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revision 1.79, Thu Nov 9 21:12:46 2006 UTC revision 1.109, Tue Sep 23 15:33:54 2008 UTC
# Line 1  Line 1 
1  #  # -*- perl -*-
2    ########################################################################
3  # Copyright (c) 2003-2006 University of Chicago and Fellowship  # Copyright (c) 2003-2006 University of Chicago and Fellowship
4  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
5  #  #
# Line 13  Line 14 
14  # at info@ci.uchicago.edu or the Fellowship for Interpretation of  # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15  # Genomes at veronika@thefig.info or download a copy from  # Genomes at veronika@thefig.info or download a copy from
16  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
17  #  ########################################################################
18    
19  package Tracer;  package Tracer;
20    
21      require Exporter;      require Exporter;
22      @ISA = ('Exporter');      @ISA = ('Exporter');
23      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn);
24      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
25      use strict;      use strict;
26      use Carp qw(longmess croak);      use Carp qw(longmess croak carp);
27      use CGI;      use CGI;
28      use Cwd;      use Cwd;
29      use FIG_Config;      use FIG_Config;
# Line 35  Line 36 
36      use Time::HiRes 'gettimeofday';      use Time::HiRes 'gettimeofday';
37      use URI::Escape;      use URI::Escape;
38      use Time::Local;      use Time::Local;
39        use POSIX qw(strftime);
40        use Time::Zone;
41        use Fcntl ':flock';
42    
43    
44  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
45    
# Line 159  Line 164 
164    
165  Sometimes, you need a way for tracing to happen automatically without putting parameters  Sometimes, you need a way for tracing to happen automatically without putting parameters
166  in a form or on the command line. Emergency tracing does this. You invoke emergency tracing  in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
167  from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.  from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
168  Emergency tracing requires you specify a tracing key. For command-line tools, the key is  that you specify a tracing key. For command-line tools, the key is
169  taken from the C<TRACING> environment variable. For web services, the key is taken from  taken from the C<TRACING> environment variable. For web services, the key is taken from
170  a cookie. Either way, the key tells the tracing facility who you are, so that you control  a cookie. Either way, the key tells the tracing facility who you are, so that you control
171  the tracing in your environment without stepping on other users.  the tracing in your environment without stepping on other users.
# Line 183  Line 188 
188    
189  The web script will look for the tracing key in the cookies, and the command-line  The web script will look for the tracing key in the cookies, and the command-line
190  script will look for it in the C<TRACING> environment variable. If you are  script will look for it in the C<TRACING> environment variable. If you are
191  using the L</StandardScript> or L</StandardSetup> methods, emergency tracing  using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
192  will be configured automatically.  will be configured automatically.
193    
 =head3 Debugging Control Panel  
   
 The debugging control panel provides several tools to assist in development of  
 SEED and Sprout software. You access the debugging control panel from the URL  
 C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,  
 for example, the panel access point for the development NMPDR system is  
 C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to  
 find out what the password is. From this page, you can also specify a tracing  
 key. If you don't specify a key, one will be generated for you.  
   
 =head4 Emergency Tracing Form  
   
 At the bottom of the debugging control panel is a form that allows you to  
 specify a trace level and tracing categories. Special and common categories  
 are listed with check boxes. You can hold your mouse over a check box to see  
 what its category does. In general, however, a category name is the same as  
 the name of the package in which the trace message occurs.  
   
 Additional categories can be entered in an input box, delimited by spaces or commas.  
   
 The B<Activate> button turns on Emergency tracing at the level you specify with the  
 specified categories active. The B<Terminate> button turns tracing off. The  
 B<Show File> button displays the current contents of the trace file. The tracing  
 form at the bottom of the control panel is designed for emergency tracing, so it  
 will only affect programs that call L</ETracing>, L</StandardScript>,  
 or L</StandardSetup>.  
   
 =head4 Script Form  
   
 The top form of the debugging control panel allows you to enter a tiny script and  
 have the output generated in a formatted table. Certain object variables are  
 predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),  
 and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.  
   
 The last line of the script must be a scalar, but it can be a reference to a hash,  
 a list, a list of lists, and various other combinations. If you select the appropriate  
 data type in the dropdown box, the output will be formatted accordingly. The form  
 also has controls for specifying tracing. These controls override any emergency  
 tracing in effect.  
   
 =head4 Database Query Forms  
   
 The forms between the script form and the emergency tracing form allow you to  
 make queries against the database. The FIG query form allows simple queries against  
 a single FIG table. The Sprout query form uses the B<GetAll> method to do a  
 multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>  
 package, and it takes five parameters.  
   
     GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);  
   
 Each of the five parameters corresponds to a text box on the query form:  
   
 =over 4  
   
 =item Objects  
   
 Comma-separated list containing the names of the entity and relationship objects to be retrieved.  
   
 =item Filter  
   
 WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  
 be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form  
 B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a  
 field, I<objectName> is the name of the entity or relationship object containing the field, and  
 I<number> is the 1-based position of the object in the object list. Any parameters  
 specified in the filter clause should be specified in the B<Params> field.  
 The fields in a filter clause can come from primary entity relations,  
 relationship relations, or secondary entity relations; however, all of the  
 entities and relationships involved must be included in the list of object names.  
   
 =item Params  
   
 List of the parameters to be substituted in for the parameters marks in the filter clause. This  
 is a comma-separated list without any quoting or escaping.  
   
 =item fields  
   
 Comma-separated list of the fields to be returned in each element of the list returned. Fields  
 are specified in the same manner as in the filter clause.  
   
 =item count  
   
 Maximum number of records to return. If omitted or 0, all available records will be returned.  
   
 =back  
   
 B<GetAll> automatically joins together the entities and relationships listed in the object  
 names. This simplifies the coding of the filter clause, but it means that some queries are  
 not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation  
 that has yet to be addressed.  
   
194  =cut  =cut
195    
196  # Declare the configuration variables.  # Declare the configuration variables.
197    
198  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
199  my $TeeFlag = 0;            # TRUE if output is going to a file and to the  my $TeeFlag = 0;            # TRUE if output is going to a file and to the
200                              # standard output                              # standard output
201  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
202                              # hash of active category names                              # hash of active category names
203    my @LevelNames = qw(error warn notice info detail);
204  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
205                              # messages                              # messages
206  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
207  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
208    my $LastLevel = 0;          # level of the last test call
209  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
210  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
211    my $SavedCGI;               # CGI object passed to ETracing
212    my $CommandLine;            # Command line passed to StandardSetup
213    umask 2;                    # Fix the damn umask so everything is group-writable.
214    
215  =head2 Public Methods  =head2 Tracing Methods
216    
217    =head3 Setups
218    
219        my $count = Tracer::Setups();
220    
221    Return the number of times L</TSetup> has been called.
222    
223    This method allows for the creation of conditional tracing setups where, for example, we
224    may want to set up tracing if nobody else has done it before us.
225    
226    =cut
227    
228    sub Setups {
229        return $SetupCount;
230    }
231    
232  =head3 TSetup  =head3 TSetup
233    
234  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
235    
236  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
237  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 347  Line 281 
281          }          }
282      }      }
283      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
284      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
285      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
286        # the standard output (tee mode).
287      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
288          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
289              $TeeFlag = 1;              $TeeFlag = 1;
290              $target = substr($target, 1);              $target = substr($target, 1);
291          }          }
292          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
293                # We need to initialize the file (which clears it).
294              open TRACEFILE, $target;              open TRACEFILE, $target;
295              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
296              close TRACEFILE;              close TRACEFILE;
297                # Set to append mode now that the file has been cleared.
298              $Destination = ">$target";              $Destination = ">$target";
299          } else {          } else {
300              $Destination = $target;              $Destination = $target;
# Line 369  Line 306 
306      $SetupCount++;      $SetupCount++;
307  }  }
308    
309  =head3 StandardSetup  =head3 SetLevel
310    
311  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
312    
313  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.  
314    
315  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.  
316    
317  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  
318    
319      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
320    
321  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.  
322    
323  =over 4  =cut
324    
325  =item SQL  sub SetLevel {
326        $TraceLevel = $_[0];
327    }
328    
329  Traces SQL commands and activity.  =head3 ParseDate
330    
331  =item Tracer      my $time = Tracer::ParseDate($dateString);
332    
333  Traces error messages and call stacks.  Convert a date into a PERL time number. This method expects a date-like string
334    and parses it into a number. The string must be vaguely date-like or it will
335    return an undefined value. Our requirement is that a month and day be
336    present and that three pieces of the date string (time of day, month and day,
337    year) be separated by likely delimiters, such as spaces, commas, and such-like.
338    
339  =back  If a time of day is present, it must be in military time with two digits for
340    everything but the hour.
341    
342  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.  
343    
344      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
345    equally innocuous. This means, however, that a sufficiently long sentence with date-like
346    parts in it may be interpreted as a date. Hopefully this will not be a problem.
347    
348  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  
349    
350  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.  
351    
352      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  =over 4
353    
354  would send the trace output to C<traceBruce.log> in the temporary directory.  =item dateString
355    
356  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.  
357    
358  You can specify a different default trace level by setting C<$options->{trace}>  =item RETURN
 prior to calling this method.  
359    
360  An example at this point would help. Consider, for example, the command-line utility  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
361  C<TransactFeatures>. It accepts a list of positional parameters plus the options  the date string is invalid. A valid date string must contain a month and day.
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
362    
363      my ($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);  
364    
365    =cut
366    
367  The call to C<ParseCommand> specifies the default values for the options and  # Universal month conversion table.
368  stores the actual options in a hash that is returned as C<$options>. The  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
369  positional parameters are returned in C<@parameters>.                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
370                                Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
371                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
372                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
373                                Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
374                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
375                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
376                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
377                                Oct =>  9, October  =>   9, '10' =>  9,
378                                Nov => 10, November =>  10, '11' => 10,
379                                Dec => 11, December =>  11, '12' => 11
380                            };
381    
382  The following is a sample command line for C<TransactFeatures>.  sub ParseDate {
383        # Get the parameters.
384        my ($dateString) = @_;
385        # Declare the return variable.
386        my $retVal;
387        # Find the month and day of month. There are two ways that can happen. We check for the
388        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
389        # won't be fooled into thinking the month is Sunday.
390        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
391            my ($mon, $mday) = (MONTHS->{$1}, $2);
392            # Insist that the month and day are valid.
393            if (defined($mon) && $2 >= 1 && $2 <= 31) {
394                # Find the time.
395                my ($hour, $min, $sec) = (0, 0, 0);
396                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
397                    ($hour, $min, $sec) = ($1, $2, $3);
398                }
399                # Find the year.
400                my $year;
401                if ($dateString =~ /\b(\d{4})\b/) {
402                    $year = $1;
403                } else {
404                    # Get the default year, which is this one. Note we must convert it to
405                    # the four-digit value expected by "timelocal".
406                    (undef, undef, undef, undef, undef, $year) = localtime();
407                    $year += 1900;
408                }
409                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
410            }
411        }
412        # Return the result.
413        return $retVal;
414    }
415    
416      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  =head3 LogErrors
417    
418  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional      Tracer::LogErrors($fileName);
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
419    
420      { trace => 2, sql => 0, safe => 0,  Route the standard error output to a log file.
       noAlias => 1, start => ' ', tblFiles => 0 }  
421    
422  Use of C<StandardSetup> in this way provides a simple way of performing  =over 4
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
423    
424  If the C<background> option is specified on the command line, then the  =item fileName
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
425    
426      -user=Bruce -background  Name of the file to receive the error output.
427    
428  then the trace output would go to C<traceBruce.log>, the standard output to  =back
 C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to  
 simplify starting a command in the background.  
429    
430  The user name is also used as the tracing key for L</Emergency Tracing>.  =cut
 Specifying a value of C<E> for the trace level causes emergency tracing to  
 be used instead of custom tracing. If the user name is not specified,  
 the tracing key is taken from the C<Tracing> environment variable. If there  
 is no value for that variable, the tracing key will be computed from the PID.  
431    
432  Finally, if the special option C<-h> is specified, the option names will  sub LogErrors {
433  be traced at level 0 and the program will exit without processing.      # Get the file name.
434  This provides a limited help capability. For example, if the user enters      my ($fileName) = @_;
435        # Open the file as the standard error output.
436        open STDERR, '>', $fileName;
437    }
438    
439      TransactFeatures -h  =head3 Trace
440    
441  he would see the following output.      Trace($message);
442    
443      TransactFeatures [options] command transactionDirectory IDfile  Write a trace message to the target location specified in L</TSetup>. If there has not been
444          -trace    tracing level (default E)  any prior call to B<TSetup>.
         -sql      trace SQL commands  
         -safe     use database transactions  
         -noAlias  do not expect aliases in CHANGE transactions  
         -start    start with this genome  
         -tblFiles output TBL files containing the corrected IDs  
445    
446  The caller has the option of modifying the tracing scheme by placing a value  =over 4
 for C<trace> in the incoming options hash. The default value can be overridden,  
 or the tracing to the standard output can be turned off by suffixing a minus  
 sign to the trace level. So, for example,  
447    
448      { trace => [0, "tracing level (default 0)"],  =item message
        ...  
449    
450  would set the default trace level to 0 instead of E, while  Message to write.
451    
452      { trace => ["2-", "tracing level (default 2)"],  =back
        ...  
453    
454  would set the default to 2, but trace only to the log file, not to the  =cut
 standard output.  
455    
456  The parameters to this method are as follows.  sub Trace {
457        # Get the parameters.
458        my ($message) = @_;
459        # Strip off any line terminators at the end of the message. We will add
460        # new-line stuff ourselves.
461        my $stripped = Strip($message);
462        # Compute the caller information.
463        my ($callPackage, $callFile, $callLine) = caller();
464        my $callFileTitle = basename($callFile);
465        # Check the caller.
466        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
467        # Get the timestamp.
468        my $timeStamp = Now();
469        # Build the prefix.
470        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
471        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
472        # Format the message.
473        my $formatted = "$prefix $stripped";
474        # Process according to the destination.
475        if ($Destination eq "TEXT") {
476            # Write the message to the standard output.
477            print "$formatted\n";
478        } elsif ($Destination eq "ERROR") {
479            # Write the message to the error output. Here, we want our prefix fields.
480            print STDERR "$formatted\n";
481        } elsif ($Destination eq "WARN") {
482            # Emit the message to the standard error output. It is presumed that the
483            # error logger will add its own prefix fields, the notable exception being
484            # the caller info.
485            print STDERR "$callerInfo$stripped\n";
486        } elsif ($Destination eq "QUEUE") {
487            # Push the message into the queue.
488            push @Queue, "$formatted";
489        } elsif ($Destination eq "HTML") {
490            # Convert the message to HTML and write it to the standard output.
491            my $escapedMessage = CGI::escapeHTML($stripped);
492            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
493        } elsif ($Destination =~ m/^>>/) {
494            # Write the trace message to an output file.
495            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
496            print TRACING "$formatted\n";
497            close TRACING;
498            # If the Tee flag is on, echo it to the standard output.
499            if ($TeeFlag) {
500                print "$formatted\n";
501            }
502        }
503    }
504    
505  =over 4  =head3 T
506    
507  =item categories      my $switch = T($category, $traceLevel);
508    
509  Reference to a list of tracing category names. These should be names of      or
 packages whose internal workings will need to be debugged to get the  
 command working.  
510    
511  =item options      my $switch = T($traceLevel);
512    
513  Reference to a hash containing the legal options for the current command mapped  Return TRUE if the trace level is at or above a specified value and the specified category
514  to their default values and descriptions. The user can override the defaults  is active, else FALSE. If no category is specified, the caller's package name is used.
 by specifying the options as command-line switches prefixed by a hyphen.  
 Tracing-related options may be added to this hash. If the C<-h> option is  
 specified on the command line, the option descriptions will be used to  
 explain the options. To turn off tracing to the standard output, add a  
 minus sign to the value for C<trace> (see above).  
515    
516  =item parmHelp  =over 4
517    
518  A string that vaguely describes the positional parameters. This is used  =item category
 if the user specifies the C<-h> option.  
519    
520  =item argv  Category to which the message belongs. If not specified, the caller's package name is
521    used.
522    
523  List of command line parameters, including the option switches, which must  =item traceLevel
524  precede the positional parameters and be prefixed by a hyphen.  
525    Relevant tracing level.
526    
527  =item RETURN  =item RETURN
528    
529  Returns a list. The first element of the list is the reference to a hash that  TRUE if a message at the specified trace level would appear in the trace, else FALSE.
 maps the command-line option switches to their values. These will either be the  
 default values or overrides specified on the command line. The remaining  
 elements of the list are the position parameters, in order.  
530    
531  =back  =back
532    
533  =cut  =cut
534    
535  sub StandardSetup {  sub T {
536        # Declare the return variable.
537        my $retVal = 0;
538        # Only proceed if tracing is turned on.
539        if ($Destination ne "NONE") {
540      # Get the parameters.      # Get the parameters.
541      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
542      # Get the default tracing key.          if (!defined $traceLevel) {
543      my $tkey = EmergencyKey();              # Here we have no category, so we need to get the calling package.
544      # Add the tracing options.              # The calling package is normally the first parameter. If it is
545      if (! exists $options->{trace}) {              # omitted, the first parameter will be the tracelevel. So, the
546          $options->{trace} = ['E', "tracing level (E for emergency tracing)"];              # first thing we do is shift the so-called category into the
547      }              # $traceLevel variable where it belongs.
548      $options->{sql} = [0, "turn on SQL tracing"];              $traceLevel = $category;
549      $options->{h} = [0, "display command-line options"];              my ($package, $fileName, $line) = caller;
550      $options->{user} = [$tkey, "tracing key"];              # If there is no calling package, we default to "main".
551      $options->{background} = [0, "spool standard and error output"];              if (!$package) {
552      # Create a parsing hash from the options hash. The parsing hash                  $category = "main";
     # contains the default values rather than the default value  
     # and the description. While we're at it, we'll memorize the  
     # length of the longest option name.  
     my $longestName = 0;  
     my %parseOptions = ();  
     for my $key (keys %{$options}) {  
         if (length $key > $longestName) {  
             $longestName = length $key;  
         }  
         $parseOptions{$key} = $options->{$key}->[0];  
     }  
     # Parse the command line.  
     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);  
     # Get the logfile suffix.  
     my $suffix = $retOptions->{user};  
     # Check for background mode.  
     if ($retOptions->{background}) {  
         my $outFileName = "$FIG_Config::temp/out$suffix.log";  
         my $errFileName = "$FIG_Config::temp/err$suffix.log";  
         open STDOUT, ">$outFileName";  
         open STDERR, ">$errFileName";  
     }  
     # Now we want to set up tracing. First, we need to know if the user  
     # wants emergency tracing.  
     if ($retOptions->{trace} eq 'E') {  
         ETracing($retOptions->{user});  
553      } else {      } else {
554          # Here the tracing is controlled from the command line.                  my @cats = split /::/, $package;
555          my @cats = @{$categories};                  $category = $cats[$#cats];
         if ($retOptions->{sql}) {  
             push @cats, "SQL";  
         }  
         # Add the default categories.  
         push @cats, "Tracer";  
         # Next, we create the category string by joining the categories.  
         my $cats = join(" ", @cats);  
         # Check to determine whether or not the caller wants to turn off tracing  
         # to the standard output.  
         my $traceLevel = $retOptions->{trace};  
         my $textOKFlag = 1;  
         if ($traceLevel =~ /^(.)-/) {  
             $traceLevel = $1;  
             $textOKFlag = 0;  
556          }          }
         # 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";  
557              }              }
558              # Close the test file.          # Save the category name and level.
559              close TESTTRACE;          $LastCategory = $category;
560          } else {          $LastLevel = $traceLevel;
561              # Here we can't trace to a file. We trace to the standard output if it's          # Convert it to lower case before we hash it.
562              # okay, and the error log otherwise.          $category = lc $category;
563              if ($textOKFlag) {          # Validate the trace level.
564                  $traceMode = "TEXT";          if (ref $traceLevel) {
565              } else {              Confess("Bad trace level.");
566                  $traceMode = "WARN";          } elsif (ref $TraceLevel) {
567                Confess("Bad trace config.");
568              }              }
569            # Make the check. Note that level 0 shows even if the category is turned off.
570            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
571          }          }
572          # Now set up the tracing.      # Return the computed result.
573          TSetup("$traceLevel $cats", $traceMode);      return $retVal;
574      }      }
575      # Check for the "h" option. If it is specified, dump the command-line  
576      # options and exit the program.  =head3 QTrace
577      if ($retOptions->{h}) {  
578          $0 =~ m#[/\\](\w+)(\.pl)?$#i;      my $data = QTrace($format);
579          print "$1 [options] $parmHelp\n";  
580          for my $key (sort keys %{$options}) {  Return the queued trace data in the specified format.
581              my $name = Pad($key, $longestName, 0, ' ');  
582              my $desc = $options->{$key}->[1];  =over 4
583              if ($options->{$key}->[0]) {  
584                  $desc .= " (default " . $options->{$key}->[0] . ")";  =item format
585    
586    C<html> to format the data as an HTML list, C<text> to format it as straight text.
587    
588    =back
589    
590    =cut
591    
592    sub QTrace {
593        # Get the parameter.
594        my ($format) = @_;
595        # Create the return variable.
596        my $retVal = "";
597        # Only proceed if there is an actual queue.
598        if (@Queue) {
599            # Process according to the format.
600            if ($format =~ m/^HTML$/i) {
601                # Convert the queue into an HTML list.
602                $retVal = "<ul>\n";
603                for my $line (@Queue) {
604                    my $escapedLine = CGI::escapeHTML($line);
605                    $retVal .= "<li>$escapedLine</li>\n";
606              }              }
607              print "  $name $desc\n";              $retVal .= "</ul>\n";
608            } elsif ($format =~ m/^TEXT$/i) {
609                # Convert the queue into a list of text lines.
610                $retVal = join("\n", @Queue) . "\n";
611          }          }
612          exit(0);          # Clear the queue.
613            @Queue = ();
614      }      }
615      # Return the parsed parameters.      # Return the formatted list.
616      return ($retOptions, @retParameters);      return $retVal;
617  }  }
618    
619  =head3 Setups  =head3 Confess
620    
621  C<< my $count = Tracer::Setups(); >>      Confess($message);
622    
623  Return the number of times L</TSetup> has been called.  Trace the call stack and abort the program with the specified message. When used with
624    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
625    So, for example
626    
627  This method allows for the creation of conditional tracing setups where, for example, we      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
628  may want to set up tracing if nobody else has done it before us.  
629    Will abort the program with a stack trace if the value of C<$recNum> is negative.
630    
631    =over 4
632    
633    =item message
634    
635    Message to include in the trace.
636    
637    =back
638    
639  =cut  =cut
640    
641  sub Setups {  sub Confess {
642      return $SetupCount;      # Get the parameters.
643        my ($message) = @_;
644        # Set up the category and level.
645        $LastCategory = "(confess)";
646        $LastLevel = 0;
647        if (! defined($FIG_Config::no_tool_hdr)) {
648            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
649            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
650            # Only proceed if the tool header file is actually present.
651            if (-f $toolHeaderFile) {
652                my $fh;
653                if (open $fh, "<$toolHeaderFile") {
654                    my @lines = <$fh>;
655                    Trace("Tool header has " . scalar(@lines) . " lines.");
656                }
657            }
658        }
659        # Trace the call stack.
660        Cluck($message);
661        # Abort the program.
662        croak(">>> $message");
663  }  }
664    
665  =head3 Open  =head3 SaveCGI
   
 C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  
666    
667  Open a file.      Tracer::SaveCGI($cgi);
668    
669  The I<$fileSpec> is essentially the second argument of the PERL C<open>  This method saves the CGI object but does not activate emergency tracing.
670  function. The mode is specified using Unix-like shell information. So, for  It is used to allow L</Warn> to work in situations where emergency
671  example,  tracing is contra-indicated (e.g. the wiki).
672    
673      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =over 4
674    
675  would open for output appended to the specified file, and  =item cgi
676    
677      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  Active CGI query object.
678    
679  would open a pipe that sorts the records written and removes duplicates. Note  =back
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
680    
681      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =cut
682    
683  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  sub SaveCGI {
684  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a      $SavedCGI = $_[0];
685  failed open will throw an exception and the third parameter will be used to construct  }
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
686    
687      Could not open "/usr/spool/news/twitlog"  =head3 Warn
688    
689  Note that the mode characters are automatically cleaned from the file name.      Warn($message, @options);
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
690    
691      Could not open "/usr/spool/news/twitlog": file not found.  This method traces an important message. If an RSS feed is configured
692    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
693    then the message will be echoed to the feed. In general, a tracing
694    destination of C<WARN> indicates that the caller is running as a web
695    service in a production environment; however, this is not a requirement.
696    
697  In some versions of PERL the only error message we get is a number, which  To force warnings into the RSS feed even when the tracing destination
698  corresponds to the C++ C<errno> value.  is not C<WARN>, simply specify the C<Feed> tracing module. This can be
699    configured automatically when L</StandardSetup> is used.
700    
701      Could not open "/usr/spool/news/twitlog": 6.  The L</Cluck> method calls this one for its final message. Since
702    L</Confess> calls L</Cluck>, this means that any error which is caught
703    and confessed will put something in the feed. This insures that someone
704    will be alerted relatively quickly when a failure occurs.
705    
706  =over 4  =over 4
707    
708  =item fileHandle  =item message
709    
710  File handle. If this parameter is C<undef>, a file handle will be generated  Message to be traced.
 and returned as the value of this method.  
711    
712  =item fileSpec  =item options
713    
714  File name and mode, as per the PERL C<open> function.  A list containing zero or more options.
715    
716  =item message (optional)  =back
717    
718  Error message to use if the open fails. If omitted, a standard error message  The permissible options are as follows.
 will be generated. In either case, the error information from the file system  
 is appended to the message. To specify a conditional open that does not throw  
 an error if it fails, use C<0>.  
719    
720  =item RETURN  =over 4
721    
722  Returns the name of the file handle assigned to the file, or C<undef> if the  =item noStack
723  open failed.  
724    If specified, then the stack trace is not included in the output.
725    
726  =back  =back
727    
728  =cut  =cut
729    
730  sub Open {  sub Warn {
731      # Get the parameters.      # Get the parameters.
732      my ($fileHandle, $fileSpec, $message) = @_;      my $message = shift @_;
733      # Attempt to open the file.      my %options = map { $_ => 1 } @_;
734      my $rv = open $fileHandle, $fileSpec;      # Save $@;
735      # If the open failed, generate an error message.      my $savedError = $@;
736      if (! $rv) {      # Trace the message.
737          # Save the system error message.      Trace($message);
738          my $sysMessage = $!;      # This will contain the lock handle. If it's defined, it means we need to unlock.
739          # See if we need a default message.      my $lock;
740          if (!$message) {      # Check for feed forcing.
741              # Clean any obvious mode characters and leading spaces from the      my $forceFeed = exists $Categories{feed};
742              # filename.      # An error here would be disastrous. Note that if debug mode is specified,
743              my ($fileName) = FindNamePart($fileSpec);      # we do this stuff even in a test environment.
744              $message = "Could not open \"$fileName\"";      eval {
745            # Do we need to put this in the RSS feed?
746            if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
747                # Probably. We need to check first, however, to see if it's from an
748                # ignored IP. For non-CGI situations, we default the IP to the self-referent.
749                my $key = "127.0.0.1";
750                if (defined $SavedCGI) {
751                    # Get the IP address.
752                    $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
753                }
754                # Is the IP address in the ignore list?
755                my $found = scalar(grep { $_ eq $key } @FIG_Config::error_ignore_ips);
756                if (! $found) {
757                    # No. We're good. We now need to compute the date, the link, and the title.
758                    # First, the date, in a very specific format.
759                    my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
760                        (tz_local_offset() / 30);
761                    # Environment data goes in here. We start with the date.
762                    my $environment = "$date.  ";
763                    # If we need to recap the message (because it's too long to be a title), we'll
764                    # put it in here.
765                    my $recap;
766                    # Copy the message and remove excess space.
767                    my $title = $message;
768                    $title =~ s/\s+/ /gs;
769                    # If it's too long, we have to split it up.
770                    if (length $title > 60) {
771                        # Put the full message in the environment string.
772                        $recap = $title;
773                        # Excerpt it as the title.
774                        $title = substr($title, 0, 50) . "...";
775                    }
776                    # If we have a CGI object, then this is a web error. Otherwise, it's
777                    # command-line.
778                    if (defined $SavedCGI) {
779                        # We're in a web service. The environment is the user's IP, and the link
780                        # is the URL that got us here.
781                        $environment .= "Event Reported at IP address $key process $$.";
782                        my $url = $SavedCGI->self_url();
783                        # We need the user agent string and (if available) the referrer.
784                        # The referrer will be the link.
785                        $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
786                        if ($ENV{HTTP_REFERER}) {
787                            my $link = $ENV{HTTP_REFERER};
788                            $environment .= " referred from <a href=\"$link\">$link</a>.";
789                        } else {
790                            $environment .= " referrer unknown.";
791                        }
792                        # Close off the sentence with the original link.
793                        $environment .= " URL of event is <a href=\"$url\">$url</a>.";
794                    } else {
795                        # No CGI object, so we're a command-line tool. Use the tracing
796                        # key and the PID as the user identifier, and add the command.
797                        my $key = EmergencyKey();
798                        $environment .= "Event Reported by $key process $$.";
799                        if ($CommandLine) {
800                            # We're in a StandardSetup script, so we have the real command line.
801                            $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
802                        } elsif ($ENV{_}) {
803                            # We're in a BASH script, so the command has been stored in the _ variable.
804                            $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
805                        }
806                    }
807                    # Build a GUID. We use the current time, the title, and the process ID,
808                    # then digest the result.
809                    my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
810                    # Finally, the description. This is a stack trace plus various environmental stuff.
811                    # The trace is optional.
812                    my $stackTrace;
813                    if ($options{noStack}) {
814                        $stackTrace = "";
815                    } else {
816                        my @trace = LongMess();
817                        # Only proceed if we got something back.
818                        if (scalar(@trace) > 0) {
819                            $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
820                            $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
821                        }
822                    }
823                    # We got the stack trace. Now it's time to put it all together.
824                    # We have a goofy thing here in that we need to HTML-escape some sections of the description
825                    # twice. They will be escaped once here, and then once when written by XML::Simple. They are
826                    # unescaped once when processed by the RSS reader, and stuff in the description is treated as
827                    # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
828                    # our <br>s and <pre>s are used to format the description.
829                    $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
830                    my $description = "$recap$environment  $stackTrace";
831                    # Okay, we have all the pieces. Create a hash of the new event.
832                    my $newItem = { title => $title,
833                                    description => $description,
834                                    category => $LastCategory,
835                                    pubDate => $date,
836                                    guid => $guid,
837                                  };
838                    # We need XML capability for this.
839                    require XML::Simple;
840                    # The RSS document goes in here.
841                    my $rss;
842                    # Get the name of the RSS file. It's in the FIG temporary directory.
843                    my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
844                    # Open the config file and lock it.
845                    $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
846                    flock $lock, LOCK_EX;
847                    # Does it exist?
848                    if (-s $fileName) {
849                        # Slurp it in.
850                        $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
851                    } else {
852                        my $size = -s $fileName;
853                        # Create an empty channel.
854                        $rss = {
855                            channel => {
856                                title => 'NMPDR Warning Feed',
857                                link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
858                                description => "Important messages regarding the status of the NMPDR.",
859                                generator => "NMPDR Trace Facility",
860                                docs => "http://blogs.law.harvard.edu/tech/rss",
861                                item => []
862                            },
863                        };
864          }          }
865          # Terminate with an error using the supplied message and the                  # Get the channel object.
866          # error message from the file system.                  my $channel = $rss->{channel};
867          Confess("$message: $!");                  # Update the last-build date.
868                    $channel->{lastBuildDate} = $date;
869                    # Get the item array.
870                    my $items = $channel->{item};
871                    # Insure it has only 100 entries.
872                    while (scalar @{$items} > 100) {
873                        pop @{$items};
874                    }
875                    # Add our new item at the front.
876                    unshift @{$items}, $newItem;
877                    # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
878                    # the requirements for those.
879                    my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
880                    # Here we put in the root and declaration. The problem is that the root has to have the version attribute
881                    # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
882                    $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
883                    # We don't use Open here because we can't afford an error.
884                    if (open XMLOUT, ">$fileName") {
885                        print XMLOUT $xml;
886                        close XMLOUT;
887      }      }
888      # Return the file handle.              }
889      return $fileHandle;          }
890        };
891        if ($@) {
892            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
893            # (which is a good thing).
894            my $error = $@;
895            Trace("Feed Error: $error") if T(Feed => 0);
896        }
897        # Be sure to unlock.
898        if ($lock) {
899            flock $lock, LOCK_UN;
900            undef $lock;
901        }
902        # Restore the error message.
903        $@ = $savedError;
904  }  }
905    
 =head3 FindNamePart  
   
 C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>  
   
 Extract the portion of a file specification that contains the file name.  
   
 A file specification is the string passed to an C<open> call. It specifies the file  
 mode and name. In a truly complex situation, it can specify a pipe sequence. This  
 method assumes that the file name is whatever follows the first angle bracket  
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
   
     >>/usr/fig/myfile.txt  
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
906    
 If the method cannot find a file name using its normal methods, it will return the  
 whole incoming string.  
907    
 =over 4  
908    
909  =item fileSpec  =head3 Assert
910    
911  File specification string from which the file name is to be extracted.      Assert($condition1, $condition2, ... $conditionN);
912    
913  =item RETURN  Return TRUE if all the conditions are true. This method can be used in conjunction with
914    the OR operator and the L</Confess> method as a debugging assert.
915    So, for example
916    
917  Returns a three-element list. The first element contains the file name portion of      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
 the specified string, or the whole string if a file name cannot be found via normal  
 methods. The second element contains the start position of the file name portion and  
 the third element contains the length.  
918    
919  =back  Will abort the program with a stack trace if the value of C<$recNum> is negative.
920    
921  =cut  =cut
922  #: Return Type $;  sub Assert {
923  sub FindNamePart {      my $retVal = 1;
924      # Get the parameters.      LOOP: for my $condition (@_) {
925      my ($fileSpec) = @_;          if (! $condition) {
926      # Default to the whole input string.              $retVal = 0;
927      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);              last LOOP;
     # Parse out the file name if we can.  
     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {  
         $retVal = $2;  
         $len = length $retVal;  
         $pos = (length $fileSpec) - (length $3) - $len;  
928      }      }
929      # Return the result.      }
930      return ($retVal, $pos, $len);      return $retVal;
931  }  }
932    
933  =head3 OpenDir  =head3 Cluck
   
 C<< my @files = OpenDir($dirName, $filtered, $flag); >>  
   
 Open a directory and return all the file names. This function essentially performs  
 the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  
 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  
 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be  
 filtered out of the return list. If the directory does not open and I<$flag> is not  
 set, an exception is thrown. So, for example,  
   
     my @files = OpenDir("/Volumes/fig/contigs", 1);  
   
 is effectively the same as  
934    
935      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");      Cluck($message);
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
936    
937  Similarly, the following code  Trace the call stack. Note that for best results, you should qualify the call with a
938    trace condition. For example,
939    
940      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);      Cluck("Starting record parse.") if T(3);
941    
942  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  will only trace the stack if the trace level for the package is 3 or more.
 automatically returns an empty list if the directory fails to open.  
943    
944  =over 4  =over 4
945    
946  =item dirName  =item message
947    
948  Name of the directory to open.  Message to include in the trace.
949    
950  =item filtered  =back
951    
952  TRUE if files whose names begin with a period (C<.>) should be automatically removed  =cut
 from the list, else FALSE.  
953    
954  =item flag  sub Cluck {
955        # Get the parameters.
956        my ($message) = @_;
957        # Trace what's happening.
958        Trace("Stack trace for event: $message");
959        # Get the stack trace.
960        my @trace = LongMess();
961        # Convert the trace to a series of messages.
962        for my $line (@trace) {
963            # Replace the tab at the beginning with spaces.
964            $line =~ s/^\t/    /;
965            # Trace the line.
966            Trace($line);
967        }
968        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
969        Warn($message);
970    }
971    
972  TRUE if a failure to open is okay, else FALSE  =head3 LongMess
973    
974  =back      my @lines = Tracer::LongMess();
975    
976    Return a stack trace with all tracing methods removed. The return will be in the form of a list
977    of message strings.
978    
979  =cut  =cut
980  #: Return Type @;  
981  sub OpenDir {  sub LongMess {
     # Get the parameters.  
     my ($dirName, $filtered, $flag) = @_;  
982      # Declare the return variable.      # Declare the return variable.
983      my @retVal = ();      my @retVal = ();
984      # Open the directory.      my $confession = longmess("");
985      if (opendir(my $dirHandle, $dirName)) {      for my $line (split /\s*\n/, $confession) {
986          # The directory opened successfully. Get the appropriate list according to the          unless ($line =~ /Tracer\.pm/) {
987          # strictures of the filter parameter.              # Here we have a line worth keeping. Push it onto the result list.
988          if ($filtered) {              push @retVal, $line;
             @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;  
         } else {  
             @retVal = readdir $dirHandle;  
989          }          }
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
990      }      }
991      # Return the result.      # Return the result.
992      return @retVal;      return @retVal;
993  }  }
994    
995  =head3 SetLevel  =head3 ETracing
996    
997  C<< Tracer::SetLevel($newLevel); >>      ETracing($parameter);
998    
999  Modify the trace level. A higher trace level will cause more messages to appear.  Set up emergency tracing. Emergency tracing is tracing that is turned
1000    on automatically for any program that calls this method. The emergency
1001    tracing parameters are stored in a a file identified by a tracing key.
1002    If this method is called with a CGI object, then the tracing key is
1003    taken from a cookie. If it is called with no parameters, then the tracing
1004    key is taken from an environment variable. If it is called with a string,
1005    the tracing key is that string.
1006    
1007  =over 4  =over 4
1008    
1009  =item newLevel  =item parameter
1010    
1011  Proposed new trace level.  A parameter from which the tracing key is computed. If it is a scalar,
1012    that scalar is used as the tracing key. If it is a CGI object, the
1013    tracing key is taken from the C<IP> cookie. If it is omitted, the
1014    tracing key is taken from the C<TRACING> environment variable. If it
1015    is a CGI object and emergency tracing is not on, the C<Trace> and
1016    C<TF> parameters will be used to determine the type of tracing.
1017    
1018  =back  =back
1019    
1020  =cut  =cut
1021    
1022  sub SetLevel {  sub ETracing {
1023      $TraceLevel = $_[0];      # Get the parameter.
1024        my ($parameter) = @_;
1025        # Check for CGI mode.
1026        if (defined $parameter && ref $parameter eq 'CGI') {
1027            $SavedCGI = $parameter;
1028        } else {
1029            $SavedCGI = undef;
1030        }
1031        # Default to no tracing except errors.
1032        my ($tracing, $dest) = ("0", "WARN");
1033        # Check for emergency tracing.
1034        my $tkey = EmergencyKey($parameter);
1035        my $emergencyFile = EmergencyFileName($tkey);
1036        if (-e $emergencyFile) {
1037            # We have the file. Read in the data.
1038            my @tracing = GetFile($emergencyFile);
1039            # Pull off the time limit.
1040            my $expire = shift @tracing;
1041            # Convert it to seconds.
1042            $expire *= 3600;
1043            # Check the file data.
1044            my $stat = stat($emergencyFile);
1045            my ($now) = gettimeofday;
1046            if ($now - $stat->mtime > $expire) {
1047                # Delete the expired file.
1048                unlink $emergencyFile;
1049            } else {
1050                # Emergency tracing is on. Pull off the destination and
1051                # the trace level;
1052                $dest = shift @tracing;
1053                my $level = shift @tracing;
1054                # Convert the destination to a real tracing destination.
1055                # temp directory.
1056                $dest = EmergencyTracingDest($tkey, $dest);
1057                # Insure Tracer is specified.
1058                my %moduleHash = map { $_ => 1 } @tracing;
1059                $moduleHash{Tracer} = 1;
1060                # Set the trace parameter.
1061                $tracing = join(" ", $level, sort keys %moduleHash);
1062            }
1063        } elsif (defined $SavedCGI) {
1064            # There's no emergency tracing, but we have a CGI object, so check
1065            # for tracing from the form parameters.
1066            if ($SavedCGI->param('Trace')) {
1067                # Here the user has requested tracing via a form.
1068                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1069                $tracing = $SavedCGI->param('Trace') . " Tracer";
1070            }
1071        }
1072        # Setup the tracing we've determined from all the stuff above.
1073        TSetup($tracing, $dest);
1074        # Check to see if we're a web script.
1075        if (defined $SavedCGI) {
1076            # Yes we are. Trace the form and environment data.
1077            TraceParms($SavedCGI);
1078            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1079            # emitted by the script in its raw form.
1080            if (T(Raw => 3)) {
1081                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1082  }  }
   
 =head3 Now  
   
 C<< my $string = Tracer::Now(); >>  
   
 Return a displayable time stamp containing the local time.  
   
 =cut  
   
 sub Now {  
     my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);  
     my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .  
                  _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);  
     return $retVal;  
1083  }  }
   
 # Pad a number to 2 digits.  
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
1084  }  }
1085    
1086  =head3 ParseTraceDate  =head3 EmergencyFileName
1087    
1088  C<< my $time = Tracer::ParseTraceDate($dateString); >>      my $fileName = Tracer::EmergencyFileName($tkey);
1089    
1090  Convert a date from the trace file into a PERL timestamp.  Return the emergency tracing file name. This is the file that specifies
1091    the tracing information.
1092    
1093  =over 4  =over 4
1094    
1095  =item dateString  =item tkey
1096    
1097  The date string from the trace file. The format of the string is determined by the  Tracing key for the current program.
 L</Now> method.  
1098    
1099  =item RETURN  =item RETURN
1100    
1101  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if  Returns the name of the file to contain the emergency tracing information.
 the time string is invalid.  
1102    
1103  =back  =back
1104    
1105  =cut  =cut
1106    
1107  sub ParseTraceDate {  sub EmergencyFileName {
1108      # Get the parameters.      # Get the parameters.
1109      my ($dateString) = @_;      my ($tkey) = @_;
1110      # Declare the return variable.      # Compute the emergency tracing file name.
1111      my $retVal;      return "$FIG_Config::temp/Emergency$tkey.txt";
     # Parse the date.  
     if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {  
         # Create a time object. Note we need to convert the day, month,  
         # and year to a different base. Years count from 1900, and  
         # the internal month value is relocated to January = 0.  
         $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);  
     }  
     # Return the result.  
     return $retVal;  
1112  }  }
1113    
1114  =head3 LogErrors  =head3 EmergencyFileTarget
1115    
1116  C<< Tracer::LogErrors($fileName); >>      my $fileName = Tracer::EmergencyFileTarget($tkey);
1117    
1118  Route the standard error output to a log file.  Return the emergency tracing target file name. This is the file that receives
1119    the tracing output for file-based tracing.
1120    
1121  =over 4  =over 4
1122    
1123  =item fileName  =item tkey
1124    
1125  Name of the file to receive the error output.  Tracing key for the current program.
1126    
1127    =item RETURN
1128    
1129    Returns the name of the file to contain the trace output.
1130    
1131  =back  =back
1132    
1133  =cut  =cut
1134    
1135  sub LogErrors {  sub EmergencyFileTarget {
1136      # Get the file name.      # Get the parameters.
1137      my ($fileName) = @_;      my ($tkey) = @_;
1138      # Open the file as the standard error output.      # Compute the emergency tracing file name.
1139      open STDERR, '>', $fileName;      return "$FIG_Config::temp/trace$tkey.log";
1140  }  }
1141    
1142  =head3 ReadOptions  =head3 EmergencyTracingDest
   
 C<< my %options = Tracer::ReadOptions($fileName); >>  
   
 Read a set of options from a file. Each option is encoded in a line of text that has the  
 format  
1143    
1144  I<optionName>C<=>I<optionValue>C<; >I<comment>      my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1145    
1146  The option name must consist entirely of letters, digits, and the punctuation characters  This method converts an emergency tracing destination to a real
1147  C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  tracing destination. The main difference is that if the
1148  character is a semi-colon will be ignored. The return hash will map each option name to  destination is C<FILE> or C<APPEND>, we convert it to file
1149  the corresponding option value.  output. If the destination is C<DUAL>, we convert it to file
1150    and standard output.
1151    
1152  =over 4  =over 4
1153    
1154  =item fileName  =item tkey
1155    
1156  Name of the file containing the option data.  Tracing key for this environment.
1157    
1158    =item myDest
1159    
1160    Destination from the emergency tracing file.
1161    
1162  =item RETURN  =item RETURN
1163    
1164  Returns a hash mapping the option names specified in the file to their corresponding option  Returns a destination that can be passed into L</TSetup>.
 value.  
1165    
1166  =back  =back
1167    
1168  =cut  =cut
1169    
1170  sub ReadOptions {  sub EmergencyTracingDest {
1171      # Get the parameters.      # Get the parameters.
1172      my ($fileName) = @_;      my ($tkey, $myDest) = @_;
1173      # Open the file.      # Declare the return variable.
1174      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");      my $retVal = $myDest;
1175      # Count the number of records read.      # Process according to the destination value.
1176      my ($records, $comments) = 0;      if ($myDest eq 'FILE') {
1177      # Create the return hash.          $retVal = ">" . EmergencyFileTarget($tkey);
1178      my %retVal = ();      } elsif ($myDest eq 'APPEND') {
1179      # Loop through the file, accumulating key-value pairs.          $retVal = ">>" . EmergencyFileTarget($tkey);
1180      while (my $line = <CONFIGFILE>) {      } elsif ($myDest eq 'DUAL') {
1181          # Denote we've read a line.          $retVal = "+>" . EmergencyFileTarget($tkey);
1182          $records++;      } elsif ($myDest eq 'WARN') {
1183          # Determine the line type.          $retVal = "WARN";
         if ($line =~ /^\s*[\n\r]/) {  
             # A blank line is a comment.  
             $comments++;  
         } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {  
             # Here we have an option assignment.  
             retVal{$1} = $2;  
         } elsif ($line =~ /^\s*;/) {  
             # Here we have a text comment.  
             $comments++;  
         } else {  
             # Here we have an invalid line.  
             Trace("Invalid option statement in record $records.") if T(0);  
         }  
1184      }      }
1185      # Return the hash created.      # Return the result.
1186      return %retVal;      return $retVal;
1187  }  }
1188    
1189  =head3 GetOptions  =head3 Emergency
1190    
1191  C<< Tracer::GetOptions(\%defaults, \%options); >>      Emergency($key, $hours, $dest, $level, @modules);
1192    
1193  Merge a specified set of options into a table of defaults. This method takes two hash references  Turn on emergency tracing. This method is normally invoked over the web from
1194  as input and uses the data from the second to update the first. If the second does not exist,  a debugging console, but it can also be called by the C<trace.pl> script.
1195  there will be no effect. An error will be thrown if one of the entries in the second hash does not  The caller specifies the duration of the emergency in hours, the desired tracing
1196  exist in the first.  destination, the trace level, and a list of the trace modules to activate.
1197    For the length of the duration, when a program in an environment with the
1198    specified tracing key active invokes a Sprout CGI script, tracing will be
1199    turned on automatically. See L</TSetup> for more about tracing setup and
1200    L</ETracing> for more about emergency tracing.
1201    
1202  Consider the following example.  =over 4
1203    
1204  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  =item tkey
1205    
1206  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  The tracing key. This is used to identify the control file and the trace file.
 B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  
 B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and  
 the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  
 will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  
1207    
1208  C<< {databaseType => 'Oracle'} >>  =item hours
1209    
1210  an error will occur because the B<databaseType> option does not exist.  Number of hours to keep emergency tracing alive.
1211    
1212  =over 4  =item dest
1213    
1214  =item defaults  Tracing destination. If no path information is specified for a file
1215    destination, it is put in the FIG temporary directory.
1216    
1217  Table of default option values.  =item level
1218    
1219  =item options  Tracing level. A higher level means more trace messages.
1220    
1221  Table of overrides, if any.  =item modules
1222    
1223    A list of the tracing modules to activate.
1224    
1225    =back
1226    
1227    =cut
1228    
1229    sub Emergency {
1230        # Get the parameters.
1231        my ($tkey, $hours, $dest, $level, @modules) = @_;
1232        # Create the emergency file.
1233        my $specFile = EmergencyFileName($tkey);
1234        my $outHandle = Open(undef, ">$specFile");
1235        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1236    }
1237    
1238    =head3 EmergencyKey
1239    
1240        my $tkey = EmergencyKey($parameter);
1241    
1242    Return the Key to be used for emergency tracing. This could be an IP address,
1243     a session ID, or a user name, depending on the environment.
1244    
1245    =over 4
1246    
1247    =item parameter
1248    
1249    Parameter defining the method for finding the tracing key. If it is a scalar,
1250    then it is presumed to be the tracing key itself. If it is a CGI object, then
1251    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1252    taken from the C<TRACING> environment variable.
1253    
1254  =item RETURN  =item RETURN
1255    
1256  Returns a reference to the default table passed in as the first parameter.  Returns the key to be used for labels in emergency tracing.
1257    
1258  =back  =back
1259    
1260  =cut  =cut
1261    
1262  sub GetOptions {  sub EmergencyKey {
1263      # Get the parameters.      # Get the parameters.
1264      my ($defaults, $options) = @_;      my ($parameter) = @_;
1265      # Check for overrides.      # Declare the return variable.
1266      if ($options) {      my $retVal;
1267          # Loop through the overrides.      # Determine the parameter type.
1268          while (my ($option, $setting) = each %{$options}) {      if (! defined $parameter) {
1269              # Insure this override exists.          # Here we're supposed to check the environment. If that fails, we
1270              if (!exists $defaults->{$option}) {          # get the effective login ID.
1271                  croak "Unrecognized option $option encountered.";          $retVal = $ENV{TRACING} || scalar getpwuid($<);
1272              } else {              } else {
1273                  # Apply the override.          my $ptype = ref $parameter;
1274                  $defaults->{$option} = $setting;          if ($ptype eq 'CGI') {
1275                # Here we were invoked from a web page. Look for a cookie.
1276                $retVal = $parameter->cookie('IP');
1277            } elsif (! $ptype) {
1278                # Here the key was passed in.
1279                $retVal = $parameter;
1280              }              }
1281          }          }
1282        # If no luck finding a key, use the PID.
1283        if (! defined $retVal) {
1284            $retVal = $$;
1285      }      }
1286      # Return the merged table.      # Return the result.
1287      return $defaults;      return $retVal;
1288  }  }
1289    
 =head3 MergeOptions  
   
 C<< Tracer::MergeOptions(\%table, \%defaults); >>  
1290    
1291  Merge default values into a hash table. This method looks at the key-value pairs in the  =head3 TraceParms
 second (default) hash, and if a matching key is not found in the first hash, the default  
 pair is copied in. The process is similar to L</GetOptions>, but there is no error-  
 checking and no return value.  
1292    
1293  =over 4      Tracer::TraceParms($cgi);
1294    
1295  =item table  Trace the CGI parameters at trace level CGI => 3 and the environment variables
1296    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1297    
1298  Hash table to be updated with the default values.  =over 4
1299    
1300  =item defaults  =item cgi
1301    
1302  Default values to be merged into the first hash table if they are not already present.  CGI query object containing the parameters to trace.
1303    
1304  =back  =back
1305    
1306  =cut  =cut
1307    
1308  sub MergeOptions {  sub TraceParms {
1309      # Get the parameters.      # Get the parameters.
1310      my ($table, $defaults) = @_;      my ($cgi) = @_;
1311      # Loop through the defaults.      if (T(CGI => 2)) {
1312      while (my ($key, $value) = each %{$defaults}) {          # Here we trace the GET-style URL for the script.
1313          if (!exists $table->{$key}) {          Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1314              $table->{$key} = $value;      }
1315        if (T(CGI => 3)) {
1316            # Here we want to trace the parameter data.
1317            my @names = $cgi->param;
1318            for my $parmName (sort @names) {
1319                # Note we skip the Trace parameters, which are for our use only.
1320                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1321                    my @values = $cgi->param($parmName);
1322                    Trace("[CGI] $parmName = " . join(", ", @values));
1323                }
1324            }
1325            # Display the request method.
1326            my $method = $cgi->request_method();
1327            Trace("Method: $method");
1328        }
1329        if (T(CGI => 4)) {
1330            # Here we want the environment data too.
1331            for my $envName (sort keys %ENV) {
1332                Trace("[ENV] $envName = $ENV{$envName}");
1333          }          }
1334      }      }
1335  }  }
1336    
1337  =head3 Trace  =head3 TraceImages
1338    
1339  C<< Trace($message); >>      Tracer::TraceImages($htmlString);
1340    
1341  Write a trace message to the target location specified in L</TSetup>. If there has not been  Trace information about all of an html document's images. The tracing
1342  any prior call to B<TSetup>.  will be for type "IMG" at level 3. The image's source string
1343    will be displayed. This is generally either the URL of the image or
1344    raw data for the image itself. If the source is too long, only the first 300
1345    characters will be shown at trace level 3. The entire source will be shown,
1346    however, at trace level 4. This method is not very smart, and might catch
1347    Javascript code, but it is still useful when debugging the arcane
1348    behavior of images in multiple browser environments.
1349    
1350  =over 4  =over 4
1351    
1352  =item message  =item htmlString
1353    
1354  Message to write.  HTML text for an outgoing web page.
1355    
1356  =back  =back
1357    
1358  =cut  =cut
1359    
1360  sub Trace {  sub TraceImages {
1361      # Get the parameters.      # Only proceed if we're at the proper trace level.
1362      my ($message) = @_;      if (T(IMG => 3)) {
1363      # Get the timestamp.          # For performance reasons we're manipulating $_[0] instead of retrieving the string
1364      my $timeStamp = Now();          # into a variable called "$htmlString". This is because we expect html strings to be
1365      # Format the message. Note we strip off any line terminators at the end.          # long, and don't want to copy them any more than we have to.
1366      my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);          Trace(length($_[0]) . " characters in web page.");
1367      # Process according to the destination.          # Loop through the HTML, culling image tags.
1368      if ($Destination eq "TEXT") {          while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1369          # Write the message to the standard output.              # Extract the source string and determine whether or not it's too long.
1370          print "$formatted\n";              my $srcString = $1;
1371      } elsif ($Destination eq "ERROR") {              my $pos = pos($_[0]) - length($srcString);
1372          # Write the message to the error output.              my $excess = length($srcString) - 300;
1373          print STDERR "$formatted\n";              # We'll put the display string in here.
1374      } elsif ($Destination eq "QUEUE") {              my $srcDisplay = $srcString;
1375          # Push the message into the queue.              # If it's a data string, split it at the comma.
1376          push @Queue, "$formatted";              $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1377      } elsif ($Destination eq "HTML") {              # If there's no excess or we're at trace level 4, we're done. At level 3 with
1378          # Convert the message to HTML and write it to the standard output.              # a long string, however, we only show the first 300 characters.
1379          my $escapedMessage = CGI::escapeHTML($message);              if ($excess > 0 && ! T(IMG => 4)) {
1380          print "<p>$formatted</p>\n";                  $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1381      } elsif ($Destination eq "WARN") {              }
1382         # Emit the message as a warning.              # Output the trace message.
1383         warn $message;              Trace("Image tag at position $pos:\n$srcDisplay");
     } 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";  
1384          }          }
1385      }      }
1386  }  }
1387    
1388  =head3 T  =head2 Command-Line Utility Methods
1389    
1390  C<< my $switch = T($category, $traceLevel); >>  =head3 SendSMS
1391    
1392      or      my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1393    
1394  C<< my $switch = T($traceLevel); >>  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1395    user name, password, and API ID for the relevant account in the hash reference variable
1396    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1397    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1398    is C<2561022>, then the FIG_Config file must contain
1399    
1400  Return TRUE if the trace level is at or above a specified value and the specified category      $phone =  { user => 'BruceTheHumanPet',
1401  is active, else FALSE. If no category is specified, the caller's package name is used.                  password => 'silly',
1402                    api_id => '2561022' };
1403    
1404    The original purpose of this method was to insure Bruce would be notified immediately when the
1405    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1406    when you call this method.
1407    
1408    The message ID will be returned if successful, and C<undef> if an error occurs.
1409    
1410  =over 4  =over 4
1411    
1412  =item category  =item phoneNumber
1413    
1414  Category to which the message belongs. If not specified, the caller's package name is  Phone number to receive the message, in international format. A United States phone number
1415  used.  would be prefixed by "1". A British phone number would be prefixed by "44".
1416    
1417  =item traceLevel  =item msg
1418    
1419  Relevant tracing level.  Message to send to the specified phone.
1420    
1421  =item RETURN  =item RETURN
1422    
1423  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  Returns the message ID if successful, and C<undef> if the message could not be sent.
1424    
1425  =back  =back
1426    
1427  =cut  =cut
1428    
1429  sub T {  sub SendSMS {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
1430          # Get the parameters.          # Get the parameters.
1431          my ($category, $traceLevel) = @_;      my ($phoneNumber, $msg) = @_;
1432          if (!defined $traceLevel) {      # Declare the return variable. If we do not change it, C<undef> will be returned.
1433              # Here we have no category, so we need to get the calling package.      my $retVal;
1434              # The calling package is normally the first parameter. If it is      # Only proceed if we have phone support.
1435              # omitted, the first parameter will be the tracelevel. So, the      if (! defined $FIG_Config::phone) {
1436              # first thing we do is shift the so-called category into the          Trace("Phone support not present in FIG_Config.") if T(1);
1437              # $traceLevel variable where it belongs.      } else {
1438              $traceLevel = $category;          # Get the phone data.
1439              my ($package, $fileName, $line) = caller;          my $parms = $FIG_Config::phone;
1440              # If there is no calling package, we default to "main".          # Get the Clickatell URL.
1441              if (!$package) {          my $url = "http://api.clickatell.com/http/";
1442                  $category = "main";          # Create the user agent.
1443            my $ua = LWP::UserAgent->new;
1444            # Request a Clickatell session.
1445            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1446                                         password => $parms->{password},
1447                                         api_id => $parms->{api_id},
1448                                         to => $phoneNumber,
1449                                         text => $msg});
1450            # Check for an error.
1451            if (! $resp->is_success) {
1452                Trace("Alert failed.") if T(1);
1453            } else {
1454                # Get the message ID.
1455                my $rstring = $resp->content;
1456                if ($rstring =~ /^ID:\s+(.*)$/) {
1457                    $retVal = $1;
1458              } else {              } else {
1459                  $category = $package;                  Trace("Phone attempt failed with $rstring") if T(1);
1460                }
1461            }
1462        }
1463        # Return the result.
1464        return $retVal;
1465    }
1466    
1467    =head3 StandardSetup
1468    
1469        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1470    
1471    This method performs standard command-line parsing and tracing setup. The return
1472    values are a hash of the command-line options and a list of the positional
1473    parameters. Tracing is automatically set up and the command-line options are
1474    validated.
1475    
1476    This is a complex method that does a lot of grunt work. The parameters can
1477    be more easily understood, however, once they are examined individually.
1478    
1479    The I<categories> parameter is the most obtuse. It is a reference to a list of
1480    special-purpose tracing categories. Most tracing categories are PERL package
1481    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1482    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1483    
1484        ["Sprout", "SproutLoad", "ERDB"]
1485    
1486    This would cause trace messages in the specified three packages to appear in
1487    the output. There are two special tracing categories that are automatically
1488    handled by this method. In other words, if you used L</TSetup> you would need
1489    to include these categories manually, but if you use this method they are turned
1490    on automatically.
1491    
1492    =over 4
1493    
1494    =item SQL
1495    
1496    Traces SQL commands and activity.
1497    
1498    =item Tracer
1499    
1500    Traces error messages and call stacks.
1501    
1502    =back
1503    
1504    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1505    The trace level is specified using the C<-trace> command-line option. For example,
1506    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1507    all tracing at level 3.
1508    
1509        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1510    
1511    Standard tracing is output to the standard output and echoed to the file
1512    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1513    process ID. You can also specify the C<user> parameter to put a user ID
1514    instead of a process ID in the trace file name. So, for example
1515    
1516    The default trace level is 2. To get all messages, specify a trace level of 4.
1517    For a genome-by-genome update, use 3.
1518    
1519        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1520    
1521    would send the trace output to C<traceBruce.log> in the temporary directory.
1522    
1523    The I<options> parameter is a reference to a hash containing the command-line
1524    options, their default values, and an explanation of what they mean. Command-line
1525    options may be in the form of switches or keywords. In the case of a switch, the
1526    option value is 1 if it is specified and 0 if it is not specified. In the case
1527    of a keyword, the value is separated from the option name by an equal sign. You
1528    can see this last in the command-line example above.
1529    
1530    You can specify a different default trace level by setting C<$options->{trace}>
1531    prior to calling this method.
1532    
1533    An example at this point would help. Consider, for example, the command-line utility
1534    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1535    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1536    the following code.
1537    
1538        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1539                            { safe => [0, "use database transactions"],
1540                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1541                              start => [' ', "start with this genome"],
1542                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1543                            "<command> <transactionDirectory> <IDfile>",
1544                          @ARGV);
1545    
1546    
1547    The call to C<ParseCommand> specifies the default values for the options and
1548    stores the actual options in a hash that is returned as C<$options>. The
1549    positional parameters are returned in C<@parameters>.
1550    
1551    The following is a sample command line for C<TransactFeatures>.
1552    
1553        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1554    
1555    Single and double hyphens are equivalent. So, you could also code the
1556    above command as
1557    
1558        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1559    
1560    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1561    parameters, and would find themselves in I<@parameters> after executing the
1562    above code fragment. The tracing would be set to level 2, and the categories
1563    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1564    and C<DocUtils> was included because it came in within the first parameter
1565    to this method. The I<$options> hash would be
1566    
1567        { trace => 2, sql => 0, safe => 0,
1568          noAlias => 1, start => ' ', tblFiles => 0 }
1569    
1570    Use of C<StandardSetup> in this way provides a simple way of performing
1571    standard tracing setup and command-line parsing. Note that the caller is
1572    not even aware of the command-line switches C<-trace> and C<-sql>, which
1573    are used by this method to control the tracing. If additional tracing features
1574    need to be added in the future, they can be processed by this method without
1575    upsetting the command-line utilities.
1576    
1577    If the C<background> option is specified on the command line, then the
1578    standard and error outputs will be directed to files in the temporary
1579    directory, using the same suffix as the trace file. So, if the command
1580    line specified
1581    
1582        -user=Bruce -background
1583    
1584    then the trace output would go to C<traceBruce.log>, the standard output to
1585    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1586    simplify starting a command in the background.
1587    
1588    The user name is also used as the tracing key for L</Emergency Tracing>.
1589    Specifying a value of C<E> for the trace level causes emergency tracing to
1590    be used instead of custom tracing. If the user name is not specified,
1591    the tracing key is taken from the C<Tracing> environment variable. If there
1592    is no value for that variable, the tracing key will be computed from the active
1593    login ID.
1594    
1595    Since the default situation in StandardSetup is to trace to the standard
1596    output, errors that occur in command-line scripts will not generate
1597    RSS events. To force the events, use the C<warn> option.
1598    
1599        TransactFeatures -background -warn register ../xacts IDs.tbl
1600    
1601    Finally, if the special option C<-help> is specified, the option
1602    names will be traced at level 0 and the program will exit without processing.
1603    This provides a limited help capability. For example, if the user enters
1604    
1605        TransactFeatures -help
1606    
1607    he would see the following output.
1608    
1609        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1610            -trace    tracing level (default E)
1611            -sql      trace SQL commands
1612            -safe     use database transactions
1613            -noAlias  do not expect aliases in CHANGE transactions
1614            -start    start with this genome
1615            -tblFiles output TBL files containing the corrected IDs
1616    
1617    The caller has the option of modifying the tracing scheme by placing a value
1618    for C<trace> in the incoming options hash. The default value can be overridden,
1619    or the tracing to the standard output can be turned off by suffixing a minus
1620    sign to the trace level. So, for example,
1621    
1622        { trace => [0, "tracing level (default 0)"],
1623           ...
1624    
1625    would set the default trace level to 0 instead of E, while
1626    
1627        { trace => ["2-", "tracing level (default 2)"],
1628           ...
1629    
1630    would set the default to 2, but trace only to the log file, not to the
1631    standard output.
1632    
1633    The parameters to this method are as follows.
1634    
1635    =over 4
1636    
1637    =item categories
1638    
1639    Reference to a list of tracing category names. These should be names of
1640    packages whose internal workings will need to be debugged to get the
1641    command working.
1642    
1643    =item options
1644    
1645    Reference to a hash containing the legal options for the current command mapped
1646    to their default values and descriptions. The user can override the defaults
1647    by specifying the options as command-line switches prefixed by a hyphen.
1648    Tracing-related options may be added to this hash. If the C<-h> option is
1649    specified on the command line, the option descriptions will be used to
1650    explain the options. To turn off tracing to the standard output, add a
1651    minus sign to the value for C<trace> (see above).
1652    
1653    =item parmHelp
1654    
1655    A string that vaguely describes the positional parameters. This is used
1656    if the user specifies the C<-h> option.
1657    
1658    =item argv
1659    
1660    List of command line parameters, including the option switches, which must
1661    precede the positional parameters and be prefixed by a hyphen.
1662    
1663    =item RETURN
1664    
1665    Returns a list. The first element of the list is the reference to a hash that
1666    maps the command-line option switches to their values. These will either be the
1667    default values or overrides specified on the command line. The remaining
1668    elements of the list are the position parameters, in order.
1669    
1670    =back
1671    
1672    =cut
1673    
1674    sub StandardSetup {
1675        # Get the parameters.
1676        my ($categories, $options, $parmHelp, @argv) = @_;
1677        # Get the default tracing key.
1678        my $tkey = EmergencyKey();
1679        # Save the command line.
1680        $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1681        # Add the tracing options.
1682        if (! exists $options->{trace}) {
1683            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1684        }
1685        $options->{sql} = [0, "turn on SQL tracing"];
1686        $options->{help} = [0, "display command-line options"];
1687        $options->{user} = [$tkey, "tracing key"];
1688        $options->{background} = [0, "spool standard and error output"];
1689        $options->{warn} = [0, "send errors to RSS feed"];
1690        # Create a parsing hash from the options hash. The parsing hash
1691        # contains the default values rather than the default value
1692        # and the description. While we're at it, we'll memorize the
1693        # length of the longest option name.
1694        my $longestName = 0;
1695        my %parseOptions = ();
1696        for my $key (keys %{$options}) {
1697            if (length $key > $longestName) {
1698                $longestName = length $key;
1699            }
1700            $parseOptions{$key} = $options->{$key}->[0];
1701        }
1702        # Parse the command line.
1703        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1704        # Get the logfile suffix.
1705        my $suffix = $retOptions->{user};
1706        # Check for background mode.
1707        if ($retOptions->{background}) {
1708            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1709            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1710            open STDOUT, ">$outFileName";
1711            open STDERR, ">$errFileName";
1712            # Check for phone support. If we have phone support and a phone number,
1713            # we want to turn it on.
1714            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1715                $retOptions->{phone} = $ENV{PHONE};
1716            }
1717        }
1718        # Now we want to set up tracing. First, we need to know if the user
1719        # wants emergency tracing.
1720        if ($retOptions->{trace} eq 'E') {
1721            ETracing($retOptions->{user});
1722        } else {
1723            # Here the tracing is controlled from the command line.
1724            my @cats = @{$categories};
1725            if ($retOptions->{sql}) {
1726                push @cats, "SQL";
1727            }
1728            if ($retOptions->{warn}) {
1729                push @cats, "Feed";
1730            }
1731            # Add the default categories.
1732            push @cats, "Tracer";
1733            # Next, we create the category string by joining the categories.
1734            my $cats = join(" ", @cats);
1735            # Check to determine whether or not the caller wants to turn off tracing
1736            # to the standard output.
1737            my $traceLevel = $retOptions->{trace};
1738            my $textOKFlag = 1;
1739            if ($traceLevel =~ /^(.)-/) {
1740                $traceLevel = $1;
1741                $textOKFlag = 0;
1742            }
1743            # Now we set up the trace mode.
1744            my $traceMode;
1745            # Verify that we can open a file in the FIG temporary directory.
1746            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1747            if (open TESTTRACE, ">$traceFileName") {
1748                # Here we can trace to a file.
1749                $traceMode = ">$traceFileName";
1750                if ($textOKFlag) {
1751                    # Echo to standard output if the text-OK flag is set.
1752                    $traceMode = "+$traceMode";
1753                }
1754                # Close the test file.
1755                close TESTTRACE;
1756            } else {
1757                # Here we can't trace to a file. Complain about this.
1758                warn "Could not open trace file $traceFileName: $!\n";
1759                # We trace to the standard output if it's
1760                # okay, and the error log otherwise.
1761                if ($textOKFlag) {
1762                    $traceMode = "TEXT";
1763                } else {
1764                    $traceMode = "WARN";
1765                }
1766            }
1767            # Now set up the tracing.
1768            TSetup("$traceLevel $cats", $traceMode);
1769        }
1770        # Check for the "help" option. If it is specified, dump the command-line
1771        # options and exit the program.
1772        if ($retOptions->{help}) {
1773            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1774            print "$1 [options] $parmHelp\n";
1775            for my $key (sort keys %{$options}) {
1776                my $name = Pad($key, $longestName, 0, ' ');
1777                my $desc = $options->{$key}->[1];
1778                if ($options->{$key}->[0]) {
1779                    $desc .= " (default " . $options->{$key}->[0] . ")";
1780              }              }
1781                print "  $name $desc\n";
1782          }          }
1783          # Save the category name.          exit(0);
         $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.");  
1784          }          }
1785          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));      # Trace the options, if applicable.
1786        if (T(3)) {
1787            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1788            Trace("Selected options: " . join(", ", sort @parms) . ".");
1789      }      }
1790      # Return the computed result.      # Return the parsed parameters.
1791      return $retVal;      return ($retOptions, @retParameters);
1792  }  }
1793    
1794  =head3 ParseCommand  =head3 ReadOptions
   
 C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  
   
 Parse a command line consisting of a list of parameters. The initial parameters may be option  
 specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  
 off and merged into a table of default options. The remainder of the command line is  
 returned as a list of positional arguments. For example, consider the following invocation.  
   
 C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  
   
 In this case, the list @words will be treated as a command line. There are two options available,  
 B<errors> and B<logFile>. If @words has the following format  
   
 C<< -logFile=error.log apple orange rutabaga >>  
   
 then at the end of the invocation, C<$options> will be  
1795    
1796  C<< { errors => 0, logFile => 'error.log' } >>      my %options = Tracer::ReadOptions($fileName);
1797    
1798  and C<@arguments> will contain  Read a set of options from a file. Each option is encoded in a line of text that has the
1799    format
1800    
1801  C<< apple orange rutabaga >>  I<optionName>C<=>I<optionValue>C<; >I<comment>
1802    
1803  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The option name must consist entirely of letters, digits, and the punctuation characters
1804  support for quote characters.  C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1805    character is a semi-colon will be ignored. The return hash will map each option name to
1806    the corresponding option value.
1807    
1808  =over 4  =over 4
1809    
1810  =item optionTable  =item fileName
   
 Table of default options.  
   
 =item inputList  
1811    
1812  List of words on the command line.  Name of the file containing the option data.
1813    
1814  =item RETURN  =item RETURN
1815    
1816  Returns a reference to the option table and a list of the positional arguments.  Returns a hash mapping the option names specified in the file to their corresponding option
1817    value.
1818    
1819  =back  =back
1820    
1821  =cut  =cut
1822    
1823  sub ParseCommand {  sub ReadOptions {
1824      # Get the parameters.      # Get the parameters.
1825      my ($optionTable, @inputList) = @_;      my ($fileName) = @_;
1826      # Process any options in the input list.      # Open the file.
1827      my %overrides = ();      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1828      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      # Count the number of records read.
1829          # Get the current option.      my ($records, $comments) = 0;
1830          my $arg = shift @inputList;      # Create the return hash.
1831          # Pull out the option name.      my %retVal = ();
1832          $arg =~ /^-([^=]*)/g;      # Loop through the file, accumulating key-value pairs.
1833          my $name = $1;      while (my $line = <CONFIGFILE>) {
1834          # Check for an option value.          # Denote we've read a line.
1835          if ($arg =~ /\G=(.*)$/g) {          $records++;
1836              # Here we have a value for the option.          # Determine the line type.
1837              $overrides{$name} = UnEscape($1);          if ($line =~ /^\s*[\n\r]/) {
1838                # A blank line is a comment.
1839                $comments++;
1840            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1841                # Here we have an option assignment.
1842                retVal{$1} = $2;
1843            } elsif ($line =~ /^\s*;/) {
1844                # Here we have a text comment.
1845                $comments++;
1846          } else {          } else {
1847              # Here there is no value, so we use 1.              # Here we have an invalid line.
1848              $overrides{$name} = 1;              Trace("Invalid option statement in record $records.") if T(0);
         }  
1849      }      }
     # Merge the options into the defaults.  
     GetOptions($optionTable, \%overrides);  
     # Translate the remaining parameters.  
     my @retVal = ();  
     for my $inputParm (@inputList) {  
         push @retVal, UnEscape($inputParm);  
1850      }      }
1851      # Return the results.      # Return the hash created.
1852      return ($optionTable, @retVal);      return %retVal;
1853  }  }
1854    
1855  =head3 Escape  =head3 GetOptions
   
 C<< my $codedString = Tracer::Escape($realString); >>  
   
 Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  
 replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
 result is to reverse the effect of L</UnEscape>.  
   
 =over 4  
   
 =item realString  
1856    
1857  String to escape.      Tracer::GetOptions(\%defaults, \%options);
1858    
1859  =item RETURN  Merge a specified set of options into a table of defaults. This method takes two hash references
1860    as input and uses the data from the second to update the first. If the second does not exist,
1861    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1862    exist in the first.
1863    
1864  Escaped equivalent of the real string.  Consider the following example.
1865    
1866  =back      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1867    
1868  =cut  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1869    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1870    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1871    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1872    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1873    
1874  sub Escape {      {databaseType => 'Oracle'}
     # Get the parameter.  
     my ($realString) = @_;  
     # Initialize the return variable.  
     my $retVal = "";  
     # Loop through the parameter string, looking for sequences to escape.  
     while (length $realString > 0) {  
         # Look for the first sequence to escape.  
         if ($realString =~ /^(.*?)([\n\t\r\\])/) {  
             # Here we found it. The text preceding the sequence is in $1. The sequence  
             # itself is in $2. First, move the clear text to the return variable.  
             $retVal .= $1;  
             # Strip the processed section off the real string.  
             $realString = substr $realString, (length $2) + (length $1);  
             # Get the matched character.  
             my $char = $2;  
             # If we have a CR, we are done.  
             if ($char ne "\r") {  
                 # It's not a CR, so encode the escape sequence.  
                 $char =~ tr/\t\n/tn/;  
                 $retVal .= "\\" . $char;  
             }  
         } else {  
             # Here there are no more escape sequences. The rest of the string is  
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
         }  
     }  
     # Return the result.  
     return $retVal;  
 }  
1875    
1876  =head3 UnEscape  an error will occur because the B<databaseType> option does not exist.
1877    
1878  C<< my $realString = Tracer::UnEscape($codedString); >>  =over 4
1879    
1880  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  =item defaults
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
1881    
1882  =over 4  Table of default option values.
1883    
1884  =item codedString  =item options
1885    
1886  String to un-escape.  Table of overrides, if any.
1887    
1888  =item RETURN  =item RETURN
1889    
1890  Returns a copy of the original string with the escape sequences converted to their actual  Returns a reference to the default table passed in as the first parameter.
 values.  
1891    
1892  =back  =back
1893    
1894  =cut  =cut
1895    
1896  sub UnEscape {  sub GetOptions {
1897      # Get the parameter.      # Get the parameters.
1898      my ($codedString) = @_;      my ($defaults, $options) = @_;
1899      # Initialize the return variable.      # Check for overrides.
1900      my $retVal = "";      if ($options) {
1901      # Only proceed if the incoming string is nonempty.          # Loop through the overrides.
1902      if (defined $codedString) {          while (my ($option, $setting) = each %{$options}) {
1903          # Loop through the parameter string, looking for escape sequences. We can't do              # Insure this override exists.
1904          # translating because it causes problems with the escaped slash. ("\\t" becomes              if (!exists $defaults->{$option}) {
1905          # "\<tab>" no matter what we do.)                  croak "Unrecognized option $option encountered.";
         while (length $codedString > 0) {  
             # Look for the first escape sequence.  
             if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {  
                 # Here we found it. The text preceding the sequence is in $1. The sequence  
                 # itself is in $2. First, move the clear text to the return variable.  
                 $retVal .= $1;  
                 $codedString = substr $codedString, (2 + length $1);  
                 # Get the escape value.  
                 my $char = $2;  
                 # If we have a "\r", we are done.  
                 if ($char ne 'r') {  
                     # Here it's not an 'r', so we convert it.  
                     $char =~ tr/\\tn/\\\t\n/;  
                     $retVal .= $char;  
                 }  
1906              } else {              } else {
1907                  # Here there are no more escape sequences. The rest of the string is                  # Apply the override.
1908                  # transferred unmodified.                  $defaults->{$option} = $setting;
                 $retVal .= $codedString;  
                 $codedString = "";  
             }  
         }  
1909      }      }
     # Return the result.  
     return $retVal;  
1910  }  }
   
 =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;  
1911      }      }
1912      # Return the result.      # Return the merged table.
1913      return @retVal;      return $defaults;
1914  }  }
1915    
1916  =head3 Merge  =head3 MergeOptions
1917    
1918  C<< my @mergedList = Tracer::Merge(@inputList); >>      Tracer::MergeOptions(\%table, \%defaults);
1919    
1920  Sort a list of strings and remove duplicates.  Merge default values into a hash table. This method looks at the key-value pairs in the
1921    second (default) hash, and if a matching key is not found in the first hash, the default
1922    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1923    checking and no return value.
1924    
1925  =over 4  =over 4
1926    
1927  =item inputList  =item table
1928    
1929  List of scalars to sort and merge.  Hash table to be updated with the default values.
1930    
1931  =item RETURN  =item defaults
1932    
1933  Returns a list containing the same elements sorted in ascending order with duplicates  Default values to be merged into the first hash table if they are not already present.
 removed.  
1934    
1935  =back  =back
1936    
1937  =cut  =cut
1938    
1939  sub Merge {  sub MergeOptions {
1940      # Get the input list in sort order.      # Get the parameters.
1941      my @inputList = sort @_;      my ($table, $defaults) = @_;
1942      # Only proceed if the list has at least two elements.      # Loop through the defaults.
1943      if (@inputList > 1) {      while (my ($key, $value) = each %{$defaults}) {
1944          # Now we want to move through the list splicing out duplicates.          if (!exists $table->{$key}) {
1945          my $i = 0;              $table->{$key} = $value;
         while ($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++;  
1946          }          }
1947      }      }
     # Return the merged list.  
     return @inputList;  
1948  }  }
1949    
1950  =head3 Percent  =head3 ParseCommand
1951    
1952  C<< my $percent = Tracer::Percent($number, $base); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1953    
1954  Returns the percent of the base represented by the given number. If the base  Parse a command line consisting of a list of parameters. The initial parameters may be option
1955  is zero, returns zero.  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1956    off and merged into a table of default options. The remainder of the command line is
1957    returned as a list of positional arguments. For example, consider the following invocation.
1958    
1959        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1960    
1961    In this case, the list @words will be treated as a command line and there are two options available,
1962    B<errors> and B<logFile>. If @words has the following format
1963    
1964        -logFile=error.log apple orange rutabaga
1965    
1966    then at the end of the invocation, C<$options> will be
1967    
1968        { errors => 0, logFile => 'error.log' }
1969    
1970    and C<@arguments> will contain
1971    
1972        apple orange rutabaga
1973    
1974    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1975    support for quote characters. Options can be specified with single or double hyphens.
1976    
1977  =over 4  =over 4
1978    
1979  =item number  =item optionTable
1980    
1981  Percent numerator.  Table of default options.
1982    
1983  =item base  =item inputList
1984    
1985  Percent base.  List of words on the command line.
1986    
1987  =item RETURN  =item RETURN
1988    
1989  Returns the percentage of the base represented by the numerator.  Returns a reference to the option table and a list of the positional arguments.
1990    
1991  =back  =back
1992    
1993  =cut  =cut
1994    
1995  sub Percent {  sub ParseCommand {
1996      # Get the parameters.      # Get the parameters.
1997      my ($number, $base) = @_;      my ($optionTable, @inputList) = @_;
1998      # Declare the return variable.      # Process any options in the input list.
1999      my $retVal = 0;      my %overrides = ();
2000      # Compute the percent.      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2001      if ($base != 0) {          # Get the current option.
2002          $retVal = $number * 100 / $base;          my $arg = shift @inputList;
2003            # Pull out the option name.
2004            $arg =~ /^--?([^=]*)/g;
2005            my $name = $1;
2006            # Check for an option value.
2007            if ($arg =~ /\G=(.*)$/g) {
2008                # Here we have a value for the option.
2009                $overrides{$name} = UnEscape($1);
2010            } else {
2011                # Here there is no value, so we use 1.
2012                $overrides{$name} = 1;
2013      }      }
     # Return the result.  
     return $retVal;  
2014  }  }
2015        # Merge the options into the defaults.
2016        GetOptions($optionTable, \%overrides);
2017        # Translate the remaining parameters.
2018        my @retVal = ();
2019        for my $inputParm (@inputList) {
2020            push @retVal, UnEscape($inputParm);
2021        }
2022        # Return the results.
2023        return ($optionTable, @retVal);
2024    }
2025    
2026    
2027    =head2 File Utility Methods
2028    
2029  =head3 GetFile  =head3 GetFile
2030    
2031  C<< my @fileContents = Tracer::GetFile($fileName); >>      my @fileContents = Tracer::GetFile($fileName);
2032    
2033      or      or
2034    
2035  C<< my $fileContents = Tracer::GetFile($fileName); >>      my $fileContents = Tracer::GetFile($fileName);
2036    
2037  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
2038  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 1646  Line 2080 
2080      }      }
2081  }  }
2082    
2083  =head3 PutFile  =head3 PutFile
   
 C<< Tracer::PutFile($fileName, \@lines); >>  
   
 Write out a file from a list of lines of text.  
   
 =over 4  
   
 =item fileName  
   
 Name of the output file.  
   
 =item lines  
   
 Reference to a list of text lines. The lines will be written to the file in order, with trailing  
 new-line characters. Alternatively, may be a string, in which case the string will be written without  
 modification.  
   
 =back  
   
 =cut  
   
 sub PutFile {  
     # Get the parameters.  
     my ($fileName, $lines) = @_;  
     # Open the output file.  
     my $handle = Open(undef, ">$fileName");  
     # Count the lines written.  
     if (ref $lines ne 'ARRAY') {  
         # Here we have a scalar, so we write it raw.  
         print $handle $lines;  
         Trace("Scalar put to file $fileName.") if T(File => 3);  
     } else {  
         # Write the lines one at a time.  
         my $count = 0;  
         for my $line (@{$lines}) {  
             print $handle "$line\n";  
             $count++;  
         }  
         Trace("$count lines put to file $fileName.") if T(File => 3);  
     }  
     # Close the output file.  
     close $handle;  
 }  
   
 =head3 QTrace  
   
 C<< my $data = QTrace($format); >>  
   
 Return the queued trace data in the specified format.  
   
 =over 4  
   
 =item format  
   
 C<html> to format the data as an HTML list, C<text> to format it as straight text.  
   
 =back  
   
 =cut  
   
 sub QTrace {  
     # Get the parameter.  
     my ($format) = @_;  
     # Create the return variable.  
     my $retVal = "";  
     # Only proceed if there is an actual queue.  
     if (@Queue) {  
         # Process according to the format.  
         if ($format =~ m/^HTML$/i) {  
             # Convert the queue into an HTML list.  
             $retVal = "<ul>\n";  
             for my $line (@Queue) {  
                 my $escapedLine = CGI::escapeHTML($line);  
                 $retVal .= "<li>$escapedLine</li>\n";  
             }  
             $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
             # Convert the queue into a list of text lines.  
             $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
     }  
     # Return the formatted list.  
     return $retVal;  
 }  
   
 =head3 Confess  
   
 C<< Confess($message); >>  
   
 Trace the call stack and abort the program with the specified message. When used with  
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
   
 C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  
   
 Will abort the program with a stack trace if the value of C<$recNum> is negative.  
   
 =over 4  
   
 =item message  
   
 Message to include in the trace.  
   
 =back  
   
 =cut  
   
 sub Confess {  
     # Get the parameters.  
     my ($message) = @_;  
     # Trace the call stack.  
     Cluck($message);  
     # Abort the program.  
     croak(">>> $message");  
 }  
   
 =head3 Assert  
   
 C<< Assert($condition1, $condition2, ... $conditionN); >>  
   
 Return TRUE if all the conditions are true. This method can be used in conjunction with  
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
   
 C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  
   
 Will abort the program with a stack trace if the value of C<$recNum> is negative.  
   
 =cut  
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
   
 =head3 Cluck  
   
 C<< Cluck($message); >>  
   
 Trace the call stack. Note that for best results, you should qualify the call with a  
 trace condition. For example,  
2084    
2085  C<< Cluck("Starting record parse.") if T(3); >>      Tracer::PutFile($fileName, \@lines);
2086    
2087  will only trace the stack if the trace level for the package is 3 or more.  Write out a file from a list of lines of text.
2088    
2089  =over 4  =over 4
2090    
2091  =item message  =item fileName
2092    
2093  Message to include in the trace.  Name of the output file.
2094    
2095    =item lines
2096    
2097    Reference to a list of text lines. The lines will be written to the file in order, with trailing
2098    new-line characters. Alternatively, may be a string, in which case the string will be written without
2099    modification.
2100    
2101  =back  =back
2102    
2103  =cut  =cut
2104    
2105  sub Cluck {  sub PutFile {
2106      # Get the parameters.      # Get the parameters.
2107      my ($message) = @_;      my ($fileName, $lines) = @_;
2108      # Trace what's happening.      # Open the output file.
2109      Trace("Stack trace for event: $message");      my $handle = Open(undef, ">$fileName");
2110      my $confession = longmess($message);      # Count the lines written.
2111      # Convert the confession to a series of trace messages. Note we skip any      if (ref $lines ne 'ARRAY') {
2112      # messages relating to calls into Tracer.          # Here we have a scalar, so we write it raw.
2113      for my $line (split /\s*\n/, $confession) {          print $handle $lines;
2114          Trace($line) if ($line !~ /Tracer\.pm/);          Trace("Scalar put to file $fileName.") if T(File => 3);
2115        } else {
2116            # Write the lines one at a time.
2117            my $count = 0;
2118            for my $line (@{$lines}) {
2119                print $handle "$line\n";
2120                $count++;
2121            }
2122            Trace("$count lines put to file $fileName.") if T(File => 3);
2123      }      }
2124        # Close the output file.
2125        close $handle;
2126  }  }
2127    
2128  =head3 Min  =head3 ParseRecord
2129    
2130  C<< my $min = Min($value1, $value2, ... $valueN); >>      my @fields = Tracer::ParseRecord($line);
2131    
2132  Return the minimum argument. The arguments are treated as numbers.  Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2133    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2134    These will automatically be converted.
2135    
2136  =over 4  =over 4
2137    
2138  =item $value1, $value2, ... $valueN  =item line
2139    
2140  List of numbers to compare.  Line of data containing the tab-delimited fields.
2141    
2142  =item RETURN  =item RETURN
2143    
2144  Returns the lowest number in the list.  Returns a list of the fields found in the data line.
2145    
2146  =back  =back
2147    
2148  =cut  =cut
2149    
2150  sub Min {  sub ParseRecord {
2151      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameter.
2152      my ($retVal, @values) = @_;      my ($line) = @_;
2153      # Loop through the remaining parameters, looking for the lowest.      # Remove the trailing new-line, if any.
2154      for my $value (@values) {      chomp $line;
2155          if ($value < $retVal) {      # Split the line read into pieces using the tab character.
2156              $retVal = $value;      my @retVal = split /\t/, $line;
2157          }      # Trim and fix the escapes in each piece.
2158        for my $value (@retVal) {
2159            # Trim leading whitespace.
2160            $value =~ s/^\s+//;
2161            # Trim trailing whitespace.
2162            $value =~ s/\s+$//;
2163            # Delete the carriage returns.
2164            $value =~ s/\r//g;
2165            # Convert the escapes into their real values.
2166            $value =~ s/\\t/"\t"/ge;
2167            $value =~ s/\\n/"\n"/ge;
2168      }      }
2169      # Return the minimum found.      # Return the result.
2170      return $retVal;      return @retVal;
2171  }  }
2172    
2173  =head3 Max  =head3 Merge
2174    
2175  C<< my $max = Max($value1, $value2, ... $valueN); >>      my @mergedList = Tracer::Merge(@inputList);
2176    
2177  Return the maximum argument. The arguments are treated as numbers.  Sort a list of strings and remove duplicates.
2178    
2179  =over 4  =over 4
2180    
2181  =item $value1, $value2, ... $valueN  =item inputList
2182    
2183  List of numbers to compare.  List of scalars to sort and merge.
2184    
2185  =item RETURN  =item RETURN
2186    
2187  Returns the highest number in the list.  Returns a list containing the same elements sorted in ascending order with duplicates
2188    removed.
2189    
2190  =back  =back
2191    
2192  =cut  =cut
2193    
2194  sub Max {  sub Merge {
2195      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the input list in sort order.
2196      my ($retVal, @values) = @_;      my @inputList = sort @_;
2197      # Loop through the remaining parameters, looking for the highest.      # Only proceed if the list has at least two elements.
2198      for my $value (@values) {      if (@inputList > 1) {
2199          if ($value > $retVal) {          # Now we want to move through the list splicing out duplicates.
2200              $retVal = $value;          my $i = 0;
2201            while ($i < @inputList) {
2202                # Get the current entry.
2203                my $thisEntry = $inputList[$i];
2204                # Find out how many elements duplicate the current entry.
2205                my $j = $i + 1;
2206                my $dup1 = $i + 1;
2207                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2208                # If the number is nonzero, splice out the duplicates found.
2209                if ($j > $dup1) {
2210                    splice @inputList, $dup1, $j - $dup1;
2211          }          }
2212                # Now the element at position $dup1 is different from the element before it
2213                # at position $i. We push $i forward one position and start again.
2214                $i++;
2215      }      }
2216      # Return the maximum found.      }
2217      return $retVal;      # Return the merged list.
2218        return @inputList;
2219  }  }
2220    
2221  =head3 AddToListMap  =head3 Open
2222    
2223  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2224    
2225  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Open a file.
 is created for the key. Otherwise, the new value is pushed onto the list.  
2226    
2227  =over 4  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2228    function. The mode is specified using Unix-like shell information. So, for
2229    example,
2230    
2231  =item hash      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2232    
2233  Reference to the target hash.  would open for output appended to the specified file, and
2234    
2235  =item key      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2236    
2237  Key for which the value is to be added.  would open a pipe that sorts the records written and removes duplicates. Note
2238    the use of file handle syntax in the Open call. To use anonymous file handles,
2239    code as follows.
2240    
2241  =item value1, value2, ... valueN      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2242    
2243  List of values to add to the key's value list.  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2244    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2245    failed open will throw an exception and the third parameter will be used to construct
2246    an error message. If the parameter is omitted, a standard message is constructed
2247    using the file spec.
2248    
2249  =back      Could not open "/usr/spool/news/twitlog"
2250    
2251  =cut  Note that the mode characters are automatically cleaned from the file name.
2252    The actual error message from the file system will be captured and appended to the
2253    message in any case.
2254    
2255  sub AddToListMap {      Could not open "/usr/spool/news/twitlog": file not found.
2256      # Get the parameters.  
2257      my ($hash, $key, @values) = @_;  In some versions of PERL the only error message we get is a number, which
2258      # Process according to whether or not the key already has a value.  corresponds to the C++ C<errno> value.
2259      if (! exists $hash->{$key}) {  
2260          $hash->{$key} = [@values];      Could not open "/usr/spool/news/twitlog": 6.
2261      } else {  
2262          push @{$hash->{$key}}, @values;  =over 4
     }  
 }  
2263    
2264  =head3 DebugMode  =item fileHandle
2265    
2266    File handle. If this parameter is C<undef>, a file handle will be generated
2267    and returned as the value of this method.
2268    
2269    =item fileSpec
2270    
2271    File name and mode, as per the PERL C<open> function.
2272    
2273  C<< if (Tracer::DebugMode) { ...code... } >>  =item message (optional)
2274    
2275    Error message to use if the open fails. If omitted, a standard error message
2276    will be generated. In either case, the error information from the file system
2277    is appended to the message. To specify a conditional open that does not throw
2278    an error if it fails, use C<0>.
2279    
2280    =item RETURN
2281    
2282  Return TRUE if debug mode has been turned on, else abort.  Returns the name of the file handle assigned to the file, or C<undef> if the
2283    open failed.
2284    
2285  Certain CGI scripts are too dangerous to exist in the production  =back
 environment. This method provides a simple way to prevent them  
 from working unless they are explicitly turned on by creating a password  
 cookie via the B<SetPassword> script.  If debugging mode  
 is not turned on, an error will occur.  
2286    
2287  =cut  =cut
2288    
2289  sub DebugMode {  sub Open {
2290      # Declare the return variable.      # Get the parameters.
2291      my $retVal = 0;      my ($fileHandle, $fileSpec, $message) = @_;
2292      # Check the debug configuration.      # Attempt to open the file.
2293      my $password = CGI::cookie("DebugMode");      my $rv = open $fileHandle, $fileSpec;
2294      my $encrypted = Digest::MD5::md5_hex($password);      # If the open failed, generate an error message.
2295      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {      if (! $rv) {
2296          $retVal = 1;          # Save the system error message.
2297      } else {          my $sysMessage = $!;
2298          # Here debug mode is off, so we generate an error.          # See if we need a default message.
2299          Confess("Cannot use this facility without logging in.");          if (!$message) {
2300                # Clean any obvious mode characters and leading spaces from the
2301                # filename.
2302                my ($fileName) = FindNamePart($fileSpec);
2303                $message = "Could not open \"$fileName\"";
2304      }      }
2305      # Return the determination indicator.          # Terminate with an error using the supplied message and the
2306      return $retVal;          # error message from the file system.
2307            Confess("$message: $!");
2308        }
2309        # Return the file handle.
2310        return $fileHandle;
2311  }  }
2312    
2313  =head3 Strip  =head3 FindNamePart
2314    
2315  C<< my $string = Tracer::Strip($line); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2316    
2317  Strip all line terminators off a string. This is necessary when dealing with files  Extract the portion of a file specification that contains the file name.
2318  that may have been transferred back and forth several times among different  
2319  operating environments.  A file specification is the string passed to an C<open> call. It specifies the file
2320    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2321    method assumes that the file name is whatever follows the first angle bracket
2322    sequence.  So, for example, in the following strings the file name is
2323    C</usr/fig/myfile.txt>.
2324    
2325        >>/usr/fig/myfile.txt
2326        </usr/fig/myfile.txt
2327        | sort -u > /usr/fig/myfile.txt
2328    
2329    If the method cannot find a file name using its normal methods, it will return the
2330    whole incoming string.
2331    
2332  =over 4  =over 4
2333    
2334  =item line  =item fileSpec
2335    
2336  Line of text to be stripped.  File specification string from which the file name is to be extracted.
2337    
2338  =item RETURN  =item RETURN
2339    
2340  The same line of text with all the line-ending characters chopped from the end.  Returns a three-element list. The first element contains the file name portion of
2341    the specified string, or the whole string if a file name cannot be found via normal
2342    methods. The second element contains the start position of the file name portion and
2343    the third element contains the length.
2344    
2345  =back  =back
2346    
2347  =cut  =cut
2348    #: Return Type $;
2349  sub Strip {  sub FindNamePart {
2350      # Get a copy of the parameter string.      # Get the parameters.
2351      my ($string) = @_;      my ($fileSpec) = @_;
2352      my $retVal = (defined $string ? $string : "");      # Default to the whole input string.
2353      # Strip the line terminator characters.      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2354      $retVal =~ s/(\r|\n)+$//g;      # Parse out the file name if we can.
2355        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2356            $retVal = $2;
2357            $len = length $retVal;
2358            $pos = (length $fileSpec) - (length $3) - $len;
2359        }
2360      # Return the result.      # Return the result.
2361      return $retVal;      return ($retVal, $pos, $len);
2362  }  }
2363    
2364  =head3 Pad  =head3 OpenDir
2365    
2366        my @files = OpenDir($dirName, $filtered, $flag);
2367    
2368  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>  Open a directory and return all the file names. This function essentially performs
2369    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2370    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2371    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2372    filtered out of the return list. If the directory does not open and I<$flag> is not
2373    set, an exception is thrown. So, for example,
2374    
2375  Pad a string to a specified length. The pad character will be a      my @files = OpenDir("/Volumes/fig/contigs", 1);
 space, and the padding will be on the right side unless specified  
 in the third parameter.  
2376    
2377  =over 4  is effectively the same as
2378    
2379  =item string      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2380        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2381    
2382  String to be padded.  Similarly, the following code
2383    
2384  =item len      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2385    
2386  Desired length of the padded string.  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2387    automatically returns an empty list if the directory fails to open.
2388    
2389  =item left (optional)  =over 4
2390    
2391  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  =item dirName
2392    
2393  =item padChar (optional)  Name of the directory to open.
2394    
2395  Character to use for padding. The default is a space.  =item filtered
2396    
2397  =item RETURN  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2398    from the list, else FALSE.
2399    
2400  Returns a copy of the original string with the pad character added to the  =item flag
2401  specified end so that it achieves the desired length.  
2402    TRUE if a failure to open is okay, else FALSE
2403    
2404  =back  =back
2405    
2406  =cut  =cut
2407    #: Return Type @;
2408  sub Pad {  sub OpenDir {
2409      # Get the parameters.      # Get the parameters.
2410      my ($string, $len, $left, $padChar) = @_;      my ($dirName, $filtered, $flag) = @_;
2411      # Compute the padding character.      # Declare the return variable.
2412      if (! defined $padChar) {      my @retVal = ();
2413          $padChar = " ";      # Open the directory.
2414      }      if (opendir(my $dirHandle, $dirName)) {
2415      # Compute the number of spaces needed.          # The directory opened successfully. Get the appropriate list according to the
2416      my $needed = $len - length $string;          # strictures of the filter parameter.
2417      # Copy the string into the return variable.          if ($filtered) {
2418      my $retVal = $string;              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
     # Only proceed if padding is needed.  
     if ($needed > 0) {  
         # Create the pad string.  
         my $pad = $padChar x $needed;  
         # Affix it to the return value.  
         if ($left) {  
             $retVal = $pad . $retVal;  
2419          } else {          } else {
2420              $retVal .= $pad;              @retVal = readdir $dirHandle;
2421          }          }
2422        } elsif (! $flag) {
2423            # Here the directory would not open and it's considered an error.
2424            Confess("Could not open directory $dirName.");
2425      }      }
2426      # Return the result.      # Return the result.
2427      return $retVal;      return @retVal;
2428  }  }
2429    
 =head3 EOF  
2430    
2431  This is a constant that is lexically greater than any useful string.  =head3 Insure
2432    
2433  =cut      Insure($dirName, $chmod);
2434    
2435  sub EOF {  Insure a directory is present.
     return "\xFF\xFF\xFF\xFF\xFF";  
 }  
2436    
2437  =head3 TICK  =over 4
2438    
2439  C<< my @results = TICK($commandString); >>  =item dirName
2440    
2441  Perform a back-tick operation on a command. If this is a Windows environment, any leading  Name of the directory to check. If it does not exist, it will be created.
 dot-slash (C<./> will be removed. So, for example, if you were doing  
2442    
2443      `./protein.cgi`  =item chmod (optional)
2444    
2445  from inside a CGI script, it would work fine in Unix, but would issue an error message  Security privileges to be given to the directory if it is created.
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
2446    
2447      TICK("./protein.cgi")  =back
2448    
2449  it will work correctly in both environments.  =cut
2450    
2451  =over 4  sub Insure {
2452        my ($dirName, $chmod) = @_;
2453        if (! -d $dirName) {
2454            Trace("Creating $dirName directory.") if T(2);
2455            eval {
2456                mkpath $dirName;
2457                # If we have permissions specified, set them here.
2458                if (defined($chmod)) {
2459                    chmod $chmod, $dirName;
2460                }
2461            };
2462            if ($@) {
2463                Confess("Error creating $dirName: $@");
2464            }
2465        }
2466    }
2467    
2468  =item commandString  =head3 ChDir
2469    
2470  The command string to pass to the system.      ChDir($dirName);
2471    
2472  =item RETURN  Change to the specified directory.
2473    
2474  Returns the standard output from the specified command, as a list.  =over 4
2475    
2476    =item dirName
2477    
2478    Name of the directory to which we want to change.
2479    
2480  =back  =back
2481    
2482  =cut  =cut
2483  #: Return Type @;  
2484  sub TICK {  sub ChDir {
2485      # Get the parameters.      my ($dirName) = @_;
2486      my ($commandString) = @_;      if (! -d $dirName) {
2487      # Chop off the dot-slash if this is Windows.          Confess("Cannot change to directory $dirName: no such directory.");
2488      if ($FIG_Config::win_mode) {      } else {
2489          $commandString =~ s!^\./!!;          Trace("Changing to directory $dirName.") if T(File => 4);
2490            my $okFlag = chdir $dirName;
2491            if (! $okFlag) {
2492                Confess("Error switching to directory $dirName.");
2493            }
2494      }      }
     # Activate the command and return the result.  
     return `$commandString`;  
2495  }  }
2496    
2497  =head3 ScriptSetup  =head3 SetPermissions
   
 C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  
2498    
2499  Perform standard tracing and debugging setup for scripts. The value returned is      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
 the CGI object followed by a pre-built variable hash.  
2500    
2501  The C<Trace> form parameter is used to determine whether or not tracing is active and  Set the permissions for a directory and all the files and folders inside it.
2502  which trace modules (other than C<Tracer> itself) should be turned on. Specifying  In addition, the group ownership will be changed to the specified value.
 the C<CGI> trace module will trace parameter and environment information. Parameters are  
 traced at level 3 and environment variables at level 4. To trace to a file instead of to  
 the web page, set C<TF> to 1. At the end of the script, the client should call  
 L</ScriptFinish> to output the web page.  
2503    
2504  In some situations, it is not practical to invoke tracing via form parameters. For this  This method is more vulnerable than most to permission and compatability
2505  situation, you can turn on emergency tracing from the debugging control panel.  problems, so it does internal error recovery.
 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>.  
2506    
2507  =over 4  =over 4
2508    
2509  =item noTrace (optional)  =item dirName
2510    
2511  If specified, tracing will be suppressed. This is useful if the script wants to set up  Name of the directory to process.
 tracing manually.  
2512    
2513  =item RETURN  =item group
2514    
2515  Returns a two-element list consisting of a CGI query object and a variable hash for  Name of the group to be assigned.
2516  the output page.  
2517    =item mask
2518    
2519    Permission mask. Bits that are C<1> in this mask will be ORed into the
2520    permission bits of any file or directory that does not already have them
2521    set to 1.
2522    
2523    =item otherMasks
2524    
2525    Map of search patterns to permission masks. If a directory name matches
2526    one of the patterns, that directory and all its members and subdirectories
2527    will be assigned the new pattern. For example, the following would
2528    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2529    
2530        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2531    
2532    The list is ordered, so the following would use 0777 for C<tmp1> and
2533    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2534    
2535        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2536                                                       '^tmp' => 0666);
2537    
2538    Note that the pattern matches are all case-insensitive, and only directory
2539    names are matched, not file names.
2540    
2541  =back  =back
2542    
2543  =cut  =cut
2544    
2545  sub ScriptSetup {  sub SetPermissions {
2546      # Get the parameters.      # Get the parameters.
2547      my ($noTrace) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2548      # Get the CGI query object.      # Set up for error recovery.
2549      my $cgi = CGI->new();      eval {
2550      # Set up tracing if it's not suppressed.          # Switch to the specified directory.
2551      ETracing($cgi) unless $noTrace;          ChDir($dirName);
2552      # Create the variable hash.          # Get the group ID.
2553      my $varHash = { results => '' };          my $gid = getgrnam($group);
2554      # Return the query object and variable hash.          # Get the mask for tracing.
2555      return ($cgi, $varHash);          my $traceMask = sprintf("%04o", $mask) . "($mask)";
2556            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2557            my $fixCount = 0;
2558            my $lookCount = 0;
2559            # @dirs will be a stack of directories to be processed.
2560            my @dirs = (getcwd());
2561            while (scalar(@dirs) > 0) {
2562                # Get the current directory.
2563                my $dir = pop @dirs;
2564                # Check for a match to one of the specified directory names. To do
2565                # that, we need to pull the individual part of the name off of the
2566                # whole path.
2567                my $simpleName = $dir;
2568                if ($dir =~ m!/([^/]+)$!) {
2569                    $simpleName = $1;
2570                }
2571                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2572                # Search for a match.
2573                my $match = 0;
2574                my $i;
2575                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2576                    my $pattern = $otherMasks[$i];
2577                    if ($simpleName =~ /$pattern/i) {
2578                        $match = 1;
2579                    }
2580                }
2581                # Check for a match. Note we use $i-1 because the loop added 2
2582                # before terminating due to the match.
2583                if ($match && $otherMasks[$i-1] != $mask) {
2584                    # This directory matches one of the incoming patterns, and it's
2585                    # a different mask, so we process it recursively with that mask.
2586                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2587                } else {
2588                    # Here we can process normally. Get all of the non-hidden members.
2589                    my @submems = OpenDir($dir, 1);
2590                    for my $submem (@submems) {
2591                        # Get the full name.
2592                        my $thisMem = "$dir/$submem";
2593                        Trace("Checking member $thisMem.") if T(4);
2594                        $lookCount++;
2595                        if ($lookCount % 1000 == 0) {
2596                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2597                        }
2598                        # Fix the group.
2599                        chown -1, $gid, $thisMem;
2600                        # Insure this member is not a symlink.
2601                        if (! -l $thisMem) {
2602                            # Get its info.
2603                            my $fileInfo = stat $thisMem;
2604                            # Only proceed if we got the info. Otherwise, it's a hard link
2605                            # and we want to skip it anyway.
2606                            if ($fileInfo) {
2607                                my $fileMode = $fileInfo->mode;
2608                                if (($fileMode & $mask) != $mask) {
2609                                    # Fix this member.
2610                                    $fileMode |= $mask;
2611                                    chmod $fileMode, $thisMem;
2612                                    $fixCount++;
2613                                }
2614                                # If it's a subdirectory, stack it.
2615                                if (-d $thisMem) {
2616                                    push @dirs, $thisMem;
2617                                }
2618                            }
2619                        }
2620                    }
2621                }
2622            }
2623            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2624        };
2625        # Check for an error.
2626        if ($@) {
2627            Confess("SetPermissions error: $@");
2628        }
2629  }  }
2630    
2631  =head3 ETracing  =head3 GetLine
2632    
2633  C<< ETracing($parameter); >>      my @data = Tracer::GetLine($handle);
2634    
2635  Set up emergency tracing. Emergency tracing is tracing that is turned  Read a line of data from a tab-delimited file.
 on automatically for any program that calls this method. The emergency  
 tracing parameters are stored in a a file identified by a tracing key.  
 If this method is called with a CGI object, then the tracing key is  
 taken from a cookie. If it is called with no parameters, then the tracing  
 key is taken from an environment variable. If it is called with a string,  
 the tracing key is that string.  
2636    
2637  =over 4  =over 4
2638    
2639  =item parameter  =item handle
2640    
2641  A parameter from which the tracing key is computed. If it is a scalar,  Open file handle from which to read.
2642  that scalar is used as the tracing key. If it is a CGI object, the  
2643  tracing key is taken from the C<IP> cookie. If it is omitted, the  =item RETURN
2644  tracing key is taken from the C<TRACING> environment variable. If it  
2645  is a CGI object and emergency tracing is not on, the C<Trace> and  Returns a list of the fields in the record read. The fields are presumed to be
2646  C<TF> parameters will be used to determine the type of tracing.  tab-delimited. If we are at the end of the file, then an empty list will be
2647    returned. If an empty line is read, a single list item consisting of a null
2648    string will be returned.
2649    
2650  =back  =back
2651    
2652  =cut  =cut
2653    
2654  sub ETracing {  sub GetLine {
2655      # Get the parameter.      # Get the parameters.
2656      my ($parameter) = @_;      my ($handle) = @_;
2657      # Check for CGI mode.      # Declare the return variable.
2658      my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);      my @retVal = ();
2659      # Default to no tracing except errors.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2660      my ($tracing, $dest) = ("0", "WARN");      # Read from the file.
2661      # Check for emergency tracing.      my $line = <$handle>;
2662      my $tkey = EmergencyKey($parameter);      # Only proceed if we found something.
2663      my $emergencyFile = EmergencyFileName($tkey);      if (defined $line) {
2664      if (-e $emergencyFile) {          # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2665          # We have the file. Read in the data.          # upload control and have a nonstandard EOL combination.
2666          my @tracing = GetFile($emergencyFile);          $line =~ s/(\r|\n)+$//;
2667          # Pull off the time limit.          # Here we do some fancy tracing to help in debugging complicated EOL marks.
2668          my $expire = shift @tracing;          if (T(File => 4)) {
2669          # Convert it to seconds.              my $escapedLine = $line;
2670          $expire *= 3600;              $escapedLine =~ s/\n/\\n/g;
2671          # Check the file data.              $escapedLine =~ s/\r/\\r/g;
2672          my $stat = stat($emergencyFile);              $escapedLine =~ s/\t/\\t/g;
2673          my ($now) = gettimeofday;              Trace("Line read: -->$escapedLine<--");
         if ($now - $stat->mtime > $expire) {  
             # Delete the expired file.  
             unlink $emergencyFile;  
         } else {  
             # Emergency tracing is on. Pull off the destination and  
             # the trace level;  
             $dest = shift @tracing;  
             my $level = shift @tracing;  
             # Convert the destination to a real tracing destination.  
             # temp directory.  
             $dest = EmergencyTracingDest($tkey, $dest);  
             # Insure Tracer is specified.  
             my %moduleHash = map { $_ => 1 } @tracing;  
             $moduleHash{Tracer} = 1;  
             # Set the trace parameter.  
             $tracing = join(" ", $level, sort keys %moduleHash);  
         }  
     } elsif (defined $cgi) {  
         # There's no emergency tracing, but we have a CGI object, so check  
         # for tracing from the form parameters.  
         if ($cgi->param('Trace')) {  
             # Here the user has requested tracing via a form.  
             $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");  
             $tracing = $cgi->param('Trace') . " Tracer";  
2674          }          }
2675            # If the line is empty, return a single empty string; otherwise, parse
2676            # it into fields.
2677            if ($line eq "") {
2678                push @retVal, "";
2679            } else {
2680                push @retVal, split /\t/,$line;
2681      }      }
2682      # Setup the tracing we've determined from all the stuff above.      } else {
2683      TSetup($tracing, $dest);          # Trace the reason the read failed.
2684      # 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);  
2685      }      }
2686        # Return the result.
2687        return @retVal;
2688  }  }
2689    
2690  =head3 EmergencyFileName  =head3 PutLine
2691    
2692  C<< my $fileName = Tracer::EmergencyFileName($tkey); >>      Tracer::PutLine($handle, \@fields, $eol);
2693    
2694  Return the emergency tracing file name. This is the file that specifies  Write a line of data to a tab-delimited file. The specified field values will be
2695  the tracing information.  output in tab-separated form, with a trailing new-line.
2696    
2697  =over 4  =over 4
2698    
2699  =item tkey  =item handle
2700    
2701  Tracing key for the current program.  Output file handle.
2702    
2703  =item RETURN  =item fields
2704    
2705  Returns the name of the file to contain the emergency tracing information.  List of field values.
2706    
2707    =item eol (optional)
2708    
2709    End-of-line character (default is "\n").
2710    
2711  =back  =back
2712    
2713  =cut  =cut
2714    
2715  sub EmergencyFileName {  sub PutLine {
2716      # Get the parameters.      # Get the parameters.
2717      my ($tkey) = @_;      my ($handle, $fields, $eol) = @_;
2718      # Compute the emergency tracing file name.      # Write the data.
2719      return "$FIG_Config::temp/Emergency$tkey.txt";      print $handle join("\t", @{$fields}) . ($eol || "\n");
2720  }  }
2721    
 =head3 EmergencyFileTarget  
   
 C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>  
2722    
2723  Return the emergency tracing target file name. This is the file that receives  =head3 PrintLine
 the tracing output for file-based tracing.  
2724    
2725  =over 4      Tracer::PrintLine($line);
2726    
2727  =item tkey  Print a line of text with a trailing new-line.
2728    
2729  Tracing key for the current program.  =over 4
2730    
2731  =item RETURN  =item line
2732    
2733  Returns the name of the file to contain the trace output.  Line of text to print.
2734    
2735  =back  =back
2736    
2737  =cut  =cut
2738    
2739  sub EmergencyFileTarget {  sub PrintLine {
2740      # Get the parameters.      # Get the parameters.
2741      my ($tkey) = @_;      my ($line) = @_;
2742      # Compute the emergency tracing file name.      # Print the line.
2743      return "$FIG_Config::temp/trace$tkey.log";      print "$line\n";
2744  }  }
2745    
 =head3 EmergencyTracingDest  
2746    
2747  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>  =head2 Other Useful Methods
2748    
2749  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.  
2750    
2751  =over 4      my $listValue = Tracer::ParseParm($string);
2752    
2753  =item tkey  Convert a parameter into a list reference. If the parameter is undefined,
2754    an undefined value will be returned. Otherwise, it will be parsed as a
2755    comma-separated list of values.
2756    
2757  Tracing key for this environment.  =over 4
2758    
2759  =item myDest  =item string
2760    
2761  Destination from the emergency tracing file.  Incoming string.
2762    
2763  =item RETURN  =item RETURN
2764    
2765  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
2766    was undefined.
2767    
2768  =back  =back
2769    
2770  =cut  =cut
2771    
2772  sub EmergencyTracingDest {  sub ParseParm {
2773      # Get the parameters.      # Get the parameters.
2774      my ($tkey, $myDest) = @_;      my ($string) = @_;
2775      # Declare the return variable.      # Declare the return variable.
2776      my $retVal;      my $retVal;
2777      # Process according to the destination value.      # Check for data.
2778      if ($myDest eq 'FILE') {      if (defined $string) {
2779          $retVal = ">" . EmergencyFileTarget($tkey);          # We have some, so split it into a list.
2780      } elsif ($myDest eq 'APPEND') {          $retVal = [ split /\s*,\s*/, $string];
         $retVal = ">>" . EmergencyFileTarget($tkey);  
     } else {  
         $retVal = $myDest;  
2781      }      }
2782      # Return the result.      # Return the result.
2783      return $retVal;      return $retVal;
2784  }  }
2785    
2786  =head3 Emergency  =head3 Now
2787    
2788        my $string = Tracer::Now();
2789    
2790    Return a displayable time stamp containing the local time. Whatever format this
2791    method produces must be parseable by L</ParseDate>.
2792    
2793    =cut
2794    
2795    sub Now {
2796        return DisplayTime(time);
2797    }
2798    
2799    =head3 DisplayTime
2800    
2801  C<< Emergency($key, $hours, $dest, $level, @modules); >>      my $string = Tracer::DisplayTime($time);
2802    
2803  Turn on emergency tracing. This method can only be invoked over the web and is  Convert a time value to a displayable time stamp. Whatever format this
2804  should not be called if debug mode is off. The caller specifies the duration of the  method produces must be parseable by L</ParseDate>.
 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.  
2805    
2806  =over 4  =over 4
2807    
2808  =item tkey  =item time
2809    
2810  The tracing key. This is used to identify the control file and the trace file.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2811    
2812  =item hours  =item RETURN
2813    
2814  Number of hours to keep emergency tracing alive.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2815    
2816  =item dest  =back
2817    
2818  Tracing destination. If no path information is specified for a file  =cut
 destination, it is put in the FIG temporary directory.  
2819    
2820  =item level  sub DisplayTime {
2821        my ($time) = @_;
2822        my $retVal = "(n/a)";
2823        if (defined $time) {
2824            my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2825            $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2826                      _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2827        }
2828        return $retVal;
2829    }
2830    
2831  Tracing level. A higher level means more trace messages.  # Pad a number to 2 digits.
2832    sub _p2 {
2833        my ($value) = @_;
2834        $value = "0$value" if ($value < 10);
2835        return $value;
2836    }
2837    
2838  =item modules  =head3 Escape
2839    
2840  A list of the tracing modules to activate.      my $codedString = Tracer::Escape($realString);
2841    
2842    Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2843    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2844    result is to reverse the effect of L</UnEscape>.
2845    
2846    =over 4
2847    
2848    =item realString
2849    
2850    String to escape.
2851    
2852    =item RETURN
2853    
2854    Escaped equivalent of the real string.
2855    
2856  =back  =back
2857    
2858  =cut  =cut
2859    
2860  sub Emergency {  sub Escape {
2861      # Get the parameters.      # Get the parameter.
2862      my ($tkey, $hours, $dest, $level, @modules) = @_;      my ($realString) = @_;
2863      # Create the emergency file.      # Initialize the return variable.
2864      my $specFile = EmergencyFileName($tkey);      my $retVal = "";
2865      my $outHandle = Open(undef, ">$specFile");      # Loop through the parameter string, looking for sequences to escape.
2866      print $outHandle join("\n", $hours, $dest, $level, @modules, "");      while (length $realString > 0) {
2867            # Look for the first sequence to escape.
2868            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2869                # Here we found it. The text preceding the sequence is in $1. The sequence
2870                # itself is in $2. First, move the clear text to the return variable.
2871                $retVal .= $1;
2872                # Strip the processed section off the real string.
2873                $realString = substr $realString, (length $2) + (length $1);
2874                # Get the matched character.
2875                my $char = $2;
2876                # If we have a CR, we are done.
2877                if ($char ne "\r") {
2878                    # It's not a CR, so encode the escape sequence.
2879                    $char =~ tr/\t\n/tn/;
2880                    $retVal .= "\\" . $char;
2881                }
2882            } else {
2883                # Here there are no more escape sequences. The rest of the string is
2884                # transferred unmodified.
2885                $retVal .= $realString;
2886                $realString = "";
2887            }
2888        }
2889        # Return the result.
2890        return $retVal;
2891  }  }
2892    
2893  =head3 EmergencyKey  =head3 UnEscape
2894    
2895  C<< my $tkey = EmergencyKey($parameter); >>      my $realString = Tracer::UnEscape($codedString);
2896    
2897  Return the Key to be used for emergency tracing. This could be an IP address,  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2898   a session ID, or a user name, depending on the environment.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2899    be deleted.
2900    
2901  =over 4  =over 4
2902    
2903  =item parameter  =item codedString
2904    
2905  Parameter defining the method for finding the tracing key. If it is a scalar,  String to un-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.  
2906    
2907  =item RETURN  =item RETURN
2908    
2909  Returns the key to be used for labels in emergency tracing.  Returns a copy of the original string with the escape sequences converted to their actual
2910    values.
2911    
2912  =back  =back
2913    
2914  =cut  =cut
2915    
2916  sub EmergencyKey {  sub UnEscape {
2917      # Get the parameters.      # Get the parameter.
2918      my ($parameter) = @_;      my ($codedString) = @_;
2919      # Declare the return variable.      # Initialize the return variable.
2920      my $retVal;      my $retVal = "";
2921      # Determine the parameter type.      # Only proceed if the incoming string is nonempty.
2922      if (! defined $parameter) {      if (defined $codedString) {
2923          # Here we're supposed to check the environment.          # Loop through the parameter string, looking for escape sequences. We can't do
2924          $retVal = $ENV{TRACING};          # translating because it causes problems with the escaped slash. ("\\t" becomes
2925            # "\<tab>" no matter what we do.)
2926            while (length $codedString > 0) {
2927                # Look for the first escape sequence.
2928                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2929                    # Here we found it. The text preceding the sequence is in $1. The sequence
2930                    # itself is in $2. First, move the clear text to the return variable.
2931                    $retVal .= $1;
2932                    $codedString = substr $codedString, (2 + length $1);
2933                    # Get the escape value.
2934                    my $char = $2;
2935                    # If we have a "\r", we are done.
2936                    if ($char ne 'r') {
2937                        # Here it's not an 'r', so we convert it.
2938                        $char =~ tr/\\tn/\\\t\n/;
2939                        $retVal .= $char;
2940                    }
2941      } else {      } else {
2942          my $ptype = ref $parameter;                  # Here there are no more escape sequences. The rest of the string is
2943          if ($ptype eq 'CGI') {                  # transferred unmodified.
2944              # Here we were invoked from a web page. Look for a cookie.                  $retVal .= $codedString;
2945              $retVal = $parameter->cookie('IP');                  $codedString = "";
         } elsif (! $ptype) {  
             # Here the key was passed in.  
             $retVal = $parameter;  
2946          }          }
2947      }      }
     # If no luck finding a key, use the PID.  
     if (! defined $retVal) {  
         $retVal = $$;  
2948      }      }
2949      # Return the result.      # Return the result.
2950      return $retVal;      return $retVal;
2951  }  }
2952    
2953    =head3 Percent
2954    
2955  =head3 TraceParms      my $percent = Tracer::Percent($number, $base);
   
 C<< Tracer::TraceParms($cgi); >>  
2956    
2957  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Returns the percent of the base represented by the given number. If the base
2958  at level CGI => 4.  is zero, returns zero.
2959    
2960  =over 4  =over 4
2961    
2962  =item cgi  =item number
2963    
2964  CGI query object containing the parameters to trace.  Percent numerator.
2965    
2966    =item base
2967    
2968    Percent base.
2969    
2970    =item RETURN
2971    
2972    Returns the percentage of the base represented by the numerator.
2973    
2974  =back  =back
2975    
2976  =cut  =cut
2977    
2978  sub TraceParms {  sub Percent {
2979      # Get the parameters.      # Get the parameters.
2980      my ($cgi) = @_;      my ($number, $base) = @_;
2981      if (T(CGI => 3)) {      # Declare the return variable.
2982          # Here we want to trace the parameter data.      my $retVal = 0;
2983          my @names = $cgi->param;      # Compute the percent.
2984          for my $parmName (sort @names) {      if ($base != 0) {
2985              # Note we skip the Trace parameters, which are for our use only.          $retVal = $number * 100 / $base;
             if ($parmName ne 'Trace' && $parmName ne 'TF') {  
                 my @values = $cgi->param($parmName);  
                 Trace("CGI: $parmName = " . join(", ", @values));  
             }  
         }  
         # Display the request method.  
         my $method = $cgi->request_method();  
         Trace("Method: $method");  
     }  
     if (T(CGI => 4)) {  
         # Here we want the environment data too.  
         for my $envName (sort keys %ENV) {  
             Trace("ENV: $envName = $ENV{$envName}");  
         }  
2986      }      }
2987        # Return the result.
2988        return $retVal;
2989  }  }
2990    
2991  =head3 ScriptFinish  =head3 Constrain
2992    
2993  C<< ScriptFinish($webData, $varHash); >>      my $constrained = Constrain($value, $min, $max);
2994    
2995  Output a web page at the end of a script. Either the string to be output or the  Modify a numeric value to bring it to a point in between a maximum and a minimum.
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
2996    
2997  A typical standard script would loook like the following.  =over 4
2998    
2999      BEGIN {  =item value
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
3000    
3001      my ($cgi, $varHash) = ScriptSetup();  Value to constrain.
     eval {  
         # ... get data from $cgi, put it in $varHash ...  
     };  
     if ($@) {  
         Trace("Script Error: $@") if T(0);  
     }  
     ScriptFinish("Html/MyTemplate.html", $varHash);  
3002    
3003  The idea here is that even if the script fails, you'll see trace messages and  =item min (optional)
 useful output.  
3004    
3005  =over 4  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3006    
3007  =item webData  =item max (optional)
3008    
3009  A string containing either the full web page to be written to the output or the  Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3010    
3011  =item varHash (optional)  =item RETURN
3012    
3013  If specified, then a reference to a hash mapping variable names for a template  Returns the incoming value, constrained according to the other parameters.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3014    
3015  =back  =back
3016    
3017  =cut  =cut
3018    
3019  sub ScriptFinish {  sub Constrain {
3020      # Get the parameters.      # Get the parameters.
3021      my ($webData, $varHash) = @_;      my ($value, $min, $max) = @_;
3022      # Check for a template file situation.      # Declare the return variable.
3023      my $outputString;      my $retVal = $value;
3024      if (defined $varHash) {      # Apply the minimum constraint.
3025          # Here we have a template file. We need to determine the template type.      if (defined $min && $retVal < $min) {
3026          my $template;          $retVal = $min;
3027          if ($FIG_Config::template_url && $webData =~ /\.php$/) {      }
3028              $template = "$FIG_Config::template_url/$webData";      # Apply the maximum constraint.
3029          } else {      if (defined $max && $retVal > $max) {
3030              $template = "<<$webData";          $retVal = $max;
         }  
         $outputString = PageBuilder::Build($template, $varHash, "Html");  
     } else {  
         # Here the user gave us a raw string.  
         $outputString = $webData;  
     }  
     # Check for trace messages.  
     if ($Destination ne "NONE" && $TraceLevel > 0) {  
         # We have trace messages, so we want to put them at the end of the body. This  
         # is either at the end of the whole string or at the beginning of the BODY  
         # end-tag.  
         my $pos = length $outputString;  
         if ($outputString =~ m#</body>#gi) {  
             $pos = (pos $outputString) - 7;  
         }  
         # If the trace messages were queued, we unroll them. Otherwise, we display the  
         # destination.  
         my $traceHtml;  
         if ($Destination eq "QUEUE") {  
             $traceHtml = QTrace('Html');  
         } elsif ($Destination =~ /^>>(.+)$/) {  
             # Here the tracing output it to a file. We code it as a hyperlink so the user  
             # can copy the file name into the clipboard easily.  
             my $actualDest = $1;  
             $traceHtml = "<p>Tracing output to $actualDest.</p>\n";  
         } else {  
             # Here we have one of the special destinations.  
             $traceHtml = "<P>Tracing output type is $Destination.</p>\n";  
         }  
         substr $outputString, $pos, 0, $traceHtml;  
3031      }      }
3032      # Write the output string.      # Return the result.
3033      print $outputString;      return $retVal;
3034  }  }
3035    
3036  =head3 Insure  =head3 Min
3037    
3038  C<< Insure($dirName); >>      my $min = Min($value1, $value2, ... $valueN);
3039    
3040  Insure a directory is present.  Return the minimum argument. The arguments are treated as numbers.
3041    
3042  =over 4  =over 4
3043    
3044  =item dirName  =item $value1, $value2, ... $valueN
3045    
3046  Name of the directory to check. If it does not exist, it will be created.  List of numbers to compare.
3047    
3048    =item RETURN
3049    
3050    Returns the lowest number in the list.
3051    
3052  =back  =back
3053    
3054  =cut  =cut
3055    
3056  sub Insure {  sub Min {
3057      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
3058      if (! -d $dirName) {      my ($retVal, @values) = @_;
3059          Trace("Creating $dirName directory.") if T(File => 2);      # Loop through the remaining parameters, looking for the lowest.
3060          eval { mkpath $dirName; };      for my $value (@values) {
3061          if ($@) {          if ($value < $retVal) {
3062              Confess("Error creating $dirName: $@");              $retVal = $value;
3063          }          }
3064      }      }
3065        # Return the minimum found.
3066        return $retVal;
3067  }  }
3068    
3069  =head3 ChDir  =head3 Max
3070    
3071  C<< ChDir($dirName); >>      my $max = Max($value1, $value2, ... $valueN);
3072    
3073  Change to the specified directory.  Return the maximum argument. The arguments are treated as numbers.
3074    
3075  =over 4  =over 4
3076    
3077  =item dirName  =item $value1, $value2, ... $valueN
3078    
3079  Name of the directory to which we want to change.  List of numbers to compare.
3080    
3081    =item RETURN
3082    
3083    Returns the highest number in the list.
3084    
3085  =back  =back
3086    
3087  =cut  =cut
3088    
3089  sub ChDir {  sub Max {
3090      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
3091      if (! -d $dirName) {      my ($retVal, @values) = @_;
3092          Confess("Cannot change to directory $dirName: no such directory.");      # Loop through the remaining parameters, looking for the highest.
3093      } else {      for my $value (@values) {
3094          Trace("Changing to directory $dirName.") if T(File => 4);          if ($value > $retVal) {
3095          my $okFlag = chdir $dirName;              $retVal = $value;
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
         }  
3096      }      }
3097  }  }
3098        # Return the maximum found.
3099        return $retVal;
3100    }
3101    
3102  =head3 SendSMS  =head3 Strip
   
 C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>  
   
 Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  
 user name, password, and API ID for the relevant account in the hash reference variable  
 I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For  
 example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID  
 is C<2561022>, then the FIG_Config file must contain  
   
     $phone =  { user => 'BruceTheHumanPet',  
                 password => 'silly',  
                 api_id => '2561022' };  
3103    
3104  The original purpose of this method was to insure Bruce would be notified immediately when the      my $string = Tracer::Strip($line);
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3105    
3106  The message ID will be returned if successful, and C<undef> if an error occurs.  Strip all line terminators off a string. This is necessary when dealing with files
3107    that may have been transferred back and forth several times among different
3108    operating environments.
3109    
3110  =over 4  =over 4
3111    
3112  =item phoneNumber  =item line
   
 Phone number to receive the message, in international format. A United States phone number  
 would be prefixed by "1". A British phone number would be prefixed by "44".  
   
 =item msg  
3113    
3114  Message to send to the specified phone.  Line of text to be stripped.
3115    
3116  =item RETURN  =item RETURN
3117    
3118  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.
3119    
3120  =back  =back
3121    
3122  =cut  =cut
3123    
3124  sub SendSMS {  sub Strip {
3125      # Get the parameters.      # Get a copy of the parameter string.
3126      my ($phoneNumber, $msg) = @_;      my ($string) = @_;
3127      # Declare the return variable. If we do not change it, C<undef> will be returned.      my $retVal = (defined $string ? $string : "");
3128      my $retVal;      # Strip the line terminator characters.
3129      # 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);  
             }  
         }  
     }  
3130      # Return the result.      # Return the result.
3131      return $retVal;      return $retVal;
3132  }  }
3133    
3134  =head3 CommaFormat  =head3 Pad
3135    
3136  C<< my $formatted = Tracer::CommaFormat($number); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3137    
3138  Insert commas into a number.  Pad a string to a specified length. The pad character will be a
3139    space, and the padding will be on the right side unless specified
3140    in the third parameter.
3141    
3142  =over 4  =over 4
3143    
3144  =item number  =item string
3145    
3146  A sequence of digits.  String to be padded.
3147    
3148    =item len
3149    
3150    Desired length of the padded string.
3151    
3152    =item left (optional)
3153    
3154    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3155    
3156    =item padChar (optional)
3157    
3158    Character to use for padding. The default is a space.
3159    
3160  =item RETURN  =item RETURN
3161    
3162  Returns the same digits with commas strategically inserted.  Returns a copy of the original string with the pad character added to the
3163    specified end so that it achieves the desired length.
3164    
3165  =back  =back
3166    
3167  =cut  =cut
3168    
3169  sub CommaFormat {  sub Pad {
3170      # Get the parameters.      # Get the parameters.
3171      my ($number) = @_;      my ($string, $len, $left, $padChar) = @_;
3172      # Pad the length up to a multiple of three.      # Compute the padding character.
3173      my $padded = "$number";      if (! defined $padChar) {
3174      $padded = " " . $padded while length($padded) % 3 != 0;          $padChar = " ";
3175      # This is a fancy PERL trick. The parentheses in the SPLIT pattern      }
3176      # cause the delimiters to be included in the output stream. The      # Compute the number of spaces needed.
3177      # GREP removes the empty strings in between the delimiters.      my $needed = $len - length $string;
3178      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));      # Copy the string into the return variable.
3179      # Clean out the spaces.      my $retVal = $string;
3180      $retVal =~ s/ //g;      # Only proceed if padding is needed.
3181        if ($needed > 0) {
3182            # Create the pad string.
3183            my $pad = $padChar x $needed;
3184            # Affix it to the return value.
3185            if ($left) {
3186                $retVal = $pad . $retVal;
3187            } else {
3188                $retVal .= $pad;
3189            }
3190        }
3191      # Return the result.      # Return the result.
3192      return $retVal;      return $retVal;
3193  }  }
 =head3 SetPermissions  
3194    
3195  C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  =head3 EOF
3196    
3197  Set the permissions for a directory and all the files and folders inside it.  This is a constant that is lexically greater than any useful string.
 In addition, the group ownership will be changed to the specified value.  
3198    
3199  This method is more vulnerable than most to permission and compatability  =cut
 problems, so it does internal error recovery.  
3200    
3201  =over 4  sub EOF {
3202        return "\xFF\xFF\xFF\xFF\xFF";
3203    }
3204    
3205  =item dirName  =head3 TICK
3206    
3207  Name of the directory to process.      my @results = TICK($commandString);
3208    
3209  =item group  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3210    dot-slash (C<./> will be removed. So, for example, if you were doing
3211    
3212  Name of the group to be assigned.      `./protein.cgi`
3213    
3214  =item mask  from inside a CGI script, it would work fine in Unix, but would issue an error message
3215    in Windows complaining that C<'.'> is not a valid command. If instead you code
3216    
3217  Permission mask. Bits that are C<1> in this mask will be ORed into the      TICK("./protein.cgi")
 permission bits of any file or directory that does not already have them  
 set to 1.  
3218    
3219  =item otherMasks  it will work correctly in both environments.
3220    
3221  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>.  
3222    
3223      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  =item commandString
3224    
3225  The list is ordered, so the following would use 0777 for C<tmp1> and  The command string to pass to the system.
 0666 for C<tmp>, C<tmp2>, or C<tmp3>.  
3226    
3227      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  =item RETURN
                                                    '^tmp' => 0666);  
3228    
3229  Note that the pattern matches are all case-insensitive, and only directory  Returns the standard output from the specified command, as a list.
 names are matched, not file names.  
3230    
3231  =back  =back
3232    
3233  =cut  =cut
3234    #: Return Type @;
3235  sub SetPermissions {  sub TICK {
3236      # Get the parameters.      # Get the parameters.
3237      my ($dirName, $group, $mask, @otherMasks) = @_;      my ($commandString) = @_;
3238      # Set up for error recovery.      # Chop off the dot-slash if this is Windows.
3239      eval {      if ($FIG_Config::win_mode) {
3240          # Switch to the specified directory.          $commandString =~ s!^\./!!;
         ChDir($dirName);  
         # Get the group ID.  
         my $gid = getgrnam($group);  
         # Get the mask for tracing.  
         my $traceMask = sprintf("%04o", $mask) . "($mask)";  
         Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);  
         my $fixCount = 0;  
         my $lookCount = 0;  
         # @dirs will be a stack of directories to be processed.  
         my @dirs = (getcwd());  
         while (scalar(@dirs) > 0) {  
             # Get the current directory.  
             my $dir = pop @dirs;  
             # Check for a match to one of the specified directory names. To do  
             # that, we need to pull the individual part of the name off of the  
             # whole path.  
             my $simpleName = $dir;  
             if ($dir =~ m!/([^/]+)$!) {  
                 $simpleName = $1;  
             }  
             Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);  
             # Search for a match.  
             my $match = 0;