(IMG => 4)) {
1327                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1328                }
1329                # Output the trace message.
1330                Trace("Image tag at position $pos:\n$srcDisplay");
1331            }
1332        }
1333    }
1334    
1335    
1336    =head3 ScriptFinish (deprecated)
1337    
1338        ScriptFinish($webData, $varHash);
1339    
1340    Output a web page at the end of a script. Either the string to be output or the
1341    name of a template file can be specified. If the second parameter is omitted,
1342    it is assumed we have a string to be output; otherwise, it is assumed we have the
1343    name of a template file. The template should have the variable C<DebugData>
1344    specified in any form that invokes a standard script. If debugging mode is turned
1345    on, a form field will be put in that allows the user to enter tracing data.
1346    Trace messages will be placed immediately before the terminal C<BODY> tag in
1347    the output, formatted as a list.
1348    
1349    A typical standard script would loook like the following.
1350    
1351        BEGIN {
1352            # Print the HTML header.
1353            print "CONTENT-TYPE: text/html\n\n";
1354        }
1355        use Tracer;
1356        use CGI;
1357        use FIG;
1358        # ... more uses ...
1359    
1360        my ($cgi, $varHash) = ScriptSetup();
1361        eval {
1362            # ... get data from $cgi, put it in $varHash ...
1363        };
1364        if ($@) {
1365            Trace("Script Error: $@") if T(0);
1366        }
1367        ScriptFinish("Html/MyTemplate.html", $varHash);
1368    
1369    The idea here is that even if the script fails, you'll see trace messages and
1370    useful output.
1371    
1372    =over 4
1373    
1374    =item webData
1375    
1376    A string containing either the full web page to be written to the output or the
1377    name of a template file from which the page is to be constructed. If the name
1378    of a template file is specified, then the second parameter must be present;
1379    otherwise, it must be absent.
1380    
1381    =item varHash (optional)
1382    
1383    If specified, then a reference to a hash mapping variable names for a template
1384    to their values. The template file will be read into memory, and variable markers
1385    will be replaced by data in this hash reference.
1386    
1387    =back
1388    
1389    =cut
1390    
1391    sub ScriptFinish {
1392        # Get the parameters.
1393        my ($webData, $varHash) = @_;
1394        # Check for a template file situation.
1395        my $outputString;
1396        if (defined $varHash) {
1397            # Here we have a template file. We need to determine the template type.
1398            my $template;
1399            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1400                $template = "$FIG_Config::template_url/$webData";
1401            } else {
1402                $template = "<<$webData";
1403            }
1404            $outputString = PageBuilder::Build($template, $varHash, "Html");
1405        } else {
1406            # Here the user gave us a raw string.
1407            $outputString = $webData;
1408        }
1409        # Check for trace messages.
1410        if ($Destination ne "NONE" && $TraceLevel > 0) {
1411            # We have trace messages, so we want to put them at the end of the body. This
1412            # is either at the end of the whole string or at the beginning of the BODY
1413            # end-tag.
1414            my $pos = length $outputString;
1415            if ($outputString =~ m#</body>#gi) {
1416                $pos = (pos $outputString) - 7;
1417            }
1418            # If the trace messages were queued, we unroll them. Otherwise, we display the
1419            # destination.
1420            my $traceHtml;
1421            if ($Destination eq "QUEUE") {
1422                $traceHtml = QTrace('Html');
1423            } elsif ($Destination =~ /^>>(.+)$/) {
1424                # Here the tracing output it to a file. We code it as a hyperlink so the user
1425                # can copy the file name into the clipboard easily.
1426                my $actualDest = $1;
1427                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1428            } else {
1429                # Here we have one of the special destinations.
1430                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1431            }
1432            substr $outputString, $pos, 0, $traceHtml;
1433        }
1434        # Write the output string.
1435        print $outputString;
1436    }
1437    
1438    =head2 Command-Line Utility Methods
1439    
1440    =head3 SendSMS
1441    
1442        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1443    
1444    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1445    user name, password, and API ID for the relevant account in the hash reference variable
1446    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1447    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1448    is C<2561022>, then the FIG_Config file must contain
1449    
1450        $phone =  { user => 'BruceTheHumanPet',
1451                    password => 'silly',
1452                    api_id => '2561022' };
1453    
1454    The original purpose of this method was to insure Bruce would be notified immediately when the
1455    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1456    when you call this method.
1457    
1458    The message ID will be returned if successful, and C<undef> if an error occurs.
1459    
1460    =over 4
1461    
1462    =item phoneNumber
1463    
1464    Phone number to receive the message, in international format. A United States phone number
1465    would be prefixed by "1". A British phone number would be prefixed by "44".
1466    
1467    =item msg
1468    
1469    Message to send to the specified phone.
1470    
1471    =item RETURN
1472    
1473    Returns the message ID if successful, and C<undef> if the message could not be sent.
1474    
1475    =back
1476    
1477    =cut
1478    
1479    sub SendSMS {
1480        # Get the parameters.
1481        my ($phoneNumber, $msg) = @_;
1482        # Declare the return variable. If we do not change it, C<undef> will be returned.
1483        my $retVal;
1484        # Only proceed if we have phone support.
1485        if (! defined $FIG_Config::phone) {
1486            Trace("Phone support not present in FIG_Config.") if T(1);
1487        } else {
1488            # Get the phone data.
1489            my $parms = $FIG_Config::phone;
1490            # Get the Clickatell URL.
1491            my $url = "http://api.clickatell.com/http/";
1492            # Create the user agent.
1493            my $ua = LWP::UserAgent->new;
1494            # Request a Clickatell session.
1495            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1496                                         password => $parms->{password},
1497                                         api_id => $parms->{api_id},
1498                                         to => $phoneNumber,
1499                                         text => $msg});
1500            # Check for an error.
1501            if (! $resp->is_success) {
1502                Trace("Alert failed.") if T(1);
1503            } else {
1504                # Get the message ID.
1505                my $rstring = $resp->content;
1506                if ($rstring =~ /^ID:\s+(.*)$/) {
1507                    $retVal = $1;
1508                } else {
1509                    Trace("Phone attempt failed with $rstring") if T(1);
1510          }          }
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
1511      }      }
1512      # Return the file handle.      }
1513      return $fileHandle;      # Return the result.
1514        return $retVal;
1515  }  }
1516    
1517  =head3 FindNamePart  =head3 StandardSetup
1518    
1519  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>      my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1520    
1521  Extract the portion of a file specification that contains the file name.  This method performs standard command-line parsing and tracing setup. The return
1522    values are a hash of the command-line options and a list of the positional
1523    parameters. Tracing is automatically set up and the command-line options are
1524    validated.
1525    
1526  A file specification is the string passed to an C<open> call. It specifies the file  This is a complex method that does a lot of grunt work. The parameters can
1527  mode and name. In a truly complex situation, it can specify a pipe sequence. This  be more easily understood, however, once they are examined individually.
 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>.  
1528    
1529      >>/usr/fig/myfile.txt  The I<categories> parameter is the most obtuse. It is a reference to a list of
1530      </usr/fig/myfile.txt  special-purpose tracing categories. Most tracing categories are PERL package
1531      | sort -u > /usr/fig/myfile.txt  names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1532    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1533    
1534  If the method cannot find a file name using its normal methods, it will return the      ["Sprout", "SproutLoad", "ERDB"]
1535  whole incoming string.  
1536    This would cause trace messages in the specified three packages to appear in
1537    the output. There are two special tracing categories that are automatically
1538    handled by this method. In other words, if you used L</TSetup> you would need
1539    to include these categories manually, but if you use this method they are turned
1540    on automatically.
1541    
1542  =over 4  =over 4
1543    
1544  =item fileSpec  =item SQL
1545    
1546  File specification string from which the file name is to be extracted.  Traces SQL commands and activity.
1547    
1548  =item RETURN  =item Tracer
1549    
1550  Returns a three-element list. The first element contains the file name portion of  Traces error messages and call stacks.
 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.  
1551    
1552  =back  =back
1553    
1554  =cut  C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1555  #: Return Type $;  The trace level is specified using the C<-trace> command-line option. For example,
1556  sub FindNamePart {  the following command line for C<TransactFeatures> turns on SQL tracing and runs
1557      # Get the parameters.  all tracing at level 3.
     my ($fileSpec) = @_;  
     # Default to the whole input string.  
     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);  
     # Parse out the file name if we can.  
     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {  
         $retVal = $2;  
         $len = length $retVal;  
         $pos = (length $fileSpec) - (length $3) - $len;  
     }  
     # Return the result.  
     return ($retVal, $pos, $len);  
 }  
1558    
1559  =head3 OpenDir      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1560    
1561  C<< my @files = OpenDir($dirName, $filtered, $flag); >>  Standard tracing is output to the standard output and echoed to the file
1562    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1563    process ID. You can also specify the C<user> parameter to put a user ID
1564    instead of a process ID in the trace file name. So, for example
1565    
1566  Open a directory and return all the file names. This function essentially performs  The default trace level is 2. To get all messages, specify a trace level of 4.
1567  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  For a genome-by-genome update, use 3.
 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  
 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,  
1568    
1569      my @files = OpenDir("/Volumes/fig/contigs", 1);      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1570    
1571  is effectively the same as  would send the trace output to C<traceBruce.log> in the temporary directory.
1572    
1573      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  The I<options> parameter is a reference to a hash containing the command-line
1574      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  options, their default values, and an explanation of what they mean. Command-line
1575    options may be in the form of switches or keywords. In the case of a switch, the
1576    option value is 1 if it is specified and 0 if it is not specified. In the case
1577    of a keyword, the value is separated from the option name by an equal sign. You
1578    can see this last in the command-line example above.
1579    
1580  Similarly, the following code  You can specify a different default trace level by setting C<$options->{trace}>
1581    prior to calling this method.
1582    
1583      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  An example at this point would help. Consider, for example, the command-line utility
1584    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1585    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1586    the following code.
1587    
1588  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1589  automatically returns an empty list if the directory fails to open.                          { safe => [0, "use database transactions"],
1590                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1591                              start => [' ', "start with this genome"],
1592                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1593                            "<command> <transactionDirectory> <IDfile>",
1594                          @ARGV);
1595    
 =over 4  
1596    
1597  =item dirName  The call to C<ParseCommand> specifies the default values for the options and
1598    stores the actual options in a hash that is returned as C<$options>. The
1599    positional parameters are returned in C<@parameters>.
1600    
1601  Name of the directory to open.  The following is a sample command line for C<TransactFeatures>.
1602    
1603  =item filtered      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1604    
1605  TRUE if files whose names begin with a period (C<.>) should be automatically removed  Single and double hyphens are equivalent. So, you could also code the
1606  from the list, else FALSE.  above command as
1607    
1608  =item flag      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1609    
1610  TRUE if a failure to open is okay, else FALSE  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1611    parameters, and would find themselves in I<@parameters> after executing the
1612    above code fragment. The tracing would be set to level 2, and the categories
1613    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1614    and C<DocUtils> was included because it came in within the first parameter
1615    to this method. The I<$options> hash would be
1616    
1617  =back      { trace => 2, sql => 0, safe => 0,
1618          noAlias => 1, start => ' ', tblFiles => 0 }
1619    
1620  =cut  Use of C<StandardSetup> in this way provides a simple way of performing
1621  #: Return Type @;  standard tracing setup and command-line parsing. Note that the caller is
1622  sub OpenDir {  not even aware of the command-line switches C<-trace> and C<-sql>, which
1623      # Get the parameters.  are used by this method to control the tracing. If additional tracing features
1624      my ($dirName, $filtered, $flag) = @_;  need to be added in the future, they can be processed by this method without
1625      # Declare the return variable.  upsetting the command-line utilities.
     my @retVal = ();  
     # Open the directory.  
     if (opendir(my $dirHandle, $dirName)) {  
         # The directory opened successfully. Get the appropriate list according to the  
         # strictures of the filter parameter.  
         if ($filtered) {  
             @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;  
         } else {  
             @retVal = readdir $dirHandle;  
         }  
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
     }  
     # Return the result.  
     return @retVal;  
 }  
1626    
1627  =head3 SetLevel  If the C<background> option is specified on the command line, then the
1628    standard and error outputs will be directed to files in the temporary
1629    directory, using the same suffix as the trace file. So, if the command
1630    line specified
1631    
1632  C<< Tracer::SetLevel($newLevel); >>      -user=Bruce -background
1633    
1634  Modify the trace level. A higher trace level will cause more messages to appear.  then the trace output would go to C<traceBruce.log>, the standard output to
1635    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1636    simplify starting a command in the background.
1637    
1638  =over 4  The user name is also used as the tracing key for L</Emergency Tracing>.
1639    Specifying a value of C<E> for the trace level causes emergency tracing to
1640    be used instead of custom tracing. If the user name is not specified,
1641    the tracing key is taken from the C<Tracing> environment variable. If there
1642    is no value for that variable, the tracing key will be computed from the PID.
1643    
1644  =item newLevel  Finally, if the special option C<-help> is specified, the option
1645    names will be traced at level 0 and the program will exit without processing.
1646    This provides a limited help capability. For example, if the user enters
1647    
1648  Proposed new trace level.      TransactFeatures -help
1649    
1650  =back  he would see the following output.
1651    
1652  =cut      TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1653            -trace    tracing level (default E)
1654            -sql      trace SQL commands
1655            -safe     use database transactions
1656            -noAlias  do not expect aliases in CHANGE transactions
1657            -start    start with this genome
1658            -tblFiles output TBL files containing the corrected IDs
1659    
1660  sub SetLevel {  The caller has the option of modifying the tracing scheme by placing a value
1661      $TraceLevel = $_[0];  for C<trace> in the incoming options hash. The default value can be overridden,
1662  }  or the tracing to the standard output can be turned off by suffixing a minus
1663    sign to the trace level. So, for example,
1664    
1665  =head3 Now      { trace => [0, "tracing level (default 0)"],
1666           ...
1667    
1668    would set the default trace level to 0 instead of E, while
1669    
1670  C<< my $string = Tracer::Now(); >>      { trace => ["2-", "tracing level (default 2)"],
1671           ...
1672    
1673  Return a displayable time stamp containing the local time.  would set the default to 2, but trace only to the log file, not to the
1674    standard output.
1675    
1676  =cut  The parameters to this method are as follows.
1677    
1678  sub Now {  =over 4
     my ($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 $retVal;  
 }  
1679    
1680  # Pad a number to 2 digits.  =item categories
1681  sub _p2 {  
1682      my ($value) = @_;  Reference to a list of tracing category names. These should be names of
1683      $value = "0$value" if ($value < 10);  packages whose internal workings will need to be debugged to get the
1684      return $value;  command working.
 }  
1685    
1686  =head3 ParseTraceDate  =item options
1687    
1688  C<< my $time = Tracer::ParseTraceDate($dateString); >>  Reference to a hash containing the legal options for the current command mapped
1689    to their default values and descriptions. The user can override the defaults
1690    by specifying the options as command-line switches prefixed by a hyphen.
1691    Tracing-related options may be added to this hash. If the C<-h> option is
1692    specified on the command line, the option descriptions will be used to
1693    explain the options. To turn off tracing to the standard output, add a
1694    minus sign to the value for C<trace> (see above).
1695    
1696  Convert a date from the trace file into a PERL timestamp.  =item parmHelp
1697    
1698  =over 4  A string that vaguely describes the positional parameters. This is used
1699    if the user specifies the C<-h> option.
1700    
1701  =item dateString  =item argv
1702    
1703  The date string from the trace file. The format of the string is determined by the  List of command line parameters, including the option switches, which must
1704  L</Now> method.  precede the positional parameters and be prefixed by a hyphen.
1705    
1706  =item RETURN  =item RETURN
1707    
1708  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if  Returns a list. The first element of the list is the reference to a hash that
1709  the time string is invalid.  maps the command-line option switches to their values. These will either be the
1710    default values or overrides specified on the command line. The remaining
1711    elements of the list are the position parameters, in order.
1712    
1713  =back  =back
1714    
1715  =cut  =cut
1716    
1717  sub ParseTraceDate {  sub StandardSetup {
1718      # Get the parameters.      # Get the parameters.
1719      my ($dateString) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
1720      # Declare the return variable.      # Get the default tracing key.
1721      my $retVal;      my $tkey = EmergencyKey();
1722      # Parse the date.      # Add the tracing options.
1723      if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {      if (! exists $options->{trace}) {
1724          # Create a time object. Note we need to convert the day, month,          $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
         # 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);  
1725      }      }
1726      # Return the result.      $options->{sql} = [0, "turn on SQL tracing"];
1727      return $retVal;      $options->{help} = [0, "display command-line options"];
1728        $options->{user} = [$tkey, "tracing key"];
1729        $options->{background} = [0, "spool standard and error output"];
1730        # Create a parsing hash from the options hash. The parsing hash
1731        # contains the default values rather than the default value
1732        # and the description. While we're at it, we'll memorize the
1733        # length of the longest option name.
1734        my $longestName = 0;
1735        my %parseOptions = ();
1736        for my $key (keys %{$options}) {
1737            if (length $key > $longestName) {
1738                $longestName = length $key;
1739  }  }
1740            $parseOptions{$key} = $options->{$key}->[0];
1741  =head3 LogErrors      }
1742        # Parse the command line.
1743  C<< Tracer::LogErrors($fileName); >>      my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1744        # Get the logfile suffix.
1745  Route the standard error output to a log file.      my $suffix = $retOptions->{user};
1746        # Check for background mode.
1747  =over 4      if ($retOptions->{background}) {
1748            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1749  =item fileName          my $errFileName = "$FIG_Config::temp/err$suffix.log";
1750            open STDOUT, ">$outFileName";
1751  Name of the file to receive the error output.          open STDERR, ">$errFileName";
1752            # Check for phone support. If we have phone support and a phone number,
1753  =back          # we want to turn it on.
1754            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1755  =cut              $retOptions->{phone} = $ENV{PHONE};
1756            }
1757  sub LogErrors {      }
1758      # Get the file name.      # Now we want to set up tracing. First, we need to know if the user
1759      my ($fileName) = @_;      # wants emergency tracing.
1760      # Open the file as the standard error output.      if ($retOptions->{trace} eq 'E') {
1761      open STDERR, '>', $fileName;          ETracing($retOptions->{user});
1762        } else {
1763            # Here the tracing is controlled from the command line.
1764            my @cats = @{$categories};
1765            if ($retOptions->{sql}) {
1766                push @cats, "SQL";
1767            }
1768            # Add the default categories.
1769            push @cats, "Tracer";
1770            # Next, we create the category string by joining the categories.
1771            my $cats = join(" ", @cats);
1772            # Check to determine whether or not the caller wants to turn off tracing
1773            # to the standard output.
1774            my $traceLevel = $retOptions->{trace};
1775            my $textOKFlag = 1;
1776            if ($traceLevel =~ /^(.)-/) {
1777                $traceLevel = $1;
1778                $textOKFlag = 0;
1779            }
1780            # Now we set up the trace mode.
1781            my $traceMode;
1782            # Verify that we can open a file in the FIG temporary directory.
1783            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1784            if (open TESTTRACE, ">$traceFileName") {
1785                # Here we can trace to a file.
1786                $traceMode = ">$traceFileName";
1787                if ($textOKFlag) {
1788                    # Echo to standard output if the text-OK flag is set.
1789                    $traceMode = "+$traceMode";
1790                }
1791                # Close the test file.
1792                close TESTTRACE;
1793            } else {
1794                # Here we can't trace to a file. Complain about this.
1795                warn "Could not open trace file $traceFileName: $!\n";
1796                # We trace to the standard output if it's
1797                # okay, and the error log otherwise.
1798                if ($textOKFlag) {
1799                    $traceMode = "TEXT";
1800                } else {
1801                    $traceMode = "WARN";
1802                }
1803            }
1804            # Now set up the tracing.
1805            TSetup("$traceLevel $cats", $traceMode);
1806        }
1807        # Check for the "help" option. If it is specified, dump the command-line
1808        # options and exit the program.
1809        if ($retOptions->{help}) {
1810            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1811            print "$1 [options] $parmHelp\n";
1812            for my $key (sort keys %{$options}) {
1813                my $name = Pad($key, $longestName, 0, ' ');
1814                my $desc = $options->{$key}->[1];
1815                if ($options->{$key}->[0]) {
1816                    $desc .= " (default " . $options->{$key}->[0] . ")";
1817                }
1818                print "  $name $desc\n";
1819            }
1820            exit(0);
1821        }
1822        # Trace the options, if applicable.
1823        if (T(3)) {
1824            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1825            Trace("Selected options: " . join(", ", sort @parms) . ".");
1826        }
1827        # Return the parsed parameters.
1828        return ($retOptions, @retParameters);
1829  }  }
1830    
1831  =head3 ReadOptions  =head3 ReadOptions
1832    
1833  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1834    
1835  Read a set of options from a file. Each option is encoded in a line of text that has the  Read a set of options from a file. Each option is encoded in a line of text that has the
1836  format  format
# Line 1069  Line 1891 
1891    
1892  =head3 GetOptions  =head3 GetOptions
1893    
1894  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1895    
1896  Merge a specified set of options into a table of defaults. This method takes two hash references  Merge a specified set of options into a table of defaults. This method takes two hash references
1897  as input and uses the data from the second to update the first. If the second does not exist,  as input and uses the data from the second to update the first. If the second does not exist,
# Line 1078  Line 1900 
1900    
1901  Consider the following example.  Consider the following example.
1902    
1903  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1904    
1905  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1906  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 1086  Line 1908 
1908  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1909  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1910    
1911  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1912    
1913  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1914    
# Line 1130  Line 1952 
1952    
1953  =head3 MergeOptions  =head3 MergeOptions
1954    
1955  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
1956    
1957  Merge default values into a hash table. This method looks at the key-value pairs in the  Merge default values into a hash table. This method looks at the key-value pairs in the
1958  second (default) hash, and if a matching key is not found in the first hash, the default  second (default) hash, and if a matching key is not found in the first hash, the default
# Line 1145  Line 1967 
1967    
1968  =item defaults  =item defaults
1969    
1970  Default values to be merged into the first hash table if they are not already present.  Default values to be merged into the first hash table if they are not already present.
1971    
1972  =back  =back
1973    
1974  =cut  =cut
1975    
1976  sub MergeOptions {  sub MergeOptions {
1977      # Get the parameters.      # Get the parameters.
1978      my ($table, $defaults) = @_;      my ($table, $defaults) = @_;
1979      # Loop through the defaults.      # Loop through the defaults.
1980      while (my ($key, $value) = each %{$defaults}) {      while (my ($key, $value) = each %{$defaults}) {
1981          if (!exists $table->{$key}) {          if (!exists $table->{$key}) {
1982              $table->{$key} = $value;              $table->{$key} = $value;
         }  
     }  
 }  
   
 =head3 Trace  
   
 C<< Trace($message); >>  
   
 Write a trace message to the target location specified in L</TSetup>. If there has not been  
 any prior call to B<TSetup>.  
   
 =over 4  
   
 =item message  
   
 Message to write.  
   
 =back  
   
 =cut  
   
 sub Trace {  
     # Get the parameters.  
     my ($message) = @_;  
     # Get the timestamp.  
     my $timeStamp = Now();  
     # Format the message. Note we strip off any line terminators at the end.  
     my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);  
     # Process according to the destination.  
     if ($Destination eq "TEXT") {  
         # Write the message to the standard output.  
         print "$formatted\n";  
     } elsif ($Destination eq "ERROR") {  
         # Write the message to the error output.  
         print STDERR "$formatted\n";  
     } elsif ($Destination eq "QUEUE") {  
         # Push the message into the queue.  
         push @Queue, "$formatted";  
     } elsif ($Destination eq "HTML") {  
         # Convert the message to HTML and write it to the standard output.  
         my $escapedMessage = CGI::escapeHTML($message);  
         print "<p>$formatted</p>\n";  
     } elsif ($Destination eq "WARN") {  
        # Emit the message as a warning.  
        warn $message;  
     } elsif ($Destination =~ m/^>>/) {  
         # Write the trace message to an output file.  
         (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";  
         print TRACING "$formatted\n";  
         close TRACING;  
         # If the Tee flag is on, echo it to the standard output.  
         if ($TeeFlag) {  
             print "$formatted\n";  
         }  
     }  
 }  
   
 =head3 T  
   
 C<< my $switch = T($category, $traceLevel); >>  
   
     or  
   
 C<< my $switch = T($traceLevel); >>  
   
 Return TRUE if the trace level is at or above a specified value and the specified category  
 is active, else FALSE. If no category is specified, the caller's package name is used.  
   
 =over 4  
   
 =item category  
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
   
 Relevant tracing level.  
   
 =item RETURN  
   
 TRUE if a message at the specified trace level would appear in the trace, else FALSE.  
   
 =back  
   
 =cut  
   
 sub T {  
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
         # Get the parameters.  
         my ($category, $traceLevel) = @_;  
         if (!defined $traceLevel) {  
             # Here we have no category, so we need to get the calling package.  
             # The calling package is normally the first parameter. If it is  
             # omitted, the first parameter will be the tracelevel. So, the  
             # first thing we do is shift the so-called category into the  
             # $traceLevel variable where it belongs.  
             $traceLevel = $category;  
             my ($package, $fileName, $line) = caller;  
             # If there is no calling package, we default to "main".  
             if (!$package) {  
                 $category = "main";  
             } else {  
                 $category = $package;  
             }  
         }  
         # Save the category name.  
         $LastCategory = $category;  
         # Convert it to lower case before we hash it.  
         $category = lc $category;  
         # Use the category and tracelevel to compute the result.  
         if (ref $traceLevel) {  
             Confess("Bad trace level.");  
         } elsif (ref $TraceLevel) {  
             Confess("Bad trace config.");  
1983          }          }
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
1984      }      }
     # Return the computed result.  
     return $retVal;  
1985  }  }
1986    
1987  =head3 ParseCommand  =head3 ParseCommand
1988    
1989  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1990    
1991  Parse a command line consisting of a list of parameters. The initial parameters may be option  Parse a command line consisting of a list of parameters. The initial parameters may be option
1992  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1993  off and merged into a table of default options. The remainder of the command line is  off and merged into a table of default options. The remainder of the command line is
1994  returned as a list of positional arguments. For example, consider the following invocation.  returned as a list of positional arguments. For example, consider the following invocation.
1995    
1996  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1997    
1998  In this case, the list @words will be treated as a command line and there are two options available,  In this case, the list @words will be treated as a command line and there are two options available,
1999  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
2000    
2001  C<< -logFile=error.log apple orange rutabaga >>      -logFile=error.log apple orange rutabaga
2002    
2003  then at the end of the invocation, C<$options> will be  then at the end of the invocation, C<$options> will be
2004    
2005  C<< { errors => 0, logFile => 'error.log' } >>      { errors => 0, logFile => 'error.log' }
2006    
2007  and C<@arguments> will contain  and C<@arguments> will contain
2008    
2009  C<< apple orange rutabaga >>      apple orange rutabaga
2010    
2011  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2012  support for quote characters. Options can be specified with single or double hyphens.  support for quote characters. Options can be specified with single or double hyphens.
# Line 1356  Line 2057 
2057          push @retVal, UnEscape($inputParm);          push @retVal, UnEscape($inputParm);
2058      }      }
2059      # Return the results.      # Return the results.
2060      return ($optionTable, @retVal);      return ($optionTable, @retVal);
 }  
   
 =head3 Escape  
   
 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  
   
 String to escape.  
   
 =item RETURN  
   
 Escaped equivalent of the real string.  
   
 =back  
   
 =cut  
   
 sub Escape {  
     # 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;  
 }  
   
 =head3 UnEscape  
   
 C<< my $realString = Tracer::UnEscape($codedString); >>  
   
 Replace escape sequences with their actual equivalents. C<\t> will be replaced by  
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
   
 =over 4  
   
 =item codedString  
   
 String to un-escape.  
   
 =item RETURN  
   
 Returns a copy of the original string with the escape sequences converted to their actual  
 values.  
   
 =back  
   
 =cut  
   
 sub UnEscape {  
     # Get the parameter.  
     my ($codedString) = @_;  
     # Initialize the return variable.  
     my $retVal = "";  
     # Only proceed if the incoming string is nonempty.  
     if (defined $codedString) {  
         # Loop through the parameter string, looking for escape sequences. We can't do  
         # translating because it causes problems with the escaped slash. ("\\t" becomes  
         # "\<tab>" no matter what we do.)  
         while (length $codedString > 0) {  
             # Look for the first escape sequence.  
             if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {  
                 # Here we found it. The text preceding the sequence is in $1. The sequence  
                 # itself is in $2. First, move the clear text to the return variable.  
                 $retVal .= $1;  
                 $codedString = substr $codedString, (2 + length $1);  
                 # Get the escape value.  
                 my $char = $2;  
                 # If we have a "\r", we are done.  
                 if ($char ne 'r') {  
                     # Here it's not an 'r', so we convert it.  
                     $char =~ tr/\\tn/\\\t\n/;  
                     $retVal .= $char;  
                 }  
             } else {  
                 # Here there are no more escape sequences. The rest of the string is  
                 # transferred unmodified.  
                 $retVal .= $codedString;  
                 $codedString = "";  
             }  
         }  
     }  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 ParseRecord  
   
 C<< my @fields = Tracer::ParseRecord($line); >>  
   
 Parse a tab-delimited data line. The data line is split into field values. Embedded tab  
 and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
 These will automatically be converted.  
   
 =over 4  
   
 =item line  
   
 Line of data containing the tab-delimited fields.  
   
 =item RETURN  
   
 Returns a list of the fields found in the data line.  
   
 =back  
   
 =cut  
   
 sub ParseRecord {  
     # Get the parameter.  
     my ($line) = @_;  
     # Remove the trailing new-line, if any.  
     chomp $line;  
     # Split the line read into pieces using the tab character.  
     my @retVal = split /\t/, $line;  
     # 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;  
     }  
     # Return the result.  
     return @retVal;  
 }  
   
 =head3 Merge  
   
 C<< my @mergedList = Tracer::Merge(@inputList); >>  
   
 Sort a list of strings and remove duplicates.  
   
 =over 4  
   
 =item inputList  
   
 List of scalars to sort and merge.  
   
 =item RETURN  
   
 Returns a list containing the same elements sorted in ascending order with duplicates  
 removed.  
   
 =back  
   
 =cut  
   
 sub Merge {  
     # Get the input list in sort order.  
     my @inputList = sort @_;  
     # Only proceed if the list has at least two elements.  
     if (@inputList > 1) {  
         # Now we want to move through the list splicing out duplicates.  
         my $i = 0;  
         while ($i < @inputList) {  
             # Get the current entry.  
             my $thisEntry = $inputList[$i];  
             # Find out how many elements duplicate the current entry.  
             my $j = $i + 1;  
             my $dup1 = $i + 1;  
             while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };  
             # If the number is nonzero, splice out the duplicates found.  
             if ($j > $dup1) {  
                 splice @inputList, $dup1, $j - $dup1;  
             }  
             # Now the element at position $dup1 is different from the element before it  
             # at position $i. We push $i forward one position and start again.  
             $i++;  
         }  
     }  
     # Return the merged list.  
     return @inputList;  
 }  
   
 =head3 Percent  
   
 C<< my $percent = Tracer::Percent($number, $base); >>  
   
 Returns the percent of the base represented by the given number. If the base  
 is zero, returns zero.  
   
 =over 4  
   
 =item number  
   
 Percent numerator.  
   
 =item base  
   
 Percent base.  
   
 =item RETURN  
   
 Returns the percentage of the base represented by the numerator.  
   
 =back  
   
 =cut  
   
 sub Percent {  
     # Get the parameters.  
     my ($number, $base) = @_;  
     # Declare the return variable.  
     my $retVal = 0;  
     # Compute the percent.  
     if ($base != 0) {  
         $retVal = $number * 100 / $base;  
     }  
     # Return the result.  
     return $retVal;  
2061  }  }
2062    
2063    
2064    =head2 File Utility Methods
2065    
2066  =head3 GetFile  =head3 GetFile
2067    
2068  C<< my @fileContents = Tracer::GetFile($fileName); >>      my @fileContents = Tracer::GetFile($fileName);
2069    
2070      or      or
2071    
2072  C<< my $fileContents = Tracer::GetFile($fileName); >>      my $fileContents = Tracer::GetFile($fileName);
2073    
2074  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
2075  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 2119 
2119    
2120  =head3 PutFile  =head3 PutFile
2121    
2122  C<< Tracer::PutFile($fileName, \@lines); >>      Tracer::PutFile($fileName, \@lines);
2123    
2124  Write out a file from a list of lines of text.  Write out a file from a list of lines of text.
2125    
# Line 1704  Line 2162 
2162      close $handle;      close $handle;
2163  }  }
2164    
2165  =head3 QTrace  =head3 ParseRecord
2166    
2167  C<< my $data = QTrace($format); >>      my @fields = Tracer::ParseRecord($line);
2168    
2169  Return the queued trace data in the specified format.  Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2170    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2171    These will automatically be converted.
2172    
2173  =over 4  =over 4
2174    
2175  =item format  =item line
2176    
2177  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Line of data containing the tab-delimited fields.
2178    
2179    =item RETURN
2180    
2181    Returns a list of the fields found in the data line.
2182    
2183  =back  =back
2184    
2185  =cut  =cut
2186    
2187  sub QTrace {  sub ParseRecord {
2188      # Get the parameter.      # Get the parameter.
2189      my ($format) = @_;      my ($line) = @_;
2190      # Create the return variable.      # Remove the trailing new-line, if any.
2191      my $retVal = "";      chomp $line;
2192      # Only proceed if there is an actual queue.      # Split the line read into pieces using the tab character.
2193      if (@Queue) {      my @retVal = split /\t/, $line;
2194          # Process according to the format.      # Trim and fix the escapes in each piece.
2195          if ($format =~ m/^HTML$/i) {      for my $value (@retVal) {
2196              # Convert the queue into an HTML list.          # Trim leading whitespace.
2197              $retVal = "<ul>\n";          $value =~ s/^\s+//;
2198              for my $line (@Queue) {          # Trim trailing whitespace.
2199                  my $escapedLine = CGI::escapeHTML($line);          $value =~ s/\s+$//;
2200                  $retVal .= "<li>$escapedLine</li>\n";          # Delete the carriage returns.
2201              }          $value =~ s/\r//g;
2202              $retVal .= "</ul>\n";          # Convert the escapes into their real values.
2203          } elsif ($format =~ m/^TEXT$/i) {          $value =~ s/\\t/"\t"/ge;
2204              # Convert the queue into a list of text lines.          $value =~ s/\\n/"\n"/ge;
             $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
2205      }      }
2206      # Return the formatted list.      # Return the result.
2207      return $retVal;      return @retVal;
2208  }  }
2209    
2210  =head3 Confess  =head3 Merge
2211    
2212  C<< Confess($message); >>      my @mergedList = Tracer::Merge(@inputList);
2213    
2214  Trace the call stack and abort the program with the specified message. When used with  Sort a list of strings and remove duplicates.
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
2215    
2216  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
2217    
2218  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item inputList
2219    
2220  =over 4  List of scalars to sort and merge.
2221    
2222  =item message  =item RETURN
2223    
2224  Message to include in the trace.  Returns a list containing the same elements sorted in ascending order with duplicates
2225    removed.
2226    
2227  =back  =back
2228    
2229  =cut  =cut
2230    
2231  sub Confess {  sub Merge {
2232      # Get the parameters.      # Get the input list in sort order.
2233      my ($message) = @_;      my @inputList = sort @_;
2234      # Trace the call stack.      # Only proceed if the list has at least two elements.
2235      Cluck($message);      if (@inputList > 1) {
2236      # Abort the program.          # Now we want to move through the list splicing out duplicates.
2237      croak(">>> $message");          my $i = 0;
2238            while ($i < @inputList) {
2239                # Get the current entry.
2240                my $thisEntry = $inputList[$i];
2241                # Find out how many elements duplicate the current entry.
2242                my $j = $i + 1;
2243                my $dup1 = $i + 1;
2244                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2245                # If the number is nonzero, splice out the duplicates found.
2246                if ($j > $dup1) {
2247                    splice @inputList, $dup1, $j - $dup1;
2248                }
2249                # Now the element at position $dup1 is different from the element before it
2250                # at position $i. We push $i forward one position and start again.
2251                $i++;
2252            }
2253        }
2254        # Return the merged list.
2255        return @inputList;
2256  }  }
2257    
2258  =head3 Assert  =head3 Open
2259    
2260  C<< Assert($condition1, $condition2, ... $conditionN); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2261    
2262  Return TRUE if all the conditions are true. This method can be used in conjunction with  Open a file.
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
2263    
2264  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2265    function. The mode is specified using Unix-like shell information. So, for
2266    example,
2267    
2268  Will abort the program with a stack trace if the value of C<$recNum> is negative.      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2269    
2270  =cut  would open for output appended to the specified file, and
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
2271    
2272  =head3 Cluck      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2273    
2274  C<< Cluck($message); >>  would open a pipe that sorts the records written and removes duplicates. Note
2275    the use of file handle syntax in the Open call. To use anonymous file handles,
2276    code as follows.
2277    
2278  Trace the call stack. Note that for best results, you should qualify the call with a      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
 trace condition. For example,  
2279    
2280  C<< Cluck("Starting record parse.") if T(3); >>  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2281    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2282    failed open will throw an exception and the third parameter will be used to construct
2283    an error message. If the parameter is omitted, a standard message is constructed
2284    using the file spec.
2285    
2286  will only trace the stack if the trace level for the package is 3 or more.      Could not open "/usr/spool/news/twitlog"
2287    
2288    Note that the mode characters are automatically cleaned from the file name.
2289    The actual error message from the file system will be captured and appended to the
2290    message in any case.
2291    
2292        Could not open "/usr/spool/news/twitlog": file not found.
2293    
2294    In some versions of PERL the only error message we get is a number, which
2295    corresponds to the C++ C<errno> value.
2296    
2297        Could not open "/usr/spool/news/twitlog": 6.
2298    
2299  =over 4  =over 4
2300    
2301  =item message  =item fileHandle
2302    
2303  Message to include in the trace.  File handle. If this parameter is C<undef>, a file handle will be generated
2304    and returned as the value of this method.
2305    
2306    =item fileSpec
2307    
2308    File name and mode, as per the PERL C<open> function.
2309    
2310    =item message (optional)
2311    
2312    Error message to use if the open fails. If omitted, a standard error message
2313    will be generated. In either case, the error information from the file system
2314    is appended to the message. To specify a conditional open that does not throw
2315    an error if it fails, use C<0>.
2316    
2317    =item RETURN
2318    
2319    Returns the name of the file handle assigned to the file, or C<undef> if the
2320    open failed.
2321    
2322  =back  =back
2323    
2324  =cut  =cut
2325    
2326  sub Cluck {  sub Open {
2327      # Get the parameters.      # Get the parameters.
2328      my ($message) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2329      # Trace what's happening.      # Attempt to open the file.
2330      Trace("Stack trace for event: $message");      my $rv = open $fileHandle, $fileSpec;
2331      my $confession = longmess($message);      # If the open failed, generate an error message.
2332      # Convert the confession to a series of trace messages. Note we skip any      if (! $rv) {
2333      # messages relating to calls into Tracer.          # Save the system error message.
2334      for my $line (split /\s*\n/, $confession) {          my $sysMessage = $!;
2335          Trace($line) if ($line !~ /Tracer\.pm/);          # See if we need a default message.
2336            if (!$message) {
2337                # Clean any obvious mode characters and leading spaces from the
2338                # filename.
2339                my ($fileName) = FindNamePart($fileSpec);
2340                $message = "Could not open \"$fileName\"";
2341            }
2342            # Terminate with an error using the supplied message and the
2343            # error message from the file system.
2344            Confess("$message: $!");
2345      }      }
2346        # Return the file handle.
2347        return $fileHandle;
2348  }  }
2349    
2350  =head3 Min  =head3 FindNamePart
2351    
2352  C<< my $min = Min($value1, $value2, ... $valueN); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2353    
2354  Return the minimum argument. The arguments are treated as numbers.  Extract the portion of a file specification that contains the file name.
2355    
2356    A file specification is the string passed to an C<open> call. It specifies the file
2357    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2358    method assumes that the file name is whatever follows the first angle bracket
2359    sequence.  So, for example, in the following strings the file name is
2360    C</usr/fig/myfile.txt>.
2361    
2362        >>/usr/fig/myfile.txt
2363        </usr/fig/myfile.txt
2364        | sort -u > /usr/fig/myfile.txt
2365    
2366    If the method cannot find a file name using its normal methods, it will return the
2367    whole incoming string.
2368    
2369  =over 4  =over 4
2370    
2371  =item $value1, $value2, ... $valueN  =item fileSpec
2372    
2373  List of numbers to compare.  File specification string from which the file name is to be extracted.
2374    
2375  =item RETURN  =item RETURN
2376    
2377  Returns the lowest number in the list.  Returns a three-element list. The first element contains the file name portion of
2378    the specified string, or the whole string if a file name cannot be found via normal
2379    methods. The second element contains the start position of the file name portion and
2380    the third element contains the length.
2381    
2382    =back
2383    
2384    =cut
2385    #: Return Type $;
2386    sub FindNamePart {
2387        # Get the parameters.
2388        my ($fileSpec) = @_;
2389        # Default to the whole input string.
2390        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2391        # Parse out the file name if we can.
2392        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2393            $retVal = $2;
2394            $len = length $retVal;
2395            $pos = (length $fileSpec) - (length $3) - $len;
2396        }
2397        # Return the result.
2398        return ($retVal, $pos, $len);
2399    }
2400    
2401    =head3 OpenDir
2402    
2403        my @files = OpenDir($dirName, $filtered, $flag);
2404    
2405    Open a directory and return all the file names. This function essentially performs
2406    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2407    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2408    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2409    filtered out of the return list. If the directory does not open and I<$flag> is not
2410    set, an exception is thrown. So, for example,
2411    
2412  =back      my @files = OpenDir("/Volumes/fig/contigs", 1);
2413    
2414  =cut  is effectively the same as
2415    
2416  sub Min {      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2417      # 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 lowest.  
     for my $value (@values) {  
         if ($value < $retVal) {  
             $retVal = $value;  
         }  
     }  
     # Return the minimum found.  
     return $retVal;  
 }  
2418    
2419  =head3 Max  Similarly, the following code
2420    
2421  C<< my $max = Max($value1, $value2, ... $valueN); >>      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2422    
2423  Return the maximum argument. The arguments are treated as numbers.  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2424    automatically returns an empty list if the directory fails to open.
2425    
2426  =over 4  =over 4
2427    
2428  =item $value1, $value2, ... $valueN  =item dirName
2429    
2430  List of numbers to compare.  Name of the directory to open.
2431    
2432  =item RETURN  =item filtered
2433    
2434  Returns the highest number in the list.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2435    from the list, else FALSE.
2436    
2437    =item flag
2438    
2439    TRUE if a failure to open is okay, else FALSE
2440    
2441  =back  =back
2442    
2443  =cut  =cut
2444    #: Return Type @;
2445  sub Max {  sub OpenDir {
2446      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2447      my ($retVal, @values) = @_;      my ($dirName, $filtered, $flag) = @_;
2448      # Loop through the remaining parameters, looking for the highest.      # Declare the return variable.
2449      for my $value (@values) {      my @retVal = ();
2450          if ($value > $retVal) {      # Open the directory.
2451              $retVal = $value;      if (opendir(my $dirHandle, $dirName)) {
2452            # The directory opened successfully. Get the appropriate list according to the
2453            # strictures of the filter parameter.
2454            if ($filtered) {
2455                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2456            } else {
2457                @retVal = readdir $dirHandle;
2458          }          }
2459        } elsif (! $flag) {
2460            # Here the directory would not open and it's considered an error.
2461            Confess("Could not open directory $dirName.");
2462      }      }
2463      # Return the maximum found.      # Return the result.
2464      return $retVal;      return @retVal;
2465  }  }
2466    
 =head3 AddToListMap  
   
 C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>  
2467    
2468  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  =head3 Insure
 is created for the key. Otherwise, the new value is pushed onto the list.  
2469    
2470  =over 4      Insure($dirName, $chmod);
2471    
2472  =item hash  Insure a directory is present.
2473    
2474  Reference to the target hash.  =over 4
2475    
2476  =item key  =item dirName
2477    
2478  Key for which the value is to be added.  Name of the directory to check. If it does not exist, it will be created.
2479    
2480  =item value1, value2, ... valueN  =item chmod (optional)
2481    
2482  List of values to add to the key's value list.  Security privileges to be given to the directory if it is created.
2483    
2484  =back  =back
2485    
2486  =cut  =cut
2487    
2488  sub AddToListMap {  sub Insure {
2489      # Get the parameters.      my ($dirName, $chmod) = @_;
2490      my ($hash, $key, @values) = @_;      if (! -d $dirName) {
2491      # Process according to whether or not the key already has a value.          Trace("Creating $dirName directory.") if T(2);
2492      if (! exists $hash->{$key}) {          eval {
2493          $hash->{$key} = [@values];              mkpath $dirName;
2494      } else {              # If we have permissions specified, set them here.
2495          push @{$hash->{$key}}, @values;              if (defined($chmod)) {
2496                    chmod $chmod, $dirName;
2497      }      }
2498            };
2499            if ($@) {
2500                Confess("Error creating $dirName: $@");
2501  }  }
   
 =head3 DebugMode  
   
 C<< if (Tracer::DebugMode) { ...code... } >>  
   
 Return TRUE if debug mode has been turned on, else abort.  
   
 Certain CGI scripts are too dangerous to exist in the production  
 environment. This method provides a simple way to prevent them  
 from working unless they are explicitly turned on by creating a password  
 cookie via the B<SetPassword> script.  If debugging mode  
 is not turned on, an error will occur.  
   
 =cut  
   
 sub DebugMode {  
     # Declare the return variable.  
     my $retVal = 0;  
     # Check the debug configuration.  
     my $password = CGI::cookie("DebugMode");  
     my $encrypted = Digest::MD5::md5_hex($password);  
     if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {  
         $retVal = 1;  
     } else {  
         # Here debug mode is off, so we generate an error.  
         Confess("Cannot use this facility without logging in.");  
2502      }      }
     # Return the determination indicator.  
     return $retVal;  
2503  }  }
2504    
2505  =head3 Strip  =head3 ChDir
2506    
2507  C<< my $string = Tracer::Strip($line); >>      ChDir($dirName);
2508    
2509  Strip all line terminators off a string. This is necessary when dealing with files  Change to the specified directory.
 that may have been transferred back and forth several times among different  
 operating environments.  
2510    
2511  =over 4  =over 4
2512    
2513  =item line  =item dirName
   
 Line of text to be stripped.  
   
 =item RETURN  
2514    
2515  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.
2516    
2517  =back  =back
2518    
2519  =cut  =cut
2520    
2521  sub Strip {  sub ChDir {
2522      # Get a copy of the parameter string.      my ($dirName) = @_;
2523      my ($string) = @_;      if (! -d $dirName) {
2524      my $retVal = (defined $string ? $string : "");          Confess("Cannot change to directory $dirName: no such directory.");
2525      # Strip the line terminator characters.      } else {
2526      $retVal =~ s/(\r|\n)+$//g;          Trace("Changing to directory $dirName.") if T(File => 4);
2527      # Return the result.          my $okFlag = chdir $dirName;
2528      return $retVal;          if (! $okFlag) {
2529                Confess("Error switching to directory $dirName.");
2530            }
2531        }
2532  }  }
2533    
2534  =head3 Pad  =head3 SetPermissions
2535    
2536  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2537    
2538  Pad a string to a specified length. The pad character will be a  Set the permissions for a directory and all the files and folders inside it.
2539  space, and the padding will be on the right side unless specified  In addition, the group ownership will be changed to the specified value.
2540  in the third parameter.  
2541    This method is more vulnerable than most to permission and compatability
2542    problems, so it does internal error recovery.
2543    
2544  =over 4  =over 4
2545    
2546  =item string  =item dirName
2547    
2548  String to be padded.  Name of the directory to process.
2549    
2550  =item len  =item group
2551    
2552  Desired length of the padded string.  Name of the group to be assigned.
2553    
2554  =item left (optional)  =item mask
2555    
2556  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  Permission mask. Bits that are C<1> in this mask will be ORed into the
2557    permission bits of any file or directory that does not already have them
2558    set to 1.
2559    
2560  =item padChar (optional)  =item otherMasks
2561    
2562  Character to use for padding. The default is a space.  Map of search patterns to permission masks. If a directory name matches
2563    one of the patterns, that directory and all its members and subdirectories
2564    will be assigned the new pattern. For example, the following would
2565    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2566    
2567  =item RETURN      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2568    
2569  Returns a copy of the original string with the pad character added to the  The list is ordered, so the following would use 0777 for C<tmp1> and
2570  specified end so that it achieves the desired length.  0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2571    
2572        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2573                                                       '^tmp' => 0666);
2574    
2575    Note that the pattern matches are all case-insensitive, and only directory
2576    names are matched, not file names.
2577    
2578  =back  =back
2579    
2580  =cut  =cut
2581    
2582  sub Pad {  sub SetPermissions {
2583      # Get the parameters.      # Get the parameters.
2584      my ($string, $len, $left, $padChar) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2585      # Compute the padding character.      # Set up for error recovery.
2586      if (! defined $padChar) {      eval {
2587          $padChar = " ";          # Switch to the specified directory.
2588            ChDir($dirName);
2589            # Get the group ID.
2590            my $gid = getgrnam($group);
2591            # Get the mask for tracing.
2592            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2593            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2594            my $fixCount = 0;
2595            my $lookCount = 0;
2596            # @dirs will be a stack of directories to be processed.
2597            my @dirs = (getcwd());
2598            while (scalar(@dirs) > 0) {
2599                # Get the current directory.
2600                my $dir = pop @dirs;
2601                # Check for a match to one of the specified directory names. To do
2602                # that, we need to pull the individual part of the name off of the
2603                # whole path.
2604                my $simpleName = $dir;
2605                if ($dir =~ m!/([^/]+)$!) {
2606                    $simpleName = $1;
2607      }      }
2608      # Compute the number of spaces needed.              Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2609      my $needed = $len - length $string;              # Search for a match.
2610      # Copy the string into the return variable.              my $match = 0;
2611      my $retVal = $string;              my $i;
2612      # Only proceed if padding is needed.              for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2613      if ($needed > 0) {                  my $pattern = $otherMasks[$i];
2614          # Create the pad string.                  if ($simpleName =~ /$pattern/i) {
2615          my $pad = $padChar x $needed;                      $match = 1;
2616          # Affix it to the return value.                  }
2617          if ($left) {              }
2618              $retVal = $pad . $retVal;              # Check for a match. Note we use $i-1 because the loop added 2
2619                # before terminating due to the match.
2620                if ($match && $otherMasks[$i-1] != $mask) {
2621                    # This directory matches one of the incoming patterns, and it's
2622                    # a different mask, so we process it recursively with that mask.
2623                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2624          } else {          } else {
2625              $retVal .= $pad;                  # Here we can process normally. Get all of the non-hidden members.
2626                    my @submems = OpenDir($dir, 1);
2627                    for my $submem (@submems) {
2628                        # Get the full name.
2629                        my $thisMem = "$dir/$submem";
2630                        Trace("Checking member $thisMem.") if T(4);
2631                        $lookCount++;
2632                        if ($lookCount % 1000 == 0) {
2633                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2634                        }
2635                        # Fix the group.
2636                        chown -1, $gid, $thisMem;
2637                        # Insure this member is not a symlink.
2638                        if (! -l $thisMem) {
2639                            # Get its info.
2640                            my $fileInfo = stat $thisMem;
2641                            # Only proceed if we got the info. Otherwise, it's a hard link
2642                            # and we want to skip it anyway.
2643                            if ($fileInfo) {
2644                                my $fileMode = $fileInfo->mode;
2645                                if (($fileMode & $mask) != $mask) {
2646                                    # Fix this member.
2647                                    $fileMode |= $mask;
2648                                    chmod $fileMode, $thisMem;
2649                                    $fixCount++;
2650                                }
2651                                # If it's a subdirectory, stack it.
2652                                if (-d $thisMem) {
2653                                    push @dirs, $thisMem;
2654          }          }
2655      }      }
     # Return the result.  
     return $retVal;  
2656  }  }
   
 =head3 EOF  
   
 This is a constant that is lexically greater than any useful string.  
   
 =cut  
   
 sub EOF {  
     return "\xFF\xFF\xFF\xFF\xFF";  
2657  }  }
   
 =head3 TICK  
   
 C<< my @results = TICK($commandString); >>  
   
 Perform a back-tick operation on a command. If this is a Windows environment, any leading  
 dot-slash (C<./> will be removed. So, for example, if you were doing  
   
     `./protein.cgi`  
   
 from inside a CGI script, it would work fine in Unix, but would issue an error message  
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
   
     TICK("./protein.cgi")  
   
 it will work correctly in both environments.  
   
 =over 4  
   
 =item commandString  
   
 The command string to pass to the system.  
   
 =item RETURN  
   
 Returns the standard output from the specified command, as a list.  
   
 =back  
   
 =cut  
 #: Return Type @;  
 sub TICK {  
     # Get the parameters.  
     my ($commandString) = @_;  
     # Chop off the dot-slash if this is Windows.  
     if ($FIG_Config::win_mode) {  
         $commandString =~ s!^\./!!;  
2658      }      }
2659      # Activate the command and return the result.          }
2660      return `$commandString`;          Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2661        };
2662        # Check for an error.
2663        if ($@) {
2664            Confess("SetPermissions error: $@");
2665        }
2666  }  }
2667    
2668  =head3 ScriptSetup  =head3 GetLine
   
 C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  
2669    
2670  Perform standard tracing and debugging setup for scripts. The value returned is      my @data = Tracer::GetLine($handle);
 the CGI object followed by a pre-built variable hash. At the end of the script,  
 the client should call L</ScriptFinish> to output the web page.  
2671    
2672  This method calls L</ETracing> to configure tracing, which allows the tracing  Read a line of data from a tab-delimited file.
 to be configured via the emergency tracing form on the debugging control panel.  
 Tracing will then be turned on automatically for all programs that use the L</ETracing>  
 method, which includes every program that uses this method or L</StandardSetup>.  
2673    
2674  =over 4  =over 4
2675    
2676  =item noTrace (optional)  =item handle
2677    
2678  If specified, tracing will be suppressed. This is useful if the script wants to set up  Open file handle from which to read.
 tracing manually.  
2679    
2680  =item RETURN  =item RETURN
2681    
2682  Returns a two-element list consisting of a CGI query object and a variable hash for  Returns a list of the fields in the record read. The fields are presumed to be
2683  the output page.  tab-delimited. If we are at the end of the file, then an empty list will be
2684    returned. If an empty line is read, a single list item consisting of a null
2685    string will be returned.
2686    
2687  =back  =back
2688    
2689  =cut  =cut
2690    
2691  sub ScriptSetup {  sub GetLine {
2692      # Get the parameters.      # Get the parameters.
2693      my ($noTrace) = @_;      my ($handle) = @_;
2694      # Get the CGI query object.      # Declare the return variable.
2695      my $cgi = CGI->new();      my @retVal = ();
2696      # Set up tracing if it's not suppressed.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2697      ETracing($cgi) unless $noTrace;      # Read from the file.
2698      # Create the variable hash.      my $line = <$handle>;
2699      my $varHash = { results => '' };      # Only proceed if we found something.
2700      # Return the query object and variable hash.      if (defined $line) {
2701      return ($cgi, $varHash);          # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2702            # upload control and have a nonstandard EOL combination.
2703            $line =~ s/(\r|\n)+$//;
2704            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2705            if (T(File => 4)) {
2706                my $escapedLine = $line;
2707                $escapedLine =~ s/\n/\\n/g;
2708                $escapedLine =~ s/\r/\\r/g;
2709                $escapedLine =~ s/\t/\\t/g;
2710                Trace("Line read: -->$escapedLine<--");
2711  }  }
2712            # If the line is empty, return a single empty string; otherwise, parse
2713  =head3 ETracing          # it into fields.
2714            if ($line eq "") {
2715  C<< ETracing($parameter); >>              push @retVal, "";
   
 Set up emergency tracing. Emergency tracing is tracing that is turned  
 on automatically for any program that calls this method. The emergency  
 tracing parameters are stored in a a file identified by a tracing key.  
 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.  
   
 =over 4  
   
 =item parameter  
   
 A parameter from which the tracing key is computed. If it is a scalar,  
 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.  
   
 =back  
   
 =cut  
   
 sub ETracing {  
     # Get the parameter.  
     my ($parameter) = @_;  
     # Check for CGI mode.  
     my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);  
     # Default to no tracing except errors.  
     my ($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 $emergencyFile;  
2716          } else {          } else {
2717              # Emergency tracing is on. Pull off the destination and              push @retVal, split /\t/,$line;
             # the trace level;  
             $dest = shift @tracing;  
             my $level = shift @tracing;  
             # Convert the destination to a real tracing destination.  
             # temp directory.  
             $dest = EmergencyTracingDest($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 = $cgi->param('Trace') . " Tracer";  
         }  
2718      }      }
2719      # Setup the tracing we've determined from all the stuff above.      } else {
2720      TSetup($tracing, $dest);          # Trace the reason the read failed.
2721      # If we're a web script, trace the parameter and environment data.          Trace("End of file: $!") if T(File => 3);
     if (defined $cgi) {  
         TraceParms($cgi);  
2722      }      }
2723        # Return the result.
2724        return @retVal;
2725  }  }
2726    
2727  =head3 EmergencyFileName  =head3 PutLine
2728    
2729  C<< my $fileName = Tracer::EmergencyFileName($tkey); >>      Tracer::PutLine($handle, \@fields, $eol);
2730    
2731  Return the emergency tracing file name. This is the file that specifies  Write a line of data to a tab-delimited file. The specified field values will be
2732  the tracing information.  output in tab-separated form, with a trailing new-line.
2733    
2734  =over 4  =over 4
2735    
2736  =item tkey  =item handle
2737    
2738  Tracing key for the current program.  Output file handle.
2739    
2740  =item RETURN  =item fields
2741    
2742  Returns the name of the file to contain the emergency tracing information.  List of field values.
2743    
2744    =item eol (optional)
2745    
2746    End-of-line character (default is "\n").
2747    
2748  =back  =back
2749    
2750  =cut  =cut
2751    
2752  sub EmergencyFileName {  sub PutLine {
2753      # Get the parameters.      # Get the parameters.
2754      my ($tkey) = @_;      my ($handle, $fields, $eol) = @_;
2755      # Compute the emergency tracing file name.      # Write the data.
2756      return "$FIG_Config::temp/Emergency$tkey.txt";      print $handle join("\t", @{$fields}) . ($eol || "\n");
2757  }  }
2758    
 =head3 EmergencyFileTarget  
   
 C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>  
2759    
2760  Return the emergency tracing target file name. This is the file that receives  =head3 PrintLine
 the tracing output for file-based tracing.  
2761    
2762  =over 4      Tracer::PrintLine($line);
2763    
2764  =item tkey  Print a line of text with a trailing new-line.
2765    
2766  Tracing key for the current program.  =over 4
2767    
2768  =item RETURN  =item line
2769    
2770  Returns the name of the file to contain the trace output.  Line of text to print.
2771    
2772  =back  =back
2773    
2774  =cut  =cut
2775    
2776  sub EmergencyFileTarget {  sub PrintLine {
2777      # Get the parameters.      # Get the parameters.
2778      my ($tkey) = @_;      my ($line) = @_;
2779      # Compute the emergency tracing file name.      # Print the line.
2780      return "$FIG_Config::temp/trace$tkey.log";      print "$line\n";
2781  }  }
2782    
 =head3 EmergencyTracingDest  
2783    
2784  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>  =head2 Other Useful Methods
2785    
2786  This method converts an emergency tracing destination to a real  =head3 ParseParm
 tracing destination. The main difference is that if the  
 destination is C<FILE> or C<APPEND>, we convert it to file  
 output. If the destination is C<DUAL>, we convert it to file  
 and standard output.  
2787    
2788  =over 4      my $listValue = Tracer::ParseParm($string);
2789    
2790  =item tkey  Convert a parameter into a list reference. If the parameter is undefined,
2791    an undefined value will be returned. Otherwise, it will be parsed as a
2792    comma-separated list of values.
2793    
2794  Tracing key for this environment.  =over 4
2795    
2796  =item myDest  =item string
2797    
2798  Destination from the emergency tracing file.  Incoming string.
2799    
2800  =item RETURN  =item RETURN
2801    
2802  Returns a destination that can be passed into L</TSetup>.  Returns a reference to a list of values, or C<undef> if the incoming value
2803    was undefined.
2804    
2805  =back  =back
2806    
2807  =cut  =cut
2808    
2809  sub EmergencyTracingDest {  sub ParseParm {
2810      # Get the parameters.      # Get the parameters.
2811      my ($tkey, $myDest) = @_;      my ($string) = @_;
2812      # Declare the return variable.      # Declare the return variable.
2813      my $retVal = $myDest;      my $retVal;
2814      # Process according to the destination value.      # Check for data.
2815      if ($myDest eq 'FILE') {      if (defined $string) {
2816          $retVal = ">" . EmergencyFileTarget($tkey);          # We have some, so split it into a list.
2817      } elsif ($myDest eq 'APPEND') {          $retVal = [ split /\s*,\s*/, $string];
         $retVal = ">>" . EmergencyFileTarget($tkey);  
     } elsif ($myDest eq 'DUAL') {  
         $retVal = "+>" . EmergencyFileTarget($tkey);  
2818      }      }
2819      # Return the result.      # Return the result.
2820      return $retVal;      return $retVal;
2821  }  }
2822    
2823  =head3 Emergency  =head3 Now
   
 C<< Emergency($key, $hours, $dest, $level, @modules); >>  
2824    
2825  Turn on emergency tracing. This method is normally invoked over the web from      my $string = Tracer::Now();
 a debugging console, but it can also be called by the C<trace.pl> script.  
 The caller specifies the duration of the emergency in hours, the desired tracing  
 destination, the trace level, and a list of the trace modules to activate.  
 For the 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.  
2826    
2827  =over 4  Return a displayable time stamp containing the local time. Whatever format this
2828    method produces must be parseable by L</ParseDate>.
2829    
2830  =item tkey  =cut
2831    
2832  The tracing key. This is used to identify the control file and the trace file.  sub Now {
2833        return DisplayTime(time);
2834    }
2835    
2836  =item hours  =head3 DisplayTime
2837    
2838  Number of hours to keep emergency tracing alive.      my $string = Tracer::DisplayTime($time);
2839    
2840  =item dest  Convert a time value to a displayable time stamp. Whatever format this
2841    method produces must be parseable by L</ParseDate>.
2842    
2843  Tracing destination. If no path information is specified for a file  =over 4
 destination, it is put in the FIG temporary directory.  
2844    
2845  =item level  =item time
2846    
2847  Tracing level. A higher level means more trace messages.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2848    
2849  =item modules  =item RETURN
2850    
2851  A list of the tracing modules to activate.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2852    
2853  =back  =back
2854    
2855  =cut  =cut
2856    
2857  sub Emergency {  sub DisplayTime {
2858      # Get the parameters.      my ($time) = @_;
2859      my ($tkey, $hours, $dest, $level, @modules) = @_;      my $retVal = "(n/a)";
2860      # Create the emergency file.      if (defined $time) {
2861      my $specFile = EmergencyFileName($tkey);          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2862      my $outHandle = Open(undef, ">$specFile");          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2863      print $outHandle join("\n", $hours, $dest, $level, @modules, "");                    _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2864        }
2865        return $retVal;
2866  }  }
2867    
2868  =head3 EmergencyKey  # Pad a number to 2 digits.
2869    sub _p2 {
2870        my ($value) = @_;
2871        $value = "0$value" if ($value < 10);
2872        return $value;
2873    }
2874    
2875  C<< my $tkey = EmergencyKey($parameter); >>  =head3 Escape
2876    
2877  Return the Key to be used for emergency tracing. This could be an IP address,      my $codedString = Tracer::Escape($realString);
2878   a session ID, or a user name, depending on the environment.  
2879    Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2880    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2881    result is to reverse the effect of L</UnEscape>.
2882    
2883  =over 4  =over 4
2884    
2885  =item parameter  =item realString
2886    
2887  Parameter defining the method for finding the tracing key. If it is a scalar,  String to escape.
 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.  
2888    
2889  =item RETURN  =item RETURN
2890    
2891  Returns the key to be used for labels in emergency tracing.  Escaped equivalent of the real string.
2892    
2893  =back  =back
2894    
2895  =cut  =cut
2896    
2897  sub EmergencyKey {  sub Escape {
2898      # Get the parameters.      # Get the parameter.
2899      my ($parameter) = @_;      my ($realString) = @_;
2900      # Declare the return variable.      # Initialize the return variable.
2901      my $retVal;      my $retVal = "";
2902      # Determine the parameter type.      # Loop through the parameter string, looking for sequences to escape.
2903      if (! defined $parameter) {      while (length $realString > 0) {
2904          # Here we're supposed to check the environment.          # Look for the first sequence to escape.
2905          $retVal = $ENV{TRACING};          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2906      } else {              # Here we found it. The text preceding the sequence is in $1. The sequence
2907          my $ptype = ref $parameter;              # itself is in $2. First, move the clear text to the return variable.
2908          if ($ptype eq 'CGI') {              $retVal .= $1;
2909              # Here we were invoked from a web page. Look for a cookie.              # Strip the processed section off the real string.
2910              $retVal = $parameter->cookie('IP');              $realString = substr $realString, (length $2) + (length $1);
2911          } elsif (! $ptype) {              # Get the matched character.
2912              # Here the key was passed in.              my $char = $2;
2913              $retVal = $parameter;              # If we have a CR, we are done.
2914                if ($char ne "\r") {
2915                    # It's not a CR, so encode the escape sequence.
2916                    $char =~ tr/\t\n/tn/;
2917                    $retVal .= "\\" . $char;
2918          }          }
2919            } else {
2920                # Here there are no more escape sequences. The rest of the string is
2921                # transferred unmodified.
2922                $retVal .= $realString;
2923                $realString = "";
2924      }      }
     # If no luck finding a key, use the PID.  
     if (! defined $retVal) {  
         $retVal = $$;  
2925      }      }
2926      # Return the result.      # Return the result.
2927      return $retVal;      return $retVal;
2928  }  }
2929    
2930    =head3 UnEscape
2931    
2932  =head3 TraceParms      my $realString = Tracer::UnEscape($codedString);
   
 C<< Tracer::TraceParms($cgi); >>  
2933    
2934  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2935  at level CGI => 4.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2936    be deleted.
2937    
2938  =over 4  =over 4
2939    
2940  =item cgi  =item codedString
2941    
2942  CGI query object containing the parameters to trace.  String to un-escape.
2943    
2944    =item RETURN
2945    
2946    Returns a copy of the original string with the escape sequences converted to their actual
2947    values.
2948    
2949  =back  =back
2950    
2951  =cut  =cut
2952    
2953  sub TraceParms {  sub UnEscape {
2954      # Get the parameters.      # Get the parameter.
2955      my ($cgi) = @_;      my ($codedString) = @_;
2956      if (T(CGI => 3)) {      # Initialize the return variable.
2957          # Here we want to trace the parameter data.      my $retVal = "";
2958          my @names = $cgi->param;      # Only proceed if the incoming string is nonempty.
2959          for my $parmName (sort @names) {      if (defined $codedString) {
2960              # Note we skip the Trace parameters, which are for our use only.          # Loop through the parameter string, looking for escape sequences. We can't do
2961              if ($parmName ne 'Trace' && $parmName ne 'TF') {          # translating because it causes problems with the escaped slash. ("\\t" becomes
2962                  my @values = $cgi->param($parmName);          # "\<tab>" no matter what we do.)
2963                  Trace("CGI: $parmName = " . join(", ", @values));          while (length $codedString > 0) {
2964              }              # Look for the first escape sequence.
2965                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2966                    # Here we found it. The text preceding the sequence is in $1. The sequence
2967                    # itself is in $2. First, move the clear text to the return variable.
2968                    $retVal .= $1;
2969                    $codedString = substr $codedString, (2 + length $1);
2970                    # Get the escape value.
2971                    my $char = $2;
2972                    # If we have a "\r", we are done.
2973                    if ($char ne 'r') {
2974                        # Here it's not an 'r', so we convert it.
2975                        $char =~ tr/\\tn/\\\t\n/;
2976                        $retVal .= $char;
2977          }          }
2978          # Display the request method.              } else {
2979          my $method = $cgi->request_method();                  # Here there are no more escape sequences. The rest of the string is
2980          Trace("Method: $method");                  # transferred unmodified.
2981                    $retVal .= $codedString;
2982                    $codedString = "";
2983      }      }
     if (T(CGI => 4)) {  
         # Here we want the environment data too.  
         for my $envName (sort keys %ENV) {  
             Trace("ENV: $envName = $ENV{$envName}");  
2984          }          }
2985      }      }
2986        # Return the result.
2987        return $retVal;
2988  }  }
2989    
2990  =head3 ScriptFinish  =head3 Percent
   
 C<< ScriptFinish($webData, $varHash); >>  
   
 Output a web page at the end of a script. Either the string to be output or the  
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
2991    
2992  A typical standard script would loook like the following.      my $percent = Tracer::Percent($number, $base);
2993    
2994      BEGIN {  Returns the percent of the base represented by the given number. If the base
2995          # Print the HTML header.  is zero, returns zero.
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
2996    
2997      my ($cgi, $varHash) = ScriptSetup();  =over 4
     eval {  
         # ... get data from $cgi, put it in $varHash ...  
     };  
     if ($@) {  
         Trace("Script Error: $@") if T(0);  
     }  
     ScriptFinish("Html/MyTemplate.html", $varHash);  
2998    
2999  The idea here is that even if the script fails, you'll see trace messages and  =item number
 useful output.  
3000    
3001  =over 4  Percent numerator.
3002    
3003  =item webData  =item base
3004    
3005  A string containing either the full web page to be written to the output or the  Percent base.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3006    
3007  =item varHash (optional)  =item RETURN
3008    
3009  If specified, then a reference to a hash mapping variable names for a template  Returns the percentage of the base represented by the numerator.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3010    
3011  =back  =back
3012    
3013  =cut  =cut
3014    
3015  sub ScriptFinish {  sub Percent {
3016      # Get the parameters.      # Get the parameters.
3017      my ($webData, $varHash) = @_;      my ($number, $base) = @_;
3018      # Check for a template file situation.      # Declare the return variable.
3019      my $outputString;      my $retVal = 0;
3020      if (defined $varHash) {      # Compute the percent.
3021          # Here we have a template file. We need to determine the template type.      if ($base != 0) {
3022          my $template;          $retVal = $number * 100 / $base;
         if ($FIG_Config::template_url && $webData =~ /\.php$/) {  
             $template = "$FIG_Config::template_url/$webData";  
         } else {  
             $template = "<<$webData";  
         }  
         $outputString = PageBuilder::Build($template, $varHash, "Html");  
     } else {  
         # Here the user gave us a raw string.  
         $outputString = $webData;  
     }  
     # Check for trace messages.  
     if ($Destination ne "NONE" && $TraceLevel > 0) {  
         # We have trace messages, so we want to put them at the end of the body. This  
         # is either at the end of the whole string or at the beginning of the BODY  
         # end-tag.  
         my $pos = length $outputString;  
         if ($outputString =~ m#</body>#gi) {  
             $pos = (pos $outputString) - 7;  
         }  
         # If the trace messages were queued, we unroll them. Otherwise, we display the  
         # destination.  
         my $traceHtml;  
         if ($Destination eq "QUEUE") {  
             $traceHtml = QTrace('Html');  
         } elsif ($Destination =~ /^>>(.+)$/) {  
             # Here the tracing output it to a file. We code it as a hyperlink so the user  
             # can copy the file name into the clipboard easily.  
             my $actualDest = $1;  
             $traceHtml = "<p>Tracing output to $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;  
3023      }      }
3024      # Write the output string.      # Return the result.
3025      print $outputString;      return $retVal;
3026  }  }
3027    
3028  =head3 Insure  =head3 Constrain
3029    
3030  C<< Insure($dirName); >>      my $constrained = Constrain($value, $min, $max);
3031    
3032  Insure a directory is present.  Modify a numeric value to bring it to a point in between a maximum and a minimum.
3033    
3034  =over 4  =over 4
3035    
3036  =item dirName  =item value
3037    
3038  Name of the directory to check. If it does not exist, it will be created.  Value to constrain.
3039    
3040    =item min (optional)
3041    
3042    Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3043    
3044    =item max (optional)
3045    
3046    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3047    
3048    =item RETURN
3049    
3050    Returns the incoming value, constrained according to the other parameters.
3051    
3052  =back  =back
3053    
3054  =cut  =cut
3055    
3056  sub Insure {  sub Constrain {
3057      my ($dirName) = @_;      # Get the parameters.
3058      if (! -d $dirName) {      my ($value, $min, $max) = @_;
3059          Trace("Creating $dirName directory.") if T(File => 2);      # Declare the return variable.
3060          eval { mkpath $dirName; };      my $retVal = $value;
3061          if ($@) {      # Apply the minimum constraint.
3062              Confess("Error creating $dirName: $@");      if (defined $min && $retVal < $min) {
3063          }          $retVal = $min;
3064        }
3065        # Apply the maximum constraint.
3066        if (defined $max && $retVal > $max) {
3067            $retVal = $max;
3068      }      }
3069        # Return the result.
3070        return $retVal;
3071  }  }
3072    
3073  =head3 ChDir  =head3 Min
3074    
3075  C<< ChDir($dirName); >>      my $min = Min($value1, $value2, ... $valueN);
3076    
3077  Change to the specified directory.  Return the minimum argument. The arguments are treated as numbers.
3078    
3079  =over 4  =over 4
3080    
3081  =item dirName  =item $value1, $value2, ... $valueN
3082    
3083  Name of the directory to which we want to change.  List of numbers to compare.
3084    
3085    =item RETURN
3086    
3087    Returns the lowest number in the list.
3088    
3089  =back  =back
3090    
3091  =cut  =cut
3092    
3093  sub ChDir {  sub Min {
3094      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
3095      if (! -d $dirName) {      my ($retVal, @values) = @_;
3096          Confess("Cannot change to directory $dirName: no such directory.");      # Loop through the remaining parameters, looking for the lowest.
3097      } else {      for my $value (@values) {
3098          Trace("Changing to directory $dirName.") if T(File => 4);          if ($value < $retVal) {
3099          my $okFlag = chdir $dirName;              $retVal = $value;
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
3100          }          }
3101      }      }
3102        # Return the minimum found.
3103        return $retVal;
3104  }  }
3105    
3106  =head3 SendSMS  =head3 Max
3107    
3108  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>      my $max = Max($value1, $value2, ... $valueN);
3109    
3110  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  Return the maximum argument. The arguments are treated as numbers.
 user name, password, and API ID for the relevant account in the hash reference variable  
 I<$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  
3111    
3112      $phone =  { user => 'BruceTheHumanPet',  =over 4
                 password => 'silly',  
                 api_id => '2561022' };  
3113    
3114  The original purpose of this method was to insure Bruce would be notified immediately when the  =item $value1, $value2, ... $valueN
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3115    
3116  The message ID will be returned if successful, and C<undef> if an error occurs.  List of numbers to compare.
3117    
3118  =over 4  =item RETURN
3119    
3120  =item phoneNumber  Returns the highest number in the list.
3121    
3122  Phone number to receive the message, in international format. A United States phone number  =back
 would be prefixed by "1". A British phone number would be prefixed by "44".  
3123    
3124  =item msg  =cut
3125    
3126  Message to send to the specified phone.  sub Max {
3127        # Get the parameters. Note that we prime the return value with the first parameter.
3128        my ($retVal, @values) = @_;
3129        # Loop through the remaining parameters, looking for the highest.
3130        for my $value (@values) {
3131            if ($value > $retVal) {
3132                $retVal = $value;
3133            }
3134        }
3135        # Return the maximum found.
3136        return $retVal;
3137    }
3138    
3139    
3140    =head3 Strip
3141    
3142        my $string = Tracer::Strip($line);
3143    
3144    Strip all line terminators off a string. This is necessary when dealing with files
3145    that may have been transferred back and forth several times among different
3146    operating environments.
3147    
3148    =over 4
3149    
3150    =item line
3151    
3152    Line of text to be stripped.
3153    
3154  =item RETURN  =item RETURN
3155    
3156  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.
3157    
3158  =back  =back
3159    
3160  =cut  =cut
3161    
3162  sub SendSMS {  sub Strip {
3163      # Get the parameters.      # Get a copy of the parameter string.
3164      my ($phoneNumber, $msg) = @_;      my ($string) = @_;
3165      # Declare the return variable. If we do not change it, C<undef> will be returned.      my $retVal = (defined $string ? $string : "");
3166      my $retVal;      # Strip the line terminator characters.
3167      # 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);  
             }  
         }  
     }  
3168      # Return the result.      # Return the result.
3169      return $retVal;      return $retVal;
3170  }  }
3171    
3172  =head3 CommaFormat  =head3 Pad
3173    
3174  C<< my $formatted = Tracer::CommaFormat($number); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3175    
3176  Insert commas into a number.  Pad a string to a specified length. The pad character will be a
3177    space, and the padding will be on the right side unless specified
3178    in the third parameter.
3179    
3180  =over 4  =over 4
3181    
3182  =item number  =item string
3183    
3184  A sequence of digits.  String to be padded.
3185    
3186    =item len
3187    
3188    Desired length of the padded string.
3189    
3190    =item left (optional)
3191    
3192    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3193    
3194    =item padChar (optional)
3195    
3196    Character to use for padding. The default is a space.
3197    
3198  =item RETURN  =item RETURN
3199    
3200  Returns the same digits with commas strategically inserted.  Returns a copy of the original string with the pad character added to the
3201    specified end so that it achieves the desired length.
3202    
3203  =back  =back
3204    
3205  =cut  =cut
3206    
3207  sub CommaFormat {  sub Pad {
3208      # Get the parameters.      # Get the parameters.
3209      my ($number) = @_;      my ($string, $len, $left, $padChar) = @_;
3210      # Pad the length up to a multiple of three.      # Compute the padding character.
3211      my $padded = "$number";      if (! defined $padChar) {
3212      $padded = " " . $padded while length($padded) % 3 != 0;          $padChar = " ";
3213      # This is a fancy PERL trick. The parentheses in the SPLIT pattern      }
3214      # cause the delimiters to be included in the output stream. The      # Compute the number of spaces needed.
3215      # GREP removes the empty strings in between the delimiters.      my $needed = $len - length $string;
3216      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));      # Copy the string into the return variable.
3217      # Clean out the spaces.      my $retVal = $string;
3218      $retVal =~ s/ //g;      # Only proceed if padding is needed.
3219        if ($needed > 0) {
3220            # Create the pad string.
3221            my $pad = $padChar x $needed;
3222            # Affix it to the return value.
3223            if ($left) {
3224                $retVal = $pad . $retVal;
3225            } else {
3226                $retVal .= $pad;
3227            }
3228        }
3229      # Return the result.      # Return the result.
3230      return $retVal;      return $retVal;
3231  }  }
 =head3 SetPermissions  
3232    
3233  C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  =head3 EOF
3234    
3235    This is a constant that is lexically greater than any useful string.
3236    
3237  Set the permissions for a directory and all the files and folders inside it.  =cut
 In addition, the group ownership will be changed to the specified value.  
3238    
3239  This method is more vulnerable than most to permission and compatability  sub EOF {
3240  problems, so it does internal error recovery.      return "\xFF\xFF\xFF\xFF\xFF";
3241    }
3242    
3243    =head3 TICK
3244    
3245        my @results = TICK($commandString);
3246    
3247    Perform a back-tick operation on a command. If this is a Windows environment, any leading
3248    dot-slash (C<./> will be removed. So, for example, if you were doing
3249    
3250        `./protein.cgi`
3251    
3252    from inside a CGI script, it would work fine in Unix, but would issue an error message
3253    in Windows complaining that C<'.'> is not a valid command. If instead you code
3254    
3255        TICK("./protein.cgi")
3256    
3257    it will work correctly in both environments.
3258    
3259  =over 4  =over 4
3260    
3261  =item dirName  =item commandString
3262    
3263  Name of the directory to process.  The command string to pass to the system.
3264    
3265  =item group  =item RETURN
3266    
3267    Returns the standard output from the specified command, as a list.
3268    
3269    =back
3270    
3271    =cut
3272    #: Return Type @;
3273    sub TICK {
3274        # Get the parameters.
3275        my ($commandString) = @_;
3276        # Chop off the dot-slash if this is Windows.
3277        if ($FIG_Config::win_mode) {
3278            $commandString =~ s!^\./!!;
3279        }
3280        # Activate the command and return the result.
3281        return `$commandString`;
3282    }
3283    
 Name of the group to be assigned.  
3284    
3285  =item mask  =head3 CommaFormat
3286    
3287  Permission mask. Bits that are C<1> in this mask will be ORed into the      my $formatted = Tracer::CommaFormat($number);
 permission bits of any file or directory that does not already have them  
 set to 1.  
3288    
3289  =item otherMasks  Insert commas into a number.
3290    
3291  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>.  
3292    
3293      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  =item number
3294    
3295  The list is ordered, so the following would use 0777 for C<tmp1> and  A sequence of digits.
 0666 for C<tmp>, C<tmp2>, or C<tmp3>.  
3296    
3297      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  =item RETURN
                                                    '^tmp' => 0666);  
3298    
3299  Note that the pattern matches are all case-insensitive, and only directory  Returns the same digits with commas strategically inserted.
 names are matched, not file names.  
3300    
3301  =back  =back
3302    
3303  =cut  =cut
3304    
3305  sub SetPermissions {  sub CommaFormat {
3306      # Get the parameters.      # Get the parameters.
3307      my ($dirName, $group, $mask, @otherMasks) = @_;      my ($number) = @_;
3308      # Set up for error recovery.      # Pad the length up to a multiple of three.
3309      eval {      my $padded = "$number";
3310          # Switch to the specified directory.      $padded = " " . $padded while length($padded) % 3 != 0;
3311          ChDir($dirName);      # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3312          # Get the group ID.      # cause the delimiters to be included in the output stream. The
3313          my $gid = getgrnam($group);      # GREP removes the empty strings in between the delimiters.
3314          # Get the mask for tracing.      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3315          my $traceMask = sprintf("%04o", $mask) . "($mask)";      # Clean out the spaces.
3316          Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);      $retVal =~ s/ //g;
3317          my $fixCount = 0;      # Return the result.
3318          my $lookCount = 0;      return $retVal;
         # @dirs will be a stack of directories to be processed.  
         my @dirs = (getcwd());  
         while (scalar(@dirs) > 0) {  
             # Get the current directory.  
             my $dir = pop @dirs;  
             # Check for a match to one of the specified directory names. To do  
             # that, we need to pull the individual part of the name off of the  
             # whole path.  
             my $simpleName = $dir;  
             if ($dir =~ m!/([^/]+)$!) {  
                 $simpleName = $1;  
             }  
             Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);  
             # Search for a match.  
             my $match = 0;  
             my $i;  
             for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {  
                 my $pattern = $otherMasks[$i];  
                 if ($simpleName =~ /$pattern/i) {  
                     $match = 1;  
                 }  
             }  
             # Check for a match. Note we use $i-1 because the loop added 2  
             # before terminating due to the match.  
             if ($match && $otherMasks[$i-1] != $mask) {  
                 # This directory matches one of the incoming patterns, and it's  
                 # a different mask, so we process it recursively with that mask.  
                 SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);  
             } else {  
                 # Here we can process normally. Get all of the non-hidden members.  
                 my @submems = OpenDir($dir, 1);  
                 for my $submem (@submems) {  
                     # Get the full name.  
                     my $thisMem = "$dir/$submem";  
                     Trace("Checking member $thisMem.") if T(4);  
                     $lookCount++;  
                     if ($lookCount % 1000 == 0) {  
                         Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);  
                     }  
                     # Fix the group.  
                     chown -1, $gid, $thisMem;  
                     # Insure this member is not a symlink.  
                     if (! -l $thisMem) {  
                         # Get its info.  
                         my $fileInfo = stat $thisMem;  
                         # Only proceed if we got the info. Otherwise, it's a hard link  
                         # and we want to skip it anyway.  
                         if ($fileInfo) {  
                &