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revision 1.86, Fri May 18 19:27:17 2007 UTC revision 1.97, Tue Apr 29 06:01:21 2008 UTC
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1  #  # -*- perl -*-
2    ########################################################################
3  # Copyright (c) 2003-2006 University of Chicago and Fellowship  # Copyright (c) 2003-2006 University of Chicago and Fellowship
4  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
5  #  #
# Line 13  Line 14 
14  # at info@ci.uchicago.edu or the Fellowship for Interpretation of  # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15  # Genomes at veronika@thefig.info or download a copy from  # Genomes at veronika@thefig.info or download a copy from
16  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
17  #  ########################################################################
18    
19  package Tracer;  package Tracer;
20    
21      require Exporter;      require Exporter;
22      @ISA = ('Exporter');      @ISA = ('Exporter');
23      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency);
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 159  Line 160 
160    
161  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
162  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
163  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
164  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
165  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
166  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
167  the tracing in your environment without stepping on other users.  the tracing in your environment without stepping on other users.
# Line 183  Line 184 
184    
185  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
186  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
187  using the L</StandardScript> or L</StandardSetup> methods, emergency tracing  using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
188  will be configured automatically.  will be configured automatically.
189    
 NOTE: to configure emergency tracing from the command line instead of the Debugging  
 Control Panel (see below), use the C<trace.pl> script.  
   
 =head3 Debugging Control Panel  
   
 The debugging control panel provides several tools to assist in development of  
 SEED and Sprout software. You access the debugging control panel from the URL  
 C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,  
 for example, the panel access point for the development NMPDR system is  
 C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to  
 find out what the password is. From this page, you can also specify a tracing  
 key. If you don't specify a key, one will be generated for you.  
   
 =head4 Emergency Tracing Form  
   
 At the bottom of the debugging control panel is a form that allows you to  
 specify a trace level and tracing categories. Special and common categories  
 are listed with check boxes. You can hold your mouse over a check box to see  
 what its category does. In general, however, a category name is the same as  
 the name of the package in which the trace message occurs.  
   
 Additional categories can be entered in an input box, delimited by spaces or commas.  
   
 The B<Activate> button turns on Emergency tracing at the level you specify with the  
 specified categories active. The B<Terminate> button turns tracing off. The  
 B<Show File> button displays the current contents of the trace file. The tracing  
 form at the bottom of the control panel is designed for emergency tracing, so it  
 will only affect programs that call L</ETracing>, L</StandardScript>,  
 or L</StandardSetup>.  
   
 =head4 Script Form  
   
 The top form of the debugging control panel allows you to enter a tiny script and  
 have the output generated in a formatted table. Certain object variables are  
 predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),  
 and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.  
   
 The last line of the script must be a scalar, but it can be a reference to a hash,  
 a list, a list of lists, and various other combinations. If you select the appropriate  
 data type in the dropdown box, the output will be formatted accordingly. The form  
 also has controls for specifying tracing. These controls override any emergency  
 tracing in effect.  
   
 =head4 Database Query Forms  
   
 The forms between the script form and the emergency tracing form allow you to  
 make queries against the database. The FIG query form allows simple queries against  
 a single FIG table. The Sprout query form uses the B<GetAll> method to do a  
 multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>  
 package, and it takes five parameters.  
   
     GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);  
   
 Each of the five parameters corresponds to a text box on the query form:  
   
 =over 4  
   
 =item Objects  
   
 Comma-separated list containing the names of the entity and relationship objects to be retrieved.  
   
 =item Filter  
   
 WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  
 be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form  
 B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a  
 field, I<objectName> is the name of the entity or relationship object containing the field, and  
 I<number> is the 1-based position of the object in the object list. Any parameters  
 specified in the filter clause should be specified in the B<Params> field.  
 The fields in a filter clause can come from primary entity relations,  
 relationship relations, or secondary entity relations; however, all of the  
 entities and relationships involved must be included in the list of object names.  
   
 =item Params  
   
 List of the parameters to be substituted in for the parameters marks in the filter clause. This  
 is a comma-separated list without any quoting or escaping.  
   
 =item fields  
   
 Comma-separated list of the fields to be returned in each element of the list returned. Fields  
 are specified in the same manner as in the filter clause.  
   
 =item count  
   
 Maximum number of records to return. If omitted or 0, all available records will be returned.  
   
 =back  
   
 B<GetAll> automatically joins together the entities and relationships listed in the object  
 names. This simplifies the coding of the filter clause, but it means that some queries are  
 not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation  
 that has yet to be addressed.  
   
190  =cut  =cut
191    
192  # Declare the configuration variables.  # Declare the configuration variables.
193    
194  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
195  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
196                              # standard output                              # standard output
197  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
198                              # hash of active category names                              # hash of active category names
199    my @LevelNames = qw(error warn notice info detail);
200  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
201                              # messages                              # messages
202  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
203  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
204    my $LastLevel = 0;          # level of the last test call
205  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
206  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
207    
208  =head2 Public Methods  =head2 Tracing Methods
209    
210    =head3 Setups
211    
212        my $count = Tracer::Setups();
213    
214    Return the number of times L</TSetup> has been called.
215    
216    This method allows for the creation of conditional tracing setups where, for example, we
217    may want to set up tracing if nobody else has done it before us.
218    
219    =cut
220    
221    sub Setups {
222        return $SetupCount;
223    }
224    
225  =head3 TSetup  =head3 TSetup
226    
227  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
228    
229  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
230  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 359  Line 283 
283          }          }
284          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
285              open TRACEFILE, $target;              open TRACEFILE, $target;
286              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [Tracer] Tracing initialized.\n";
287              close TRACEFILE;              close TRACEFILE;
288              $Destination = ">$target";              $Destination = ">$target";
289          } else {          } else {
# Line 372  Line 296 
296      $SetupCount++;      $SetupCount++;
297  }  }
298    
299  =head3 StandardSetup  =head3 SetLevel
300    
301  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
302    
303  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.  
304    
305  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.  
306    
307  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  
308    
309      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
310    
311  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.  
312    
313  =over 4  =cut
314    
315  =item SQL  sub SetLevel {
316        $TraceLevel = $_[0];
317    }
318    
319  Traces SQL commands and activity.  =head3 ParseDate
320    
321  =item Tracer      my $time = Tracer::ParseDate($dateString);
322    
323  Traces error messages and call stacks.  Convert a date into a PERL time number. This method expects a date-like string
324    and parses it into a number. The string must be vaguely date-like or it will
325    return an undefined value. Our requirement is that a month and day be
326    present and that three pieces of the date string (time of day, month and day,
327    year) be separated by likely delimiters, such as spaces, commas, and such-like.
328    
329  =back  If a time of day is present, it must be in military time with two digits for
330    everything but the hour.
331    
332  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.  
333    
334      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
335    equally innocuous. This means, however, that a sufficiently long sentence with date-like
336    parts in it may be interpreted as a date. Hopefully this will not be a problem.
337    
338  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  
339    
340  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.  
341    
342      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  =over 4
343    
344  would send the trace output to C<traceBruce.log> in the temporary directory.  =item dateString
345    
346  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.  
347    
348  You can specify a different default trace level by setting C<$options->{trace}>  =item RETURN
 prior to calling this method.  
349    
350  An example at this point would help. Consider, for example, the command-line utility  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
351  C<TransactFeatures>. It accepts a list of positional parameters plus the options  the date string is invalid. A valid date string must contain a month and day.
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
352    
353      my ($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);  
354    
355    =cut
356    
357  The call to C<ParseCommand> specifies the default values for the options and  # Universal month conversion table.
358  stores the actual options in a hash that is returned as C<$options>. The  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
359  positional parameters are returned in C<@parameters>.                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
360                                Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
361                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
362                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
363                                Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
364                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
365                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
366                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
367                                Oct =>  9, October  =>   9, '10' =>  9,
368                                Nov => 10, November =>  10, '11' => 10,
369                                Dec => 11, December =>  11, '12' => 11
370                            };
371    
372  The following is a sample command line for C<TransactFeatures>.  sub ParseDate {
373        # Get the parameters.
374        my ($dateString) = @_;
375        # Declare the return variable.
376        my $retVal;
377        # Find the month and day of month. There are two ways that can happen. We check for the
378        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
379        # won't be fooled into thinking the month is Sunday.
380        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
381            my ($mon, $mday) = (MONTHS->{$1}, $2);
382            # Insist that the month and day are valid.
383            if (defined($mon) && $2 >= 1 && $2 <= 31) {
384                # Find the time.
385                my ($hour, $min, $sec) = (0, 0, 0);
386                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
387                    ($hour, $min, $sec) = ($1, $2, $3);
388                }
389                # Find the year.
390                my $year;
391                if ($dateString =~ /\b(\d{4})\b/) {
392                    $year = $1;
393                } else {
394                    # Get the default year, which is this one. Note we must convert it to
395                    # the four-digit value expected by "timelocal".
396                    (undef, undef, undef, undef, undef, $year) = localtime();
397                    $year += 1900;
398                }
399                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
400            }
401        }
402        # Return the result.
403        return $retVal;
404    }
405    
406      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  =head3 LogErrors
407    
408  Single and double hyphens are equivalent. So, you could also code the      Tracer::LogErrors($fileName);
 above command as  
409    
410      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl  Route the standard error output to a log file.
411    
412  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  =over 4
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
413    
414      { trace => 2, sql => 0, safe => 0,  =item fileName
       noAlias => 1, start => ' ', tblFiles => 0 }  
415    
416  Use of C<StandardSetup> in this way provides a simple way of performing  Name of the file to receive the error output.
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
417    
418  If the C<background> option is specified on the command line, then the  =back
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
419    
420      -user=Bruce -background  =cut
421    
422  then the trace output would go to C<traceBruce.log>, the standard output to  sub LogErrors {
423  C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to      # Get the file name.
424  simplify starting a command in the background.      my ($fileName) = @_;
425        # Open the file as the standard error output.
426        open STDERR, '>', $fileName;
427    }
428    
429  The user name is also used as the tracing key for L</Emergency Tracing>.  =head3 Trace
 Specifying a value of C<E> for the trace level causes emergency tracing to  
 be used instead of custom tracing. If the user name is not specified,  
 the tracing key is taken from the C<Tracing> environment variable. If there  
 is no value for that variable, the tracing key will be computed from the PID.  
430    
431  Finally, if the special option C<-help> is specified, the option      Trace($message);
 names will be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
432    
433      TransactFeatures -help  Write a trace message to the target location specified in L</TSetup>. If there has not been
434    any prior call to B<TSetup>.
435    
436  he would see the following output.  =over 4
437    
438      TransactFeatures [options] <command> <transactionDirectory> <IDfile>  =item message
         -trace    tracing level (default E)  
         -sql      trace SQL commands  
         -safe     use database transactions  
         -noAlias  do not expect aliases in CHANGE transactions  
         -start    start with this genome  
         -tblFiles output TBL files containing the corrected IDs  
439    
440  The caller has the option of modifying the tracing scheme by placing a value  Message to write.
 for C<trace> in the incoming options hash. The default value can be overridden,  
 or the tracing to the standard output can be turned off by suffixing a minus  
 sign to the trace level. So, for example,  
441    
442      { trace => [0, "tracing level (default 0)"],  =back
        ...  
443    
444  would set the default trace level to 0 instead of E, while  =cut
445    
446      { trace => ["2-", "tracing level (default 2)"],  sub Trace {
447         ...      # Get the parameters.
448        my ($message) = @_;
449        # Strip off any line terminators at the end of the message. We will add
450        # new-line stuff ourselves.
451        my $stripped = Strip($message);
452        # Compute the caller information.
453        my ($callPackage, $callFile, $callLine) = caller();
454        my $callFileTitle = basename($callFile);
455        # Check the caller.
456        if ($callFileTitle ne "Tracer\.pm") {
457            # The caller isn't us, so add the caller info to the message.
458            $stripped = "[$callFileTitle $callLine] $stripped";
459        }
460        # Get the timestamp.
461        my $timeStamp = Now();
462        # Build the prefix.
463        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
464        my $prefix = "[$timeStamp] [$level] ";
465        # Format the message.
466        my $formatted = "$prefix $stripped";
467        # Process according to the destination.
468        if ($Destination eq "TEXT") {
469            # Write the message to the standard output.
470            print "$formatted\n";
471        } elsif ($Destination eq "ERROR") {
472            # Write the message to the error output. Here, we want our prefix fields.
473            print STDERR "$formatted\n";
474        } elsif ($Destination eq "WARN") {
475            # Emit the message to the standard error output. It is presumed that the
476            # error logger will add its own prefix fields
477            print STDERR "$stripped\n";
478        } elsif ($Destination eq "QUEUE") {
479            # Push the message into the queue.
480            push @Queue, "$formatted";
481        } elsif ($Destination eq "HTML") {
482            # Convert the message to HTML and write it to the standard output.
483            my $escapedMessage = CGI::escapeHTML($stripped);
484            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
485        } elsif ($Destination =~ m/^>>/) {
486            # Write the trace message to an output file.
487            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
488            print TRACING "$formatted\n";
489            close TRACING;
490            # If the Tee flag is on, echo it to the standard output.
491            if ($TeeFlag) {
492                print "$formatted\n";
493            }
494        }
495    }
496    
497  would set the default to 2, but trace only to the log file, not to the  =head3 T
 standard output.  
498    
499  The parameters to this method are as follows.      my $switch = T($category, $traceLevel);
500    
501  =over 4      or
502    
503  =item categories      my $switch = T($traceLevel);
504    
505  Reference to a list of tracing category names. These should be names of  Return TRUE if the trace level is at or above a specified value and the specified category
506  packages whose internal workings will need to be debugged to get the  is active, else FALSE. If no category is specified, the caller's package name is used.
 command working.  
507    
508  =item options  =over 4
509    
510  Reference to a hash containing the legal options for the current command mapped  =item category
 to their default values and descriptions. The user can override the defaults  
 by specifying the options as command-line switches prefixed by a hyphen.  
 Tracing-related options may be added to this hash. If the C<-h> option is  
 specified on the command line, the option descriptions will be used to  
 explain the options. To turn off tracing to the standard output, add a  
 minus sign to the value for C<trace> (see above).  
511    
512  =item parmHelp  Category to which the message belongs. If not specified, the caller's package name is
513    used.
514    
515    =item traceLevel
516    
517    Relevant tracing level.
518    
519    =item RETURN
520    
521    TRUE if a message at the specified trace level would appear in the trace, else FALSE.
522    
523    =back
524    
525    =cut
526    
527    sub T {
528        # Declare the return variable.
529        my $retVal = 0;
530        # Only proceed if tracing is turned on.
531        if ($Destination ne "NONE") {
532            # Get the parameters.
533            my ($category, $traceLevel) = @_;
534            if (!defined $traceLevel) {
535                # Here we have no category, so we need to get the calling package.
536                # The calling package is normally the first parameter. If it is
537                # omitted, the first parameter will be the tracelevel. So, the
538                # first thing we do is shift the so-called category into the
539                # $traceLevel variable where it belongs.
540                $traceLevel = $category;
541                my ($package, $fileName, $line) = caller;
542                # If there is no calling package, we default to "main".
543                if (!$package) {
544                    $category = "main";
545                } else {
546                    my @cats = split /::/, $package;
547                    $category = $cats[$#cats];
548                }
549            }
550            # Save the category name and level.
551            $LastCategory = $category;
552            $LastLevel = $traceLevel;
553            # Convert it to lower case before we hash it.
554            $category = lc $category;
555            # Use the category and tracelevel to compute the result.
556            if (ref $traceLevel) {
557                Confess("Bad trace level.");
558            } elsif (ref $TraceLevel) {
559                Confess("Bad trace config.");
560            }
561            $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
562        }
563        # Return the computed result.
564        return $retVal;
565    }
566    
567    =head3 QTrace
568    
569        my $data = QTrace($format);
570    
571    Return the queued trace data in the specified format.
572    
573    =over 4
574    
575    =item format
576    
577    C<html> to format the data as an HTML list, C<text> to format it as straight text.
578    
579    =back
580    
581    =cut
582    
583    sub QTrace {
584        # Get the parameter.
585        my ($format) = @_;
586        # Create the return variable.
587        my $retVal = "";
588        # Only proceed if there is an actual queue.
589        if (@Queue) {
590            # Process according to the format.
591            if ($format =~ m/^HTML$/i) {
592                # Convert the queue into an HTML list.
593                $retVal = "<ul>\n";
594                for my $line (@Queue) {
595                    my $escapedLine = CGI::escapeHTML($line);
596                    $retVal .= "<li>$escapedLine</li>\n";
597                }
598                $retVal .= "</ul>\n";
599            } elsif ($format =~ m/^TEXT$/i) {
600                # Convert the queue into a list of text lines.
601                $retVal = join("\n", @Queue) . "\n";
602            }
603            # Clear the queue.
604            @Queue = ();
605        }
606        # Return the formatted list.
607        return $retVal;
608    }
609    
610    =head3 Confess
611    
612        Confess($message);
613    
614    Trace the call stack and abort the program with the specified message. When used with
615    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
616    So, for example
617    
618        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
619    
620    Will abort the program with a stack trace if the value of C<$recNum> is negative.
621    
622    =over 4
623    
624    =item message
625    
626    Message to include in the trace.
627    
628    =back
629    
630    =cut
631    
632    sub Confess {
633        # Get the parameters.
634        my ($message) = @_;
635        # Set up the category and level.
636        $LastCategory = "(confess)";
637        $LastLevel = 0;
638        if (! defined($FIG_Config::no_tool_hdr)) {
639            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
640            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
641            # Only proceed if the tool header file is actually present.
642            if (-f $toolHeaderFile) {
643                my $fh;
644                if (open $fh, "<$toolHeaderFile") {
645                    my @lines = <$fh>;
646                    Trace("Tool header has " . scalar(@lines) . " lines.");
647                }
648            }
649        }
650        # Trace the call stack.
651        Cluck($message);
652        # Abort the program.
653        croak(">>> $message");
654    }
655    
656    =head3 Assert
657    
658        Assert($condition1, $condition2, ... $conditionN);
659    
660    Return TRUE if all the conditions are true. This method can be used in conjunction with
661    the OR operator and the L</Confess> method as a debugging assert.
662    So, for example
663    
664        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
665    
666    Will abort the program with a stack trace if the value of C<$recNum> is negative.
667    
668    =cut
669    sub Assert {
670        my $retVal = 1;
671        LOOP: for my $condition (@_) {
672            if (! $condition) {
673                $retVal = 0;
674                last LOOP;
675            }
676        }
677        return $retVal;
678    }
679    
680    =head3 Cluck
681    
682        Cluck($message);
683    
684    Trace the call stack. Note that for best results, you should qualify the call with a
685    trace condition. For example,
686    
687        Cluck("Starting record parse.") if T(3);
688    
689    will only trace the stack if the trace level for the package is 3 or more.
690    
691    =over 4
692    
693    =item message
694    
695    Message to include in the trace.
696    
697    =back
698    
699    =cut
700    
701    sub Cluck {
702        # Get the parameters.
703        my ($message) = @_;
704        # Trace what's happening.
705        Trace("Stack trace for event: $message");
706        my $confession = longmess($message);
707        # Convert the confession to a series of trace messages.
708        for my $line (split /\s*\n/, $confession) {
709            # Only proceed if this call trace is for a method outside Tracer itself.
710            if ($line !~ /Tracer\.pm/) {
711                # Replace the leading tab with a series of spaces.
712                $line =~ s/\t/    /;
713                # Trace the line.
714                Trace($line);
715            }
716        }
717    }
718    
719    =head3 ScriptSetup (deprecated)
720    
721        my ($cgi, $varHash) = ScriptSetup($noTrace);
722    
723    Perform standard tracing and debugging setup for scripts. The value returned is
724    the CGI object followed by a pre-built variable hash. At the end of the script,
725    the client should call L</ScriptFinish> to output the web page.
726    
727    This method calls L</ETracing> to configure tracing, which allows the tracing
728    to be configured via the emergency tracing form on the debugging control panel.
729    Tracing will then be turned on automatically for all programs that use the L</ETracing>
730    method, which includes every program that uses this method or L</StandardSetup>.
731    
732    =over 4
733    
734    =item noTrace (optional)
735    
736    If specified, tracing will be suppressed. This is useful if the script wants to set up
737    tracing manually.
738    
739    =item RETURN
740    
741    Returns a two-element list consisting of a CGI query object and a variable hash for
742    the output page.
743    
744    =back
745    
746    =cut
747    
748    sub ScriptSetup {
749        # Get the parameters.
750        my ($noTrace) = @_;
751        # Get the CGI query object.
752        my $cgi = CGI->new();
753        # Set up tracing if it's not suppressed.
754        ETracing($cgi) unless $noTrace;
755        # Create the variable hash.
756        my $varHash = { results => '' };
757        # Return the query object and variable hash.
758        return ($cgi, $varHash);
759    }
760    
761    =head3 ETracing
762    
763        ETracing($parameter);
764    
765    Set up emergency tracing. Emergency tracing is tracing that is turned
766    on automatically for any program that calls this method. The emergency
767    tracing parameters are stored in a a file identified by a tracing key.
768    If this method is called with a CGI object, then the tracing key is
769    taken from a cookie. If it is called with no parameters, then the tracing
770    key is taken from an environment variable. If it is called with a string,
771    the tracing key is that string.
772    
773    =over 4
774    
775    =item parameter
776    
777    A parameter from which the tracing key is computed. If it is a scalar,
778    that scalar is used as the tracing key. If it is a CGI object, the
779    tracing key is taken from the C<IP> cookie. If it is omitted, the
780    tracing key is taken from the C<TRACING> environment variable. If it
781    is a CGI object and emergency tracing is not on, the C<Trace> and
782    C<TF> parameters will be used to determine the type of tracing.
783    
784    =back
785    
786    =cut
787    
788    sub ETracing {
789        # Get the parameter.
790        my ($parameter) = @_;
791        # Check for CGI mode.
792        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
793        # Default to no tracing except errors.
794        my ($tracing, $dest) = ("0", "WARN");
795        # Check for emergency tracing.
796        my $tkey = EmergencyKey($parameter);
797        my $emergencyFile = EmergencyFileName($tkey);
798        if (-e $emergencyFile) {
799            # We have the file. Read in the data.
800            my @tracing = GetFile($emergencyFile);
801            # Pull off the time limit.
802            my $expire = shift @tracing;
803            # Convert it to seconds.
804            $expire *= 3600;
805            # Check the file data.
806            my $stat = stat($emergencyFile);
807            my ($now) = gettimeofday;
808            if ($now - $stat->mtime > $expire) {
809                # Delete the expired file.
810                unlink $emergencyFile;
811            } else {
812                # Emergency tracing is on. Pull off the destination and
813                # the trace level;
814                $dest = shift @tracing;
815                my $level = shift @tracing;
816                # Convert the destination to a real tracing destination.
817                # temp directory.
818                $dest = EmergencyTracingDest($tkey, $dest);
819                # Insure Tracer is specified.
820                my %moduleHash = map { $_ => 1 } @tracing;
821                $moduleHash{Tracer} = 1;
822                # Set the trace parameter.
823                $tracing = join(" ", $level, sort keys %moduleHash);
824            }
825        } elsif (defined $cgi) {
826            # There's no emergency tracing, but we have a CGI object, so check
827            # for tracing from the form parameters.
828            if ($cgi->param('Trace')) {
829                # Here the user has requested tracing via a form.
830                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
831                $tracing = $cgi->param('Trace') . " Tracer";
832            }
833        }
834        # Setup the tracing we've determined from all the stuff above.
835        TSetup($tracing, $dest);
836        # Check to see if we're a web script.
837        if (defined $cgi) {
838            # Yes we are. Trace the form and environment data.
839            TraceParms($cgi);
840            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
841            # emitted by the script in its raw form.
842            if (T(Raw => 3)) {
843                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
844            }
845        }
846    }
847    
848  A string that vaguely describes the positional parameters. This is used  =head3 EmergencyFileName
 if the user specifies the C<-h> option.  
849    
850  =item argv      my $fileName = Tracer::EmergencyFileName($tkey);
851    
852  List of command line parameters, including the option switches, which must  Return the emergency tracing file name. This is the file that specifies
853  precede the positional parameters and be prefixed by a hyphen.  the tracing information.
854    
855    =over 4
856    
857    =item tkey
858    
859    Tracing key for the current program.
860    
861  =item RETURN  =item RETURN
862    
863  Returns a list. The first element of the list is the reference to a hash that  Returns the name of the file to contain the emergency tracing information.
 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.  
864    
865  =back  =back
866    
867  =cut  =cut
868    
869  sub StandardSetup {  sub EmergencyFileName {
870      # Get the parameters.      # Get the parameters.
871      my ($categories, $options, $parmHelp, @argv) = @_;      my ($tkey) = @_;
872      # Get the default tracing key.      # Compute the emergency tracing file name.
873      my $tkey = EmergencyKey();      return "$FIG_Config::temp/Emergency$tkey.txt";
     # Add the tracing options.  
     if (! exists $options->{trace}) {  
         $options->{trace} = ['2', "tracing level (E for emergency tracing)"];  
874      }      }
875      $options->{sql} = [0, "turn on SQL tracing"];  
876      $options->{help} = [0, "display command-line options"];  =head3 EmergencyFileTarget
877      $options->{user} = [$tkey, "tracing key"];  
878      $options->{background} = [0, "spool standard and error output"];      my $fileName = Tracer::EmergencyFileTarget($tkey);
879      # Create a parsing hash from the options hash. The parsing hash  
880      # contains the default values rather than the default value  Return the emergency tracing target file name. This is the file that receives
881      # and the description. While we're at it, we'll memorize the  the tracing output for file-based tracing.
882      # length of the longest option name.  
883      my $longestName = 0;  =over 4
884      my %parseOptions = ();  
885      for my $key (keys %{$options}) {  =item tkey
886          if (length $key > $longestName) {  
887              $longestName = length $key;  Tracing key for the current program.
888    
889    =item RETURN
890    
891    Returns the name of the file to contain the trace output.
892    
893    =back
894    
895    =cut
896    
897    sub EmergencyFileTarget {
898        # Get the parameters.
899        my ($tkey) = @_;
900        # Compute the emergency tracing file name.
901        return "$FIG_Config::temp/trace$tkey.log";
902          }          }
903          $parseOptions{$key} = $options->{$key}->[0];  
904    =head3 EmergencyTracingDest
905    
906        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
907    
908    This method converts an emergency tracing destination to a real
909    tracing destination. The main difference is that if the
910    destination is C<FILE> or C<APPEND>, we convert it to file
911    output. If the destination is C<DUAL>, we convert it to file
912    and standard output.
913    
914    =over 4
915    
916    =item tkey
917    
918    Tracing key for this environment.
919    
920    =item myDest
921    
922    Destination from the emergency tracing file.
923    
924    =item RETURN
925    
926    Returns a destination that can be passed into L</TSetup>.
927    
928    =back
929    
930    =cut
931    
932    sub EmergencyTracingDest {
933        # Get the parameters.
934        my ($tkey, $myDest) = @_;
935        # Declare the return variable.
936        my $retVal = $myDest;
937        # Process according to the destination value.
938        if ($myDest eq 'FILE') {
939            $retVal = ">" . EmergencyFileTarget($tkey);
940        } elsif ($myDest eq 'APPEND') {
941            $retVal = ">>" . EmergencyFileTarget($tkey);
942        } elsif ($myDest eq 'DUAL') {
943            $retVal = "+>" . EmergencyFileTarget($tkey);
944        } elsif ($myDest eq 'WARN') {
945            $retVal = "WARN";
946      }      }
947      # Parse the command line.      # Return the result.
948      my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);      return $retVal;
     # 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";  
949      }      }
950      # Now we want to set up tracing. First, we need to know if the user  
951      # wants emergency tracing.  =head3 Emergency
952      if ($retOptions->{trace} eq 'E') {  
953          ETracing($retOptions->{user});      Emergency($key, $hours, $dest, $level, @modules);
954    
955    Turn on emergency tracing. This method is normally invoked over the web from
956    a debugging console, but it can also be called by the C<trace.pl> script.
957    The caller specifies the duration of the emergency in hours, the desired tracing
958    destination, the trace level, and a list of the trace modules to activate.
959    For the length of the duration, when a program in an environment with the
960    specified tracing key active invokes a Sprout CGI script, tracing will be
961    turned on automatically. See L</TSetup> for more about tracing setup and
962    L</ETracing> for more about emergency tracing.
963    
964    =over 4
965    
966    =item tkey
967    
968    The tracing key. This is used to identify the control file and the trace file.
969    
970    =item hours
971    
972    Number of hours to keep emergency tracing alive.
973    
974    =item dest
975    
976    Tracing destination. If no path information is specified for a file
977    destination, it is put in the FIG temporary directory.
978    
979    =item level
980    
981    Tracing level. A higher level means more trace messages.
982    
983    =item modules
984    
985    A list of the tracing modules to activate.
986    
987    =back
988    
989    =cut
990    
991    sub Emergency {
992        # Get the parameters.
993        my ($tkey, $hours, $dest, $level, @modules) = @_;
994        # Create the emergency file.
995        my $specFile = EmergencyFileName($tkey);
996        my $outHandle = Open(undef, ">$specFile");
997        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
998    }
999    
1000    =head3 EmergencyKey
1001    
1002        my $tkey = EmergencyKey($parameter);
1003    
1004    Return the Key to be used for emergency tracing. This could be an IP address,
1005     a session ID, or a user name, depending on the environment.
1006    
1007    =over 4
1008    
1009    =item parameter
1010    
1011    Parameter defining the method for finding the tracing key. If it is a scalar,
1012    then it is presumed to be the tracing key itself. If it is a CGI object, then
1013    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1014    taken from the C<TRACING> environment variable.
1015    
1016    =item RETURN
1017    
1018    Returns the key to be used for labels in emergency tracing.
1019    
1020    =back
1021    
1022    =cut
1023    
1024    sub EmergencyKey {
1025        # Get the parameters.
1026        my ($parameter) = @_;
1027        # Declare the return variable.
1028        my $retVal;
1029        # Determine the parameter type.
1030        if (! defined $parameter) {
1031            # Here we're supposed to check the environment.
1032            $retVal = $ENV{TRACING};
1033      } else {      } else {
1034          # Here the tracing is controlled from the command line.          my $ptype = ref $parameter;
1035          my @cats = @{$categories};          if ($ptype eq 'CGI') {
1036          if ($retOptions->{sql}) {              # Here we were invoked from a web page. Look for a cookie.
1037              push @cats, "SQL";              $retVal = $parameter->cookie('IP');
1038            } elsif (! $ptype) {
1039                # Here the key was passed in.
1040                $retVal = $parameter;
1041            }
1042        }
1043        # If no luck finding a key, use the PID.
1044        if (! defined $retVal) {
1045            $retVal = $$;
1046        }
1047        # Return the result.
1048        return $retVal;
1049    }
1050    
1051    
1052    =head3 TraceParms
1053    
1054        Tracer::TraceParms($cgi);
1055    
1056    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1057    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1058    
1059    =over 4
1060    
1061    =item cgi
1062    
1063    CGI query object containing the parameters to trace.
1064    
1065    =back
1066    
1067    =cut
1068    
1069    sub TraceParms {
1070        # Get the parameters.
1071        my ($cgi) = @_;
1072        if (T(CGI => 2)) {
1073            # Here we trace the GET-style URL for the script.
1074            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1075          }          }
1076          # Add the default categories.      if (T(CGI => 3)) {
1077          push @cats, "Tracer";          # Here we want to trace the parameter data.
1078          # Next, we create the category string by joining the categories.          my @names = $cgi->param;
1079          my $cats = join(" ", @cats);          for my $parmName (sort @names) {
1080          # Check to determine whether or not the caller wants to turn off tracing              # Note we skip the Trace parameters, which are for our use only.
1081          # to the standard output.              if ($parmName ne 'Trace' && $parmName ne 'TF') {
1082          my $traceLevel = $retOptions->{trace};                  my @values = $cgi->param($parmName);
1083          my $textOKFlag = 1;                  Trace("[CGI] $parmName = " . join(", ", @values));
         if ($traceLevel =~ /^(.)-/) {  
             $traceLevel = $1;  
             $textOKFlag = 0;  
1084          }          }
         # 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";  
1085              }              }
1086              # Close the test file.          # Display the request method.
1087              close TESTTRACE;          my $method = $cgi->request_method();
1088          } else {          Trace("Method: $method");
             # Here we can't trace to a file. We trace to the standard output if it's  
             # okay, and the error log otherwise.  
             if ($textOKFlag) {  
                 $traceMode = "TEXT";  
             } else {  
                 $traceMode = "WARN";  
1089              }              }
1090        if (T(CGI => 4)) {
1091            # Here we want the environment data too.
1092            for my $envName (sort keys %ENV) {
1093                Trace("[ENV] $envName = $ENV{$envName}");
1094          }          }
         # Now set up the tracing.  
         TSetup("$traceLevel $cats", $traceMode);  
1095      }      }
     # Check for the "h" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($retOptions->{help}) {  
         $0 =~ m#[/\\](\w+)(\.pl)?$#i;  
         print "$1 [options] $parmHelp\n";  
         for my $key (sort keys %{$options}) {  
             my $name = Pad($key, $longestName, 0, ' ');  
             my $desc = $options->{$key}->[1];  
             if ($options->{$key}->[0]) {  
                 $desc .= " (default " . $options->{$key}->[0] . ")";  
1096              }              }
1097              print "  $name $desc\n";  
1098    =head3 TraceImages
1099    
1100        Tracer::TraceImages($htmlString);
1101    
1102    Trace information about all of an html document's images. The tracing
1103    will be for type "IMG" at level 3. The image's source string
1104    will be displayed. This is generally either the URL of the image or
1105    raw data for the image itself. If the source is too long, only the first 300
1106    characters will be shown at trace level 3. The entire source will be shown,
1107    however, at trace level 4. This method is not very smart, and might catch
1108    Javascript code, but it is still useful when debugging the arcane
1109    behavior of images in multiple browser environments.
1110    
1111    =over 4
1112    
1113    =item htmlString
1114    
1115    HTML text for an outgoing web page.
1116    
1117    =back
1118    
1119    =cut
1120    
1121    sub TraceImages {
1122        # Only proceed if we're at the proper trace level.
1123        if (T(IMG => 3)) {
1124            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1125            # into a variable called "$htmlString". This is because we expect html strings to be
1126            # long, and don't want to copy them any more than we have to.
1127            Trace(length($_[0]) . " characters in web page.");
1128            # Loop through the HTML, culling image tags.
1129            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1130                # Extract the source string and determine whether or not it's too long.
1131                my $srcString = $1;
1132                my $pos = pos($_[0]) - length($srcString);
1133                my $excess = length($srcString) - 300;
1134                # We'll put the display string in here.
1135                my $srcDisplay = $srcString;
1136                # If it's a data string, split it at the comma.
1137                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1138                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1139                # a long string, however, we only show the first 300 characters.
1140                if ($excess > 0 && ! T(IMG => 4)) {
1141                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1142          }          }
1143          exit(0);              # Output the trace message.
1144                Trace("Image tag at position $pos:\n$srcDisplay");
1145      }      }
     # Trace the options, if applicable.  
     if (T(3)) {  
         my @parms = grep { $retOptions->{$_} } keys %{$retOptions};  
         Trace("Selected options: " . join(", ", sort @parms) . ".");  
1146      }      }
     # Return the parsed parameters.  
     return ($retOptions, @retParameters);  
1147  }  }
1148    
 =head3 Setups  
1149    
1150  C<< my $count = Tracer::Setups(); >>  =head3 ScriptFinish (deprecated)
1151    
1152  Return the number of times L</TSetup> has been called.      ScriptFinish($webData, $varHash);
1153    
1154  This method allows for the creation of conditional tracing setups where, for example, we  Output a web page at the end of a script. Either the string to be output or the
1155  may want to set up tracing if nobody else has done it before us.  name of a template file can be specified. If the second parameter is omitted,
1156    it is assumed we have a string to be output; otherwise, it is assumed we have the
1157    name of a template file. The template should have the variable C<DebugData>
1158    specified in any form that invokes a standard script. If debugging mode is turned
1159    on, a form field will be put in that allows the user to enter tracing data.
1160    Trace messages will be placed immediately before the terminal C<BODY> tag in
1161    the output, formatted as a list.
1162    
1163  =cut  A typical standard script would loook like the following.
1164    
1165  sub Setups {      BEGIN {
1166      return $SetupCount;          # Print the HTML header.
1167            print "CONTENT-TYPE: text/html\n\n";
1168  }  }
1169        use Tracer;
1170        use CGI;
1171        use FIG;
1172        # ... more uses ...
1173    
1174  =head3 Open      my ($cgi, $varHash) = ScriptSetup();
1175        eval {
1176            # ... get data from $cgi, put it in $varHash ...
1177        };
1178        if ($@) {
1179            Trace("Script Error: $@") if T(0);
1180        }
1181        ScriptFinish("Html/MyTemplate.html", $varHash);
1182    
1183  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  The idea here is that even if the script fails, you'll see trace messages and
1184    useful output.
1185    
1186  Open a file.  =over 4
1187    
1188  The I<$fileSpec> is essentially the second argument of the PERL C<open>  =item webData
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
1189    
1190      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  A string containing either the full web page to be written to the output or the
1191    name of a template file from which the page is to be constructed. If the name
1192    of a template file is specified, then the second parameter must be present;
1193    otherwise, it must be absent.
1194    
1195  would open for output appended to the specified file, and  =item varHash (optional)
1196    
1197      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  If specified, then a reference to a hash mapping variable names for a template
1198    to their values. The template file will be read into memory, and variable markers
1199    will be replaced by data in this hash reference.
1200    
1201  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.  
1202    
1203      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =cut
1204    
1205  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  sub ScriptFinish {
1206  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a      # Get the parameters.
1207  failed open will throw an exception and the third parameter will be used to construct      my ($webData, $varHash) = @_;
1208  an error message. If the parameter is omitted, a standard message is constructed      # Check for a template file situation.
1209  using the file spec.      my $outputString;
1210        if (defined $varHash) {
1211            # Here we have a template file. We need to determine the template type.
1212            my $template;
1213            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1214                $template = "$FIG_Config::template_url/$webData";
1215            } else {
1216                $template = "<<$webData";
1217            }
1218            $outputString = PageBuilder::Build($template, $varHash, "Html");
1219        } else {
1220            # Here the user gave us a raw string.
1221            $outputString = $webData;
1222        }
1223        # Check for trace messages.
1224        if ($Destination ne "NONE" && $TraceLevel > 0) {
1225            # We have trace messages, so we want to put them at the end of the body. This
1226            # is either at the end of the whole string or at the beginning of the BODY
1227            # end-tag.
1228            my $pos = length $outputString;
1229            if ($outputString =~ m#</body>#gi) {
1230                $pos = (pos $outputString) - 7;
1231            }
1232            # If the trace messages were queued, we unroll them. Otherwise, we display the
1233            # destination.
1234            my $traceHtml;
1235            if ($Destination eq "QUEUE") {
1236                $traceHtml = QTrace('Html');
1237            } elsif ($Destination =~ /^>>(.+)$/) {
1238                # Here the tracing output it to a file. We code it as a hyperlink so the user
1239                # can copy the file name into the clipboard easily.
1240                my $actualDest = $1;
1241                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1242            } else {
1243                # Here we have one of the special destinations.
1244                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1245            }
1246            substr $outputString, $pos, 0, $traceHtml;
1247        }
1248        # Write the output string.
1249        print $outputString;
1250    }
1251    
1252      Could not open "/usr/spool/news/twitlog"  =head2 Command-Line Utility Methods
1253    
1254  Note that the mode characters are automatically cleaned from the file name.  =head3 SendSMS
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
1255    
1256      Could not open "/usr/spool/news/twitlog": file not found.      my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1257    
1258  In some versions of PERL the only error message we get is a number, which  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1259  corresponds to the C++ C<errno> value.  user name, password, and API ID for the relevant account in the hash reference variable
1260    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1261    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1262    is C<2561022>, then the FIG_Config file must contain
1263    
1264      Could not open "/usr/spool/news/twitlog": 6.      $phone =  { user => 'BruceTheHumanPet',
1265                    password => 'silly',
1266                    api_id => '2561022' };
1267    
1268  =over 4  The original purpose of this method was to insure Bruce would be notified immediately when the
1269    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1270    when you call this method.
1271    
1272  =item fileHandle  The message ID will be returned if successful, and C<undef> if an error occurs.
1273    
1274  File handle. If this parameter is C<undef>, a file handle will be generated  =over 4
 and returned as the value of this method.  
1275    
1276  =item fileSpec  =item phoneNumber
1277    
1278  File name and mode, as per the PERL C<open> function.  Phone number to receive the message, in international format. A United States phone number
1279    would be prefixed by "1". A British phone number would be prefixed by "44".
1280    
1281  =item message (optional)  =item msg
1282    
1283  Error message to use if the open fails. If omitted, a standard error message  Message to send to the specified phone.
 will be generated. In either case, the error information from the file system  
 is appended to the message. To specify a conditional open that does not throw  
 an error if it fails, use C<0>.  
1284    
1285  =item RETURN  =item RETURN
1286    
1287  Returns the name of the file handle assigned to the file, or C<undef> if the  Returns the message ID if successful, and C<undef> if the message could not be sent.
 open failed.  
1288    
1289  =back  =back
1290    
1291  =cut  =cut
1292    
1293  sub Open {  sub SendSMS {
1294      # Get the parameters.      # Get the parameters.
1295      my ($fileHandle, $fileSpec, $message) = @_;      my ($phoneNumber, $msg) = @_;
1296      # Attempt to open the file.      # Declare the return variable. If we do not change it, C<undef> will be returned.
1297      my $rv = open $fileHandle, $fileSpec;      my $retVal;
1298      # If the open failed, generate an error message.      # Only proceed if we have phone support.
1299      if (! $rv) {      if (! defined $FIG_Config::phone) {
1300          # Save the system error message.          Trace("Phone support not present in FIG_Config.") if T(1);
1301          my $sysMessage = $!;      } else {
1302          # See if we need a default message.          # Get the phone data.
1303          if (!$message) {          my $parms = $FIG_Config::phone;
1304              # Clean any obvious mode characters and leading spaces from the          # Get the Clickatell URL.
1305              # filename.          my $url = "http://api.clickatell.com/http/";
1306              my ($fileName) = FindNamePart($fileSpec);          # Create the user agent.
1307              $message = "Could not open \"$fileName\"";          my $ua = LWP::UserAgent->new;
1308            # Request a Clickatell session.
1309            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1310                                         password => $parms->{password},
1311                                         api_id => $parms->{api_id},
1312                                         to => $phoneNumber,
1313                                         text => $msg});
1314            # Check for an error.
1315            if (! $resp->is_success) {
1316                Trace("Alert failed.") if T(1);
1317            } else {
1318                # Get the message ID.
1319                my $rstring = $resp->content;
1320                if ($rstring =~ /^ID:\s+(.*)$/) {
1321                    $retVal = $1;
1322                } else {
1323                    Trace("Phone attempt failed with $rstring") if T(1);
1324          }          }
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
1325      }      }
1326      # Return the file handle.      }
1327      return $fileHandle;      # Return the result.
1328        return $retVal;
1329  }  }
1330    
1331  =head3 FindNamePart  =head3 StandardSetup
1332    
1333  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>      my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1334    
1335  Extract the portion of a file specification that contains the file name.  This method performs standard command-line parsing and tracing setup. The return
1336    values are a hash of the command-line options and a list of the positional
1337    parameters. Tracing is automatically set up and the command-line options are
1338    validated.
1339    
1340  A file specification is the string passed to an C<open> call. It specifies the file  This is a complex method that does a lot of grunt work. The parameters can
1341  mode and name. In a truly complex situation, it can specify a pipe sequence. This  be more easily understood, however, once they are examined individually.
 method assumes that the file name is whatever follows the first angle bracket  
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
1342    
1343      >>/usr/fig/myfile.txt  The I<categories> parameter is the most obtuse. It is a reference to a list of
1344      </usr/fig/myfile.txt  special-purpose tracing categories. Most tracing categories are PERL package
1345      | sort -u > /usr/fig/myfile.txt  names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1346    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1347    
1348  If the method cannot find a file name using its normal methods, it will return the      ["Sprout", "SproutLoad", "ERDB"]
1349  whole incoming string.  
1350    This would cause trace messages in the specified three packages to appear in
1351    the output. There are two special tracing categories that are automatically
1352    handled by this method. In other words, if you used L</TSetup> you would need
1353    to include these categories manually, but if you use this method they are turned
1354    on automatically.
1355    
1356  =over 4  =over 4
1357    
1358  =item fileSpec  =item SQL
1359    
1360  File specification string from which the file name is to be extracted.  Traces SQL commands and activity.
1361    
1362  =item RETURN  =item Tracer
1363    
1364  Returns a three-element list. The first element contains the file name portion of  Traces error messages and call stacks.
 the specified string, or the whole string if a file name cannot be found via normal  
 methods. The second element contains the start position of the file name portion and  
 the third element contains the length.  
1365    
1366  =back  =back
1367    
1368  =cut  C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1369  #: Return Type $;  The trace level is specified using the C<-trace> command-line option. For example,
1370  sub FindNamePart {  the following command line for C<TransactFeatures> turns on SQL tracing and runs
1371      # Get the parameters.  all tracing at level 3.
     my ($fileSpec) = @_;  
     # Default to the whole input string.  
     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);  
     # Parse out the file name if we can.  
     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {  
         $retVal = $2;  
         $len = length $retVal;  
         $pos = (length $fileSpec) - (length $3) - $len;  
     }  
     # Return the result.  
     return ($retVal, $pos, $len);  
 }  
1372    
1373  =head3 OpenDir      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1374    
1375  C<< my @files = OpenDir($dirName, $filtered, $flag); >>  Standard tracing is output to the standard output and echoed to the file
1376    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1377    process ID. You can also specify the C<user> parameter to put a user ID
1378    instead of a process ID in the trace file name. So, for example
1379    
1380  Open a directory and return all the file names. This function essentially performs  The default trace level is 2. To get all messages, specify a trace level of 4.
1381  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  For a genome-by-genome update, use 3.
 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  
 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be  
 filtered out of the return list. If the directory does not open and I<$flag> is not  
 set, an exception is thrown. So, for example,  
1382    
1383      my @files = OpenDir("/Volumes/fig/contigs", 1);      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1384    
1385  is effectively the same as  would send the trace output to C<traceBruce.log> in the temporary directory.
1386    
1387      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  The I<options> parameter is a reference to a hash containing the command-line
1388      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  options, their default values, and an explanation of what they mean. Command-line
1389    options may be in the form of switches or keywords. In the case of a switch, the
1390    option value is 1 if it is specified and 0 if it is not specified. In the case
1391    of a keyword, the value is separated from the option name by an equal sign. You
1392    can see this last in the command-line example above.
1393    
1394  Similarly, the following code  You can specify a different default trace level by setting C<$options->{trace}>
1395    prior to calling this method.
1396    
1397      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  An example at this point would help. Consider, for example, the command-line utility
1398    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1399    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1400    the following code.
1401    
1402  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1403  automatically returns an empty list if the directory fails to open.                          { safe => [0, "use database transactions"],
1404                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1405                              start => [' ', "start with this genome"],
1406                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1407                            "<command> <transactionDirectory> <IDfile>",
1408                          @ARGV);
1409    
 =over 4  
1410    
1411  =item dirName  The call to C<ParseCommand> specifies the default values for the options and
1412    stores the actual options in a hash that is returned as C<$options>. The
1413    positional parameters are returned in C<@parameters>.
1414    
1415  Name of the directory to open.  The following is a sample command line for C<TransactFeatures>.
1416    
1417  =item filtered      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1418    
1419  TRUE if files whose names begin with a period (C<.>) should be automatically removed  Single and double hyphens are equivalent. So, you could also code the
1420  from the list, else FALSE.  above command as
1421    
1422  =item flag      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1423    
1424  TRUE if a failure to open is okay, else FALSE  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1425    parameters, and would find themselves in I<@parameters> after executing the
1426    above code fragment. The tracing would be set to level 2, and the categories
1427    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1428    and C<DocUtils> was included because it came in within the first parameter
1429    to this method. The I<$options> hash would be
1430    
1431  =back      { trace => 2, sql => 0, safe => 0,
1432          noAlias => 1, start => ' ', tblFiles => 0 }
1433    
1434  =cut  Use of C<StandardSetup> in this way provides a simple way of performing
1435  #: Return Type @;  standard tracing setup and command-line parsing. Note that the caller is
1436  sub OpenDir {  not even aware of the command-line switches C<-trace> and C<-sql>, which
1437      # Get the parameters.  are used by this method to control the tracing. If additional tracing features
1438      my ($dirName, $filtered, $flag) = @_;  need to be added in the future, they can be processed by this method without
1439      # Declare the return variable.  upsetting the command-line utilities.
     my @retVal = ();  
     # Open the directory.  
     if (opendir(my $dirHandle, $dirName)) {  
         # The directory opened successfully. Get the appropriate list according to the  
         # strictures of the filter parameter.  
         if ($filtered) {  
             @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;  
         } else {  
             @retVal = readdir $dirHandle;  
         }  
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
     }  
     # Return the result.  
     return @retVal;  
 }  
1440    
1441  =head3 SetLevel  If the C<background> option is specified on the command line, then the
1442    standard and error outputs will be directed to files in the temporary
1443    directory, using the same suffix as the trace file. So, if the command
1444    line specified
1445    
1446  C<< Tracer::SetLevel($newLevel); >>      -user=Bruce -background
1447    
1448  Modify the trace level. A higher trace level will cause more messages to appear.  then the trace output would go to C<traceBruce.log>, the standard output to
1449    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1450    simplify starting a command in the background.
1451    
1452  =over 4  The user name is also used as the tracing key for L</Emergency Tracing>.
1453    Specifying a value of C<E> for the trace level causes emergency tracing to
1454    be used instead of custom tracing. If the user name is not specified,
1455    the tracing key is taken from the C<Tracing> environment variable. If there
1456    is no value for that variable, the tracing key will be computed from the PID.
1457    
1458  =item newLevel  Finally, if the special option C<-help> is specified, the option
1459    names will be traced at level 0 and the program will exit without processing.
1460    This provides a limited help capability. For example, if the user enters
1461    
1462  Proposed new trace level.      TransactFeatures -help
1463    
1464  =back  he would see the following output.
1465    
1466  =cut      TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1467            -trace    tracing level (default E)
1468            -sql      trace SQL commands
1469            -safe     use database transactions
1470            -noAlias  do not expect aliases in CHANGE transactions
1471            -start    start with this genome
1472            -tblFiles output TBL files containing the corrected IDs
1473    
1474  sub SetLevel {  The caller has the option of modifying the tracing scheme by placing a value
1475      $TraceLevel = $_[0];  for C<trace> in the incoming options hash. The default value can be overridden,
1476  }  or the tracing to the standard output can be turned off by suffixing a minus
1477    sign to the trace level. So, for example,
1478    
1479  =head3 Now      { trace => [0, "tracing level (default 0)"],
1480           ...
1481    
1482  C<< my $string = Tracer::Now(); >>  would set the default trace level to 0 instead of E, while
1483    
1484  Return a displayable time stamp containing the local time.      { trace => ["2-", "tracing level (default 2)"],
1485           ...
1486    
1487  =cut  would set the default to 2, but trace only to the log file, not to the
1488    standard output.
1489    
1490  sub Now {  The parameters to this method are as follows.
     my ($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 $retVal;  
 }  
1491    
1492  # Pad a number to 2 digits.  =over 4
1493  sub _p2 {  
1494      my ($value) = @_;  =item categories
1495      $value = "0$value" if ($value < 10);  
1496      return $value;  Reference to a list of tracing category names. These should be names of
1497  }  packages whose internal workings will need to be debugged to get the
1498    command working.
1499    
1500  =head3 ParseTraceDate  =item options
1501    
1502  C<< my $time = Tracer::ParseTraceDate($dateString); >>  Reference to a hash containing the legal options for the current command mapped
1503    to their default values and descriptions. The user can override the defaults
1504    by specifying the options as command-line switches prefixed by a hyphen.
1505    Tracing-related options may be added to this hash. If the C<-h> option is
1506    specified on the command line, the option descriptions will be used to
1507    explain the options. To turn off tracing to the standard output, add a
1508    minus sign to the value for C<trace> (see above).
1509    
1510  Convert a date from the trace file into a PERL timestamp.  =item parmHelp
1511    
1512  =over 4  A string that vaguely describes the positional parameters. This is used
1513    if the user specifies the C<-h> option.
1514    
1515  =item dateString  =item argv
1516    
1517  The date string from the trace file. The format of the string is determined by the  List of command line parameters, including the option switches, which must
1518  L</Now> method.  precede the positional parameters and be prefixed by a hyphen.
1519    
1520  =item RETURN  =item RETURN
1521    
1522  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if  Returns a list. The first element of the list is the reference to a hash that
1523  the time string is invalid.  maps the command-line option switches to their values. These will either be the
1524    default values or overrides specified on the command line. The remaining
1525    elements of the list are the position parameters, in order.
1526    
1527  =back  =back
1528    
1529  =cut  =cut
1530    
1531  sub ParseTraceDate {  sub StandardSetup {
1532      # Get the parameters.      # Get the parameters.
1533      my ($dateString) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
1534      # Declare the return variable.      # Get the default tracing key.
1535      my $retVal;      my $tkey = EmergencyKey();
1536      # Parse the date.      # Add the tracing options.
1537      if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {      if (! exists $options->{trace}) {
1538          # Create a time object. Note we need to convert the day, month,          $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
         # and year to a different base. Years count from 1900, and  
         # the internal month value is relocated to January = 0.  
         $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);  
1539      }      }
1540      # Return the result.      $options->{sql} = [0, "turn on SQL tracing"];
1541      return $retVal;      $options->{help} = [0, "display command-line options"];
1542        $options->{user} = [$tkey, "tracing key"];
1543        $options->{background} = [0, "spool standard and error output"];
1544        # Create a parsing hash from the options hash. The parsing hash
1545        # contains the default values rather than the default value
1546        # and the description. While we're at it, we'll memorize the
1547        # length of the longest option name.
1548        my $longestName = 0;
1549        my %parseOptions = ();
1550        for my $key (keys %{$options}) {
1551            if (length $key > $longestName) {
1552                $longestName = length $key;
1553  }  }
1554            $parseOptions{$key} = $options->{$key}->[0];
1555  =head3 LogErrors      }
1556        # Parse the command line.
1557  C<< Tracer::LogErrors($fileName); >>      my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1558        # Get the logfile suffix.
1559  Route the standard error output to a log file.      my $suffix = $retOptions->{user};
1560        # Check for background mode.
1561  =over 4      if ($retOptions->{background}) {
1562            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1563  =item fileName          my $errFileName = "$FIG_Config::temp/err$suffix.log";
1564            open STDOUT, ">$outFileName";
1565  Name of the file to receive the error output.          open STDERR, ">$errFileName";
1566            # Check for phone support. If we have phone support and a phone number,
1567  =back          # we want to turn it on.
1568            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1569  =cut              $retOptions->{phone} = $ENV{PHONE};
1570            }
1571  sub LogErrors {      }
1572      # Get the file name.      # Now we want to set up tracing. First, we need to know if the user
1573      my ($fileName) = @_;      # wants emergency tracing.
1574      # Open the file as the standard error output.      if ($retOptions->{trace} eq 'E') {
1575      open STDERR, '>', $fileName;          ETracing($retOptions->{user});
1576        } else {
1577            # Here the tracing is controlled from the command line.
1578            my @cats = @{$categories};
1579            if ($retOptions->{sql}) {
1580                push @cats, "SQL";
1581            }
1582            # Add the default categories.
1583            push @cats, "Tracer";
1584            # Next, we create the category string by joining the categories.
1585            my $cats = join(" ", @cats);
1586            # Check to determine whether or not the caller wants to turn off tracing
1587            # to the standard output.
1588            my $traceLevel = $retOptions->{trace};
1589            my $textOKFlag = 1;
1590            if ($traceLevel =~ /^(.)-/) {
1591                $traceLevel = $1;
1592                $textOKFlag = 0;
1593            }
1594            # Now we set up the trace mode.
1595            my $traceMode;
1596            # Verify that we can open a file in the FIG temporary directory.
1597            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1598            if (open TESTTRACE, ">$traceFileName") {
1599                # Here we can trace to a file.
1600                $traceMode = ">$traceFileName";
1601                if ($textOKFlag) {
1602                    # Echo to standard output if the text-OK flag is set.
1603                    $traceMode = "+$traceMode";
1604                }
1605                # Close the test file.
1606                close TESTTRACE;
1607            } else {
1608                # Here we can't trace to a file. We trace to the standard output if it's
1609                # okay, and the error log otherwise.
1610                if ($textOKFlag) {
1611                    $traceMode = "TEXT";
1612                } else {
1613                    $traceMode = "WARN";
1614                }
1615            }
1616            # Now set up the tracing.
1617            TSetup("$traceLevel $cats", $traceMode);
1618        }
1619        # Check for the "help" option. If it is specified, dump the command-line
1620        # options and exit the program.
1621        if ($retOptions->{help}) {
1622            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1623            print "$1 [options] $parmHelp\n";
1624            for my $key (sort keys %{$options}) {
1625                my $name = Pad($key, $longestName, 0, ' ');
1626                my $desc = $options->{$key}->[1];
1627                if ($options->{$key}->[0]) {
1628                    $desc .= " (default " . $options->{$key}->[0] . ")";
1629                }
1630                print "  $name $desc\n";
1631            }
1632            exit(0);
1633        }
1634        # Trace the options, if applicable.
1635        if (T(3)) {
1636            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1637            Trace("Selected options: " . join(", ", sort @parms) . ".");
1638        }
1639        # Return the parsed parameters.
1640        return ($retOptions, @retParameters);
1641  }  }
1642    
1643  =head3 ReadOptions  =head3 ReadOptions
1644    
1645  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1646    
1647  Read a set of options from a file. Each option is encoded in a line of text that has the  Read a set of options from a file. Each option is encoded in a line of text that has the
1648  format  format
# Line 1069  Line 1703 
1703    
1704  =head3 GetOptions  =head3 GetOptions
1705    
1706  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1707    
1708  Merge a specified set of options into a table of defaults. This method takes two hash references  Merge a specified set of options into a table of defaults. This method takes two hash references
1709  as input and uses the data from the second to update the first. If the second does not exist,  as input and uses the data from the second to update the first. If the second does not exist,
# Line 1078  Line 1712 
1712    
1713  Consider the following example.  Consider the following example.
1714    
1715  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1716    
1717  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1718  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 1086  Line 1720 
1720  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1721  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1722    
1723  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1724    
1725  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1726    
# Line 1130  Line 1764 
1764    
1765  =head3 MergeOptions  =head3 MergeOptions
1766    
1767  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
1768    
1769  Merge default values into a hash table. This method looks at the key-value pairs in the  Merge default values into a hash table. This method looks at the key-value pairs in the
1770  second (default) hash, and if a matching key is not found in the first hash, the default  second (default) hash, and if a matching key is not found in the first hash, the default
# Line 1148  Line 1782 
1782  Default values to be merged into the first hash table if they are not already present.  Default values to be merged into the first hash table if they are not already present.
1783    
1784  =back  =back
1785    
1786  =cut  =cut
1787    
1788  sub MergeOptions {  sub MergeOptions {
1789      # Get the parameters.      # Get the parameters.
1790      my ($table, $defaults) = @_;      my ($table, $defaults) = @_;
1791      # Loop through the defaults.      # Loop through the defaults.
1792      while (my ($key, $value) = each %{$defaults}) {      while (my ($key, $value) = each %{$defaults}) {
1793          if (!exists $table->{$key}) {          if (!exists $table->{$key}) {
1794              $table->{$key} = $value;              $table->{$key} = $value;
         }  
     }  
 }  
   
 =head3 Trace  
   
 C<< Trace($message); >>  
   
 Write a trace message to the target location specified in L</TSetup>. If there has not been  
 any prior call to B<TSetup>.  
   
 =over 4  
   
 =item message  
   
 Message to write.  
   
 =back  
   
 =cut  
   
 sub Trace {  
     # Get the parameters.  
     my ($message) = @_;  
     # Get the timestamp.  
     my $timeStamp = Now();  
     # Format the message. Note we strip off any line terminators at the end.  
     my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);  
     # Process according to the destination.  
     if ($Destination eq "TEXT") {  
         # Write the message to the standard output.  
         print "$formatted\n";  
     } elsif ($Destination eq "ERROR") {  
         # Write the message to the error output.  
         print STDERR "$formatted\n";  
     } elsif ($Destination eq "QUEUE") {  
         # Push the message into the queue.  
         push @Queue, "$formatted";  
     } elsif ($Destination eq "HTML") {  
         # Convert the message to HTML and write it to the standard output.  
         my $escapedMessage = CGI::escapeHTML($message);  
         print "<p>$formatted</p>\n";  
     } elsif ($Destination eq "WARN") {  
        # Emit the message as a warning.  
        warn $message;  
     } elsif ($Destination =~ m/^>>/) {  
         # Write the trace message to an output file.  
         (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";  
         print TRACING "$formatted\n";  
         close TRACING;  
         # If the Tee flag is on, echo it to the standard output.  
         if ($TeeFlag) {  
             print "$formatted\n";  
         }  
     }  
 }  
   
 =head3 T  
   
 C<< my $switch = T($category, $traceLevel); >>  
   
     or  
   
 C<< my $switch = T($traceLevel); >>  
   
 Return TRUE if the trace level is at or above a specified value and the specified category  
 is active, else FALSE. If no category is specified, the caller's package name is used.  
   
 =over 4  
   
 =item category  
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
   
 Relevant tracing level.  
   
 =item RETURN  
   
 TRUE if a message at the specified trace level would appear in the trace, else FALSE.  
   
 =back  
   
 =cut  
   
 sub T {  
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
         # Get the parameters.  
         my ($category, $traceLevel) = @_;  
         if (!defined $traceLevel) {  
             # Here we have no category, so we need to get the calling package.  
             # The calling package is normally the first parameter. If it is  
             # omitted, the first parameter will be the tracelevel. So, the  
             # first thing we do is shift the so-called category into the  
             # $traceLevel variable where it belongs.  
             $traceLevel = $category;  
             my ($package, $fileName, $line) = caller;  
             # If there is no calling package, we default to "main".  
             if (!$package) {  
                 $category = "main";  
             } else {  
                 $category = $package;  
             }  
         }  
         # Save the category name.  
         $LastCategory = $category;  
         # Convert it to lower case before we hash it.  
         $category = lc $category;  
         # Use the category and tracelevel to compute the result.  
         if (ref $traceLevel) {  
             Confess("Bad trace level.");  
         } elsif (ref $TraceLevel) {  
             Confess("Bad trace config.");  
1795          }          }
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
1796      }      }
     # Return the computed result.  
     return $retVal;  
1797  }  }
1798    
1799  =head3 ParseCommand  =head3 ParseCommand
1800    
1801  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1802    
1803  Parse a command line consisting of a list of parameters. The initial parameters may be option  Parse a command line consisting of a list of parameters. The initial parameters may be option
1804  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1805  off and merged into a table of default options. The remainder of the command line is  off and merged into a table of default options. The remainder of the command line is
1806  returned as a list of positional arguments. For example, consider the following invocation.  returned as a list of positional arguments. For example, consider the following invocation.
1807    
1808  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1809    
1810  In this case, the list @words will be treated as a command line and there are two options available,  In this case, the list @words will be treated as a command line and there are two options available,
1811  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
1812    
1813  C<< -logFile=error.log apple orange rutabaga >>      -logFile=error.log apple orange rutabaga
1814    
1815  then at the end of the invocation, C<$options> will be  then at the end of the invocation, C<$options> will be
1816    
1817  C<< { errors => 0, logFile => 'error.log' } >>      { errors => 0, logFile => 'error.log' }
1818    
1819  and C<@arguments> will contain  and C<@arguments> will contain
1820    
1821  C<< apple orange rutabaga >>      apple orange rutabaga
1822    
1823  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1824  support for quote characters. Options can be specified with single or double hyphens.  support for quote characters. Options can be specified with single or double hyphens.
# Line 1359  Line 1872 
1872      return ($optionTable, @retVal);      return ($optionTable, @retVal);
1873  }  }
1874    
 =head3 Escape  
   
 C<< my $codedString = Tracer::Escape($realString); >>  
   
 Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  
 replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
 result is to reverse the effect of L</UnEscape>.  
   
 =over 4  
   
 =item realString  
   
 String to escape.  
   
 =item RETURN  
   
 Escaped equivalent of the real string.  
   
 =back  
   
 =cut  
   
 sub Escape {  
     # Get the parameter.  
     my ($realString) = @_;  
     # Initialize the return variable.  
     my $retVal = "";  
     # Loop through the parameter string, looking for sequences to escape.  
     while (length $realString > 0) {  
         # Look for the first sequence to escape.  
         if ($realString =~ /^(.*?)([\n\t\r\\])/) {  
             # Here we found it. The text preceding the sequence is in $1. The sequence  
             # itself is in $2. First, move the clear text to the return variable.  
             $retVal .= $1;  
             # Strip the processed section off the real string.  
             $realString = substr $realString, (length $2) + (length $1);  
             # Get the matched character.  
             my $char = $2;  
             # If we have a CR, we are done.  
             if ($char ne "\r") {  
                 # It's not a CR, so encode the escape sequence.  
                 $char =~ tr/\t\n/tn/;  
                 $retVal .= "\\" . $char;  
             }  
         } else {  
             # Here there are no more escape sequences. The rest of the string is  
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
         }  
     }  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 UnEscape  
   
 C<< my $realString = Tracer::UnEscape($codedString); >>  
   
 Replace escape sequences with their actual equivalents. C<\t> will be replaced by  
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
   
 =over 4  
   
 =item codedString  
   
 String to un-escape.  
   
 =item RETURN  
   
 Returns a copy of the original string with the escape sequences converted to their actual  
 values.  
   
 =back  
   
 =cut  
   
 sub UnEscape {  
     # Get the parameter.  
     my ($codedString) = @_;  
     # Initialize the return variable.  
     my $retVal = "";  
     # Only proceed if the incoming string is nonempty.  
     if (defined $codedString) {  
         # Loop through the parameter string, looking for escape sequences. We can't do  
         # translating because it causes problems with the escaped slash. ("\\t" becomes  
         # "\<tab>" no matter what we do.)  
         while (length $codedString > 0) {  
             # Look for the first escape sequence.  
             if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {  
                 # Here we found it. The text preceding the sequence is in $1. The sequence  
                 # itself is in $2. First, move the clear text to the return variable.  
                 $retVal .= $1;  
                 $codedString = substr $codedString, (2 + length $1);  
                 # Get the escape value.  
                 my $char = $2;  
                 # If we have a "\r", we are done.  
                 if ($char ne 'r') {  
                     # Here it's not an 'r', so we convert it.  
                     $char =~ tr/\\tn/\\\t\n/;  
                     $retVal .= $char;  
                 }  
             } else {  
                 # Here there are no more escape sequences. The rest of the string is  
                 # transferred unmodified.  
                 $retVal .= $codedString;  
                 $codedString = "";  
             }  
         }  
     }  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 ParseRecord  
   
 C<< my @fields = Tracer::ParseRecord($line); >>  
   
 Parse a tab-delimited data line. The data line is split into field values. Embedded tab  
 and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
 These will automatically be converted.  
   
 =over 4  
   
 =item line  
   
 Line of data containing the tab-delimited fields.  
   
 =item RETURN  
   
 Returns a list of the fields found in the data line.  
   
 =back  
   
 =cut  
   
 sub ParseRecord {  
     # Get the parameter.  
     my ($line) = @_;  
     # Remove the trailing new-line, if any.  
     chomp $line;  
     # Split the line read into pieces using the tab character.  
     my @retVal = split /\t/, $line;  
     # Trim and fix the escapes in each piece.  
     for my $value (@retVal) {  
         # Trim leading whitespace.  
         $value =~ s/^\s+//;  
         # Trim trailing whitespace.  
         $value =~ s/\s+$//;  
         # Delete the carriage returns.  
         $value =~ s/\r//g;  
         # Convert the escapes into their real values.  
         $value =~ s/\\t/"\t"/ge;  
         $value =~ s/\\n/"\n"/ge;  
     }  
     # Return the result.  
     return @retVal;  
 }  
   
 =head3 Merge  
   
 C<< my @mergedList = Tracer::Merge(@inputList); >>  
   
 Sort a list of strings and remove duplicates.  
   
 =over 4  
   
 =item inputList  
   
 List of scalars to sort and merge.  
   
 =item RETURN  
   
 Returns a list containing the same elements sorted in ascending order with duplicates  
 removed.  
   
 =back  
   
 =cut  
   
 sub Merge {  
     # Get the input list in sort order.  
     my @inputList = sort @_;  
     # Only proceed if the list has at least two elements.  
     if (@inputList > 1) {  
         # Now we want to move through the list splicing out duplicates.  
         my $i = 0;  
         while ($i < @inputList) {  
             # Get the current entry.  
             my $thisEntry = $inputList[$i];  
             # Find out how many elements duplicate the current entry.  
             my $j = $i + 1;  
             my $dup1 = $i + 1;  
             while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };  
             # If the number is nonzero, splice out the duplicates found.  
             if ($j > $dup1) {  
                 splice @inputList, $dup1, $j - $dup1;  
             }  
             # Now the element at position $dup1 is different from the element before it  
             # at position $i. We push $i forward one position and start again.  
             $i++;  
         }  
     }  
     # Return the merged list.  
     return @inputList;  
 }  
   
 =head3 Percent  
   
 C<< my $percent = Tracer::Percent($number, $base); >>  
   
 Returns the percent of the base represented by the given number. If the base  
 is zero, returns zero.  
   
 =over 4  
   
 =item number  
   
 Percent numerator.  
   
 =item base  
   
 Percent base.  
   
 =item RETURN  
   
 Returns the percentage of the base represented by the numerator.  
   
 =back  
   
 =cut  
1875    
1876  sub Percent {  =head2 File Utility Methods
     # Get the parameters.  
     my ($number, $base) = @_;  
     # Declare the return variable.  
     my $retVal = 0;  
     # Compute the percent.  
     if ($base != 0) {  
         $retVal = $number * 100 / $base;  
     }  
     # Return the result.  
     return $retVal;  
 }  
1877    
1878  =head3 GetFile  =head3 GetFile
1879    
1880  C<< my @fileContents = Tracer::GetFile($fileName); >>      my @fileContents = Tracer::GetFile($fileName);
1881    
1882      or      or
1883    
1884  C<< my $fileContents = Tracer::GetFile($fileName); >>      my $fileContents = Tracer::GetFile($fileName);
1885    
1886  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
1887  each line is a list element. In scalar context, line-ends are replaced by C<\n>.  each line is a list element. In scalar context, line-ends are replaced by C<\n>.
# Line 1661  Line 1931 
1931    
1932  =head3 PutFile  =head3 PutFile
1933    
1934  C<< Tracer::PutFile($fileName, \@lines); >>      Tracer::PutFile($fileName, \@lines);
1935    
1936  Write out a file from a list of lines of text.  Write out a file from a list of lines of text.
1937    
# Line 1704  Line 1974 
1974      close $handle;      close $handle;
1975  }  }
1976    
1977  =head3 QTrace  =head3 ParseRecord
1978    
1979        my @fields = Tracer::ParseRecord($line);
1980    
1981    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1982    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1983    These will automatically be converted.
1984    
1985  C<< my $data = QTrace($format); >>  =over 4
1986    
1987  Return the queued trace data in the specified format.  =item line
1988    
1989  =over 4  Line of data containing the tab-delimited fields.
1990    
1991  =item format  =item RETURN
1992    
1993  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Returns a list of the fields found in the data line.
1994    
1995  =back  =back
1996    
1997  =cut  =cut
1998    
1999  sub QTrace {  sub ParseRecord {
2000      # Get the parameter.      # Get the parameter.
2001      my ($format) = @_;      my ($line) = @_;
2002      # Create the return variable.      # Remove the trailing new-line, if any.
2003      my $retVal = "";      chomp $line;
2004      # Only proceed if there is an actual queue.      # Split the line read into pieces using the tab character.
2005      if (@Queue) {      my @retVal = split /\t/, $line;
2006          # Process according to the format.      # Trim and fix the escapes in each piece.
2007          if ($format =~ m/^HTML$/i) {      for my $value (@retVal) {
2008              # Convert the queue into an HTML list.          # Trim leading whitespace.
2009              $retVal = "<ul>\n";          $value =~ s/^\s+//;
2010              for my $line (@Queue) {          # Trim trailing whitespace.
2011                  my $escapedLine = CGI::escapeHTML($line);          $value =~ s/\s+$//;
2012                  $retVal .= "<li>$escapedLine</li>\n";          # Delete the carriage returns.
2013              }          $value =~ s/\r//g;
2014              $retVal .= "</ul>\n";          # Convert the escapes into their real values.
2015          } elsif ($format =~ m/^TEXT$/i) {          $value =~ s/\\t/"\t"/ge;
2016              # Convert the queue into a list of text lines.          $value =~ s/\\n/"\n"/ge;
             $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
2017      }      }
2018      # Return the formatted list.      # Return the result.
2019      return $retVal;      return @retVal;
2020  }  }
2021    
2022  =head3 Confess  =head3 Merge
2023    
2024  C<< Confess($message); >>      my @mergedList = Tracer::Merge(@inputList);
2025    
2026  Trace the call stack and abort the program with the specified message. When used with  Sort a list of strings and remove duplicates.
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
2027    
2028  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
2029    
2030  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item inputList
2031    
2032  =over 4  List of scalars to sort and merge.
2033    
2034  =item message  =item RETURN
2035    
2036  Message to include in the trace.  Returns a list containing the same elements sorted in ascending order with duplicates
2037    removed.
2038    
2039  =back  =back
2040    
2041  =cut  =cut
2042    
2043  sub Confess {  sub Merge {
2044      # Get the parameters.      # Get the input list in sort order.
2045      my ($message) = @_;      my @inputList = sort @_;
2046      # Trace the call stack.      # Only proceed if the list has at least two elements.
2047      Cluck($message);      if (@inputList > 1) {
2048      # Abort the program.          # Now we want to move through the list splicing out duplicates.
2049      croak(">>> $message");          my $i = 0;
2050            while ($i < @inputList) {
2051                # Get the current entry.
2052                my $thisEntry = $inputList[$i];
2053                # Find out how many elements duplicate the current entry.
2054                my $j = $i + 1;
2055                my $dup1 = $i + 1;
2056                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2057                # If the number is nonzero, splice out the duplicates found.
2058                if ($j > $dup1) {
2059                    splice @inputList, $dup1, $j - $dup1;
2060                }
2061                # Now the element at position $dup1 is different from the element before it
2062                # at position $i. We push $i forward one position and start again.
2063                $i++;
2064            }
2065        }
2066        # Return the merged list.
2067        return @inputList;
2068  }  }
2069    
2070  =head3 Assert  =head3 Open
   
 C<< Assert($condition1, $condition2, ... $conditionN); >>  
2071    
2072  Return TRUE if all the conditions are true. This method can be used in conjunction with      my $handle = Open($fileHandle, $fileSpec, $message);
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
2073    
2074  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  Open a file.
2075    
2076  Will abort the program with a stack trace if the value of C<$recNum> is negative.  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2077    function. The mode is specified using Unix-like shell information. So, for
2078    example,
2079    
2080  =cut      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
2081    
2082  =head3 Cluck  would open for output appended to the specified file, and
2083    
2084  C<< Cluck($message); >>      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2085    
2086  Trace the call stack. Note that for best results, you should qualify the call with a  would open a pipe that sorts the records written and removes duplicates. Note
2087  trace condition. For example,  the use of file handle syntax in the Open call. To use anonymous file handles,
2088    code as follows.
2089    
2090  C<< Cluck("Starting record parse.") if T(3); >>      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2091    
2092  will only trace the stack if the trace level for the package is 3 or more.  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2093    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2094    failed open will throw an exception and the third parameter will be used to construct
2095    an error message. If the parameter is omitted, a standard message is constructed
2096    using the file spec.
2097    
2098  =over 4      Could not open "/usr/spool/news/twitlog"
2099    
2100  =item message  Note that the mode characters are automatically cleaned from the file name.
2101    The actual error message from the file system will be captured and appended to the
2102    message in any case.
2103    
2104  Message to include in the trace.      Could not open "/usr/spool/news/twitlog": file not found.
2105    
2106  =back  In some versions of PERL the only error message we get is a number, which
2107    corresponds to the C++ C<errno> value.
2108    
2109  =cut      Could not open "/usr/spool/news/twitlog": 6.
2110    
2111  sub Cluck {  =over 4
     # Get the parameters.  
     my ($message) = @_;  
     # Trace what's happening.  
     Trace("Stack trace for event: $message");  
     my $confession = longmess($message);  
     # Convert the confession to a series of trace messages. Note we skip any  
     # messages relating to calls into Tracer.  
     for my $line (split /\s*\n/, $confession) {  
         Trace($line) if ($line !~ /Tracer\.pm/);  
     }  
 }  
2112    
2113  =head3 Min  =item fileHandle
2114    
2115  C<< my $min = Min($value1, $value2, ... $valueN); >>  File handle. If this parameter is C<undef>, a file handle will be generated
2116    and returned as the value of this method.
2117    
2118  Return the minimum argument. The arguments are treated as numbers.  =item fileSpec
2119    
2120  =over 4  File name and mode, as per the PERL C<open> function.
2121    
2122  =item $value1, $value2, ... $valueN  =item message (optional)
2123    
2124  List of numbers to compare.  Error message to use if the open fails. If omitted, a standard error message
2125    will be generated. In either case, the error information from the file system
2126    is appended to the message. To specify a conditional open that does not throw
2127    an error if it fails, use C<0>.
2128    
2129  =item RETURN  =item RETURN
2130    
2131  Returns the lowest number in the list.  Returns the name of the file handle assigned to the file, or C<undef> if the
2132    open failed.
2133    
2134  =back  =back
2135    
2136  =cut  =cut
2137    
2138  sub Min {  sub Open {
2139      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2140      my ($retVal, @values) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2141      # Loop through the remaining parameters, looking for the lowest.      # Attempt to open the file.
2142      for my $value (@values) {      my $rv = open $fileHandle, $fileSpec;
2143          if ($value < $retVal) {      # If the open failed, generate an error message.
2144              $retVal = $value;      if (! $rv) {
2145            # Save the system error message.
2146            my $sysMessage = $!;
2147            # See if we need a default message.
2148            if (!$message) {
2149                # Clean any obvious mode characters and leading spaces from the
2150                # filename.
2151                my ($fileName) = FindNamePart($fileSpec);
2152                $message = "Could not open \"$fileName\"";
2153          }          }
2154            # Terminate with an error using the supplied message and the
2155            # error message from the file system.
2156            Confess("$message: $!");
2157      }      }
2158      # Return the minimum found.      # Return the file handle.
2159      return $retVal;      return $fileHandle;
2160  }  }
2161    
2162  =head3 Max  =head3 FindNamePart
2163    
2164  C<< my $max = Max($value1, $value2, ... $valueN); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2165    
2166  Return the maximum argument. The arguments are treated as numbers.  Extract the portion of a file specification that contains the file name.
2167    
2168    A file specification is the string passed to an C<open> call. It specifies the file
2169    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2170    method assumes that the file name is whatever follows the first angle bracket
2171    sequence.  So, for example, in the following strings the file name is
2172    C</usr/fig/myfile.txt>.
2173    
2174        >>/usr/fig/myfile.txt
2175        </usr/fig/myfile.txt
2176        | sort -u > /usr/fig/myfile.txt
2177    
2178    If the method cannot find a file name using its normal methods, it will return the
2179    whole incoming string.
2180    
2181  =over 4  =over 4
2182    
2183  =item $value1, $value2, ... $valueN  =item fileSpec
2184    
2185    File specification string from which the file name is to be extracted.
2186    
2187    =item RETURN
2188    
2189    Returns a three-element list. The first element contains the file name portion of
2190    the specified string, or the whole string if a file name cannot be found via normal
2191    methods. The second element contains the start position of the file name portion and
2192    the third element contains the length.
2193    
2194    =back
2195    
2196    =cut
2197    #: Return Type $;
2198    sub FindNamePart {
2199        # Get the parameters.
2200        my ($fileSpec) = @_;
2201        # Default to the whole input string.
2202        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2203        # Parse out the file name if we can.
2204        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2205            $retVal = $2;
2206            $len = length $retVal;
2207            $pos = (length $fileSpec) - (length $3) - $len;
2208        }
2209        # Return the result.
2210        return ($retVal, $pos, $len);
2211    }
2212    
2213  List of numbers to compare.  =head3 OpenDir
2214    
2215  =item RETURN      my @files = OpenDir($dirName, $filtered, $flag);
2216    
2217  Returns the highest number in the list.  Open a directory and return all the file names. This function essentially performs
2218    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2219    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2220    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2221    filtered out of the return list. If the directory does not open and I<$flag> is not
2222    set, an exception is thrown. So, for example,
2223    
2224  =back      my @files = OpenDir("/Volumes/fig/contigs", 1);
2225    
2226  =cut  is effectively the same as
2227    
2228  sub Max {      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2229      # Get the parameters. Note that we prime the return value with the first parameter.      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
     my ($retVal, @values) = @_;  
     # Loop through the remaining parameters, looking for the highest.  
     for my $value (@values) {  
         if ($value > $retVal) {  
             $retVal = $value;  
         }  
     }  
     # Return the maximum found.  
     return $retVal;  
 }  
2230    
2231  =head3 AddToListMap  Similarly, the following code
2232    
2233  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2234    
2235  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2236  is created for the key. Otherwise, the new value is pushed onto the list.  automatically returns an empty list if the directory fails to open.
2237    
2238  =over 4  =over 4
2239    
2240  =item hash  =item dirName
2241    
2242  Reference to the target hash.  Name of the directory to open.
2243    
2244  =item key  =item filtered
2245    
2246  Key for which the value is to be added.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2247    from the list, else FALSE.
2248    
2249  =item value1, value2, ... valueN  =item flag
2250    
2251  List of values to add to the key's value list.  TRUE if a failure to open is okay, else FALSE
2252    
2253  =back  =back
2254    
2255  =cut  =cut
2256    #: Return Type @;
2257  sub AddToListMap {  sub OpenDir {
2258      # Get the parameters.      # Get the parameters.
2259      my ($hash, $key, @values) = @_;      my ($dirName, $filtered, $flag) = @_;
     # Process according to whether or not the key already has a value.  
     if (! exists $hash->{$key}) {  
         $hash->{$key} = [@values];  
     } else {  
         push @{$hash->{$key}}, @values;  
     }  
 }  
   
 =head3 DebugMode  
   
 C<< if (Tracer::DebugMode) { ...code... } >>  
   
 Return TRUE if debug mode has been turned on, else abort.  
   
 Certain CGI scripts are too dangerous to exist in the production  
 environment. This method provides a simple way to prevent them  
 from working unless they are explicitly turned on by creating a password  
 cookie via the B<SetPassword> script.  If debugging mode  
 is not turned on, an error will occur.  
   
 =cut  
   
 sub DebugMode {  
2260      # Declare the return variable.      # Declare the return variable.
2261      my $retVal = 0;      my @retVal = ();
2262      # Check the debug configuration.      # Open the directory.
2263      my $password = CGI::cookie("DebugMode");      if (opendir(my $dirHandle, $dirName)) {
2264      my $encrypted = Digest::MD5::md5_hex($password);          # The directory opened successfully. Get the appropriate list according to the
2265      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {          # strictures of the filter parameter.
2266          $retVal = 1;          if ($filtered) {
2267                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2268      } else {      } else {
2269          # Here debug mode is off, so we generate an error.              @retVal = readdir $dirHandle;
         Confess("Cannot use this facility without logging in.");  
2270      }      }
2271      # Return the determination indicator.      } elsif (! $flag) {
2272      return $retVal;          # Here the directory would not open and it's considered an error.
2273            Confess("Could not open directory $dirName.");
2274        }
2275        # Return the result.
2276        return @retVal;
2277  }  }
2278    
 =head3 Strip  
2279    
2280  C<< my $string = Tracer::Strip($line); >>  =head3 Insure
2281    
2282        Insure($dirName, $chmod);
2283    
2284  Strip all line terminators off a string. This is necessary when dealing with files  Insure a directory is present.
 that may have been transferred back and forth several times among different  
 operating environments.  
2285    
2286  =over 4  =over 4
2287    
2288  =item line  =item dirName
2289    
2290  Line of text to be stripped.  Name of the directory to check. If it does not exist, it will be created.
2291    
2292  =item RETURN  =item chmod (optional)
2293    
2294  The same line of text with all the line-ending characters chopped from the end.  Security privileges to be given to the directory if it is created.
2295    
2296  =back  =back
2297    
2298  =cut  =cut
2299    
2300  sub Strip {  sub Insure {
2301      # Get a copy of the parameter string.      my ($dirName, $chmod) = @_;
2302      my ($string) = @_;      if (! -d $dirName) {
2303      my $retVal = (defined $string ? $string : "");          Trace("Creating $dirName directory.") if T(2);
2304      # Strip the line terminator characters.          eval {
2305      $retVal =~ s/(\r|\n)+$//g;              mkpath $dirName;
2306      # Return the result.              # If we have permissions specified, set them here.
2307      return $retVal;              if (defined($chmod)) {
2308                    chmod $chmod, $dirName;
2309                }
2310            };
2311            if ($@) {
2312                Confess("Error creating $dirName: $@");
2313            }
2314        }
2315  }  }
2316    
2317  =head3 Pad  =head3 ChDir
2318    
2319  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      ChDir($dirName);
2320    
2321  Pad a string to a specified length. The pad character will be a  Change to the specified directory.
 space, and the padding will be on the right side unless specified  
 in the third parameter.  
2322    
2323  =over 4  =over 4
2324    
2325  =item string  =item dirName
   
 String to be padded.  
   
 =item len  
   
 Desired length of the padded string.  
   
 =item left (optional)  
   
 TRUE if the string is to be left-padded; otherwise it will be padded on the right.  
   
 =item padChar (optional)  
   
 Character to use for padding. The default is a space.  
   
 =item RETURN  
2326    
2327  Returns a copy of the original string with the pad character added to the  Name of the directory to which we want to change.
 specified end so that it achieves the desired length.  
2328    
2329  =back  =back
2330    
2331  =cut  =cut
2332    
2333  sub Pad {  sub ChDir {
2334      # Get the parameters.      my ($dirName) = @_;
2335      my ($string, $len, $left, $padChar) = @_;      if (! -d $dirName) {
2336      # Compute the padding character.          Confess("Cannot change to directory $dirName: no such directory.");
     if (! defined $padChar) {  
         $padChar = " ";  
     }  
     # Compute the number of spaces needed.  
     my $needed = $len - length $string;  
     # Copy the string into the return variable.  
     my $retVal = $string;  
     # Only proceed if padding is needed.  
     if ($needed > 0) {  
         # Create the pad string.  
         my $pad = $padChar x $needed;  
         # Affix it to the return value.  
         if ($left) {  
             $retVal = $pad . $retVal;  
2337          } else {          } else {
2338              $retVal .= $pad;          Trace("Changing to directory $dirName.") if T(File => 4);
2339            my $okFlag = chdir $dirName;
2340            if (! $okFlag) {
2341                Confess("Error switching to directory $dirName.");
2342          }          }
2343      }      }
     # Return the result.  
     return $retVal;  
2344  }  }
2345    
2346  =head3 EOF  =head3 SetPermissions
2347    
2348  This is a constant that is lexically greater than any useful string.      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2349    
2350  =cut  Set the permissions for a directory and all the files and folders inside it.
2351    In addition, the group ownership will be changed to the specified value.
2352    
2353  sub EOF {  This method is more vulnerable than most to permission and compatability
2354      return "\xFF\xFF\xFF\xFF\xFF";  problems, so it does internal error recovery.
 }  
2355    
2356  =head3 TICK  =over 4
2357    
2358  C<< my @results = TICK($commandString); >>  =item dirName
2359    
2360  Perform a back-tick operation on a command. If this is a Windows environment, any leading  Name of the directory to process.
 dot-slash (C<./> will be removed. So, for example, if you were doing  
2361    
2362      `./protein.cgi`  =item group
2363    
2364  from inside a CGI script, it would work fine in Unix, but would issue an error message  Name of the group to be assigned.
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
2365    
2366      TICK("./protein.cgi")  =item mask
2367    
2368  it will work correctly in both environments.  Permission mask. Bits that are C<1> in this mask will be ORed into the
2369    permission bits of any file or directory that does not already have them
2370    set to 1.
2371    
2372  =over 4  =item otherMasks
2373    
2374  =item commandString  Map of search patterns to permission masks. If a directory name matches
2375    one of the patterns, that directory and all its members and subdirectories
2376    will be assigned the new pattern. For example, the following would
2377    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2378    
2379  The command string to pass to the system.      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2380    
2381  =item RETURN  The list is ordered, so the following would use 0777 for C<tmp1> and
2382    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2383    
2384  Returns the standard output from the specified command, as a list.      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2385                                                       '^tmp' => 0666);
2386    
2387    Note that the pattern matches are all case-insensitive, and only directory
2388    names are matched, not file names.
2389    
2390  =back  =back
2391    
2392  =cut  =cut
2393  #: Return Type @;  
2394  sub TICK {  sub SetPermissions {
2395      # Get the parameters.      # Get the parameters.
2396      my ($commandString) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2397      # Chop off the dot-slash if this is Windows.      # Set up for error recovery.
2398      if ($FIG_Config::win_mode) {      eval {
2399          $commandString =~ s!^\./!!;          # Switch to the specified directory.
2400            ChDir($dirName);
2401            # Get the group ID.
2402            my $gid = getgrnam($group);
2403            # Get the mask for tracing.
2404            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2405            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2406            my $fixCount = 0;
2407            my $lookCount = 0;
2408            # @dirs will be a stack of directories to be processed.
2409            my @dirs = (getcwd());
2410            while (scalar(@dirs) > 0) {
2411                # Get the current directory.
2412                my $dir = pop @dirs;
2413                # Check for a match to one of the specified directory names. To do
2414                # that, we need to pull the individual part of the name off of the
2415                # whole path.
2416                my $simpleName = $dir;
2417                if ($dir =~ m!/([^/]+)$!) {
2418                    $simpleName = $1;
2419                }
2420                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2421                # Search for a match.
2422                my $match = 0;
2423                my $i;
2424                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2425                    my $pattern = $otherMasks[$i];
2426                    if ($simpleName =~ /$pattern/i) {
2427                        $match = 1;
2428                    }
2429                }
2430                # Check for a match. Note we use $i-1 because the loop added 2
2431                # before terminating due to the match.
2432                if ($match && $otherMasks[$i-1] != $mask) {
2433                    # This directory matches one of the incoming patterns, and it's
2434                    # a different mask, so we process it recursively with that mask.
2435                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2436                } else {
2437                    # Here we can process normally. Get all of the non-hidden members.
2438                    my @submems = OpenDir($dir, 1);
2439                    for my $submem (@submems) {
2440                        # Get the full name.
2441                        my $thisMem = "$dir/$submem";
2442                        Trace("Checking member $thisMem.") if T(4);
2443                        $lookCount++;
2444                        if ($lookCount % 1000 == 0) {
2445                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2446                        }
2447                        # Fix the group.
2448                        chown -1, $gid, $thisMem;
2449                        # Insure this member is not a symlink.
2450                        if (! -l $thisMem) {
2451                            # Get its info.
2452                            my $fileInfo = stat $thisMem;
2453                            # Only proceed if we got the info. Otherwise, it's a hard link
2454                            # and we want to skip it anyway.
2455                            if ($fileInfo) {
2456                                my $fileMode = $fileInfo->mode;
2457                                if (($fileMode & $mask) != $mask) {
2458                                    # Fix this member.
2459                                    $fileMode |= $mask;
2460                                    chmod $fileMode, $thisMem;
2461                                    $fixCount++;
2462                                }
2463                                # If it's a subdirectory, stack it.
2464                                if (-d $thisMem) {
2465                                    push @dirs, $thisMem;
2466                                }
2467                            }
2468                        }
2469                    }
2470                }
2471            }
2472            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2473        };
2474        # Check for an error.
2475        if ($@) {
2476            Confess("SetPermissions error: $@");
2477      }      }
     # Activate the command and return the result.  
     return `$commandString`;  
2478  }  }
2479    
2480  =head3 ScriptSetup  =head3 GetLine
   
 C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  
2481    
2482  Perform standard tracing and debugging setup for scripts. The value returned is      my @data = Tracer::GetLine($handle);
 the CGI object followed by a pre-built variable hash. At the end of the script,  
 the client should call L</ScriptFinish> to output the web page.  
2483    
2484  This method calls L</ETracing> to configure tracing, which allows the tracing  Read a line of data from a tab-delimited file.
 to be configured via the emergency tracing form on the debugging control panel.  
 Tracing will then be turned on automatically for all programs that use the L</ETracing>  
 method, which includes every program that uses this method or L</StandardSetup>.  
2485    
2486  =over 4  =over 4
2487    
2488  =item noTrace (optional)  =item handle
2489    
2490  If specified, tracing will be suppressed. This is useful if the script wants to set up  Open file handle from which to read.
 tracing manually.  
2491    
2492  =item RETURN  =item RETURN
2493    
2494  Returns a two-element list consisting of a CGI query object and a variable hash for  Returns a list of the fields in the record read. The fields are presumed to be
2495  the output page.  tab-delimited. If we are at the end of the file, then an empty list will be
2496    returned. If an empty line is read, a single list item consisting of a null
2497    string will be returned.
2498    
2499  =back  =back
2500    
2501  =cut  =cut
2502    
2503  sub ScriptSetup {  sub GetLine {
2504      # Get the parameters.      # Get the parameters.
2505      my ($noTrace) = @_;      my ($handle) = @_;
2506      # Get the CGI query object.      # Declare the return variable.
2507      my $cgi = CGI->new();      my @retVal = ();
2508      # Set up tracing if it's not suppressed.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2509      ETracing($cgi) unless $noTrace;      # Read from the file.
2510      # Create the variable hash.      my $line = <$handle>;
2511      my $varHash = { results => '' };      # Only proceed if we found something.
2512      # Return the query object and variable hash.      if (defined $line) {
2513      return ($cgi, $varHash);          # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2514            # upload control and have a nonstandard EOL combination.
2515            $line =~ s/(\r|\n)+$//;
2516            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2517            if (T(File => 4)) {
2518                my $escapedLine = $line;
2519                $escapedLine =~ s/\n/\\n/g;
2520                $escapedLine =~ s/\r/\\r/g;
2521                $escapedLine =~ s/\t/\\t/g;
2522                Trace("Line read: -->$escapedLine<--");
2523  }  }
2524            # If the line is empty, return a single empty string; otherwise, parse
2525  =head3 ETracing          # it into fields.
2526            if ($line eq "") {
2527  C<< ETracing($parameter); >>              push @retVal, "";
   
 Set up emergency tracing. Emergency tracing is tracing that is turned  
 on automatically for any program that calls this method. The emergency  
 tracing parameters are stored in a a file identified by a tracing key.  
 If this method is called with a CGI object, then the tracing key is  
 taken from a cookie. If it is called with no parameters, then the tracing  
 key is taken from an environment variable. If it is called with a string,  
 the tracing key is that string.  
   
 =over 4  
   
 =item parameter  
   
 A parameter from which the tracing key is computed. If it is a scalar,  
 that scalar is used as the tracing key. If it is a CGI object, the  
 tracing key is taken from the C<IP> cookie. If it is omitted, the  
 tracing key is taken from the C<TRACING> environment variable. If it  
 is a CGI object and emergency tracing is not on, the C<Trace> and  
 C<TF> parameters will be used to determine the type of tracing.  
   
 =back  
   
 =cut  
   
 sub ETracing {  
     # Get the parameter.  
     my ($parameter) = @_;  
     # Check for CGI mode.  
     my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);  
     # Default to no tracing except errors.  
     my ($tracing, $dest) = ("0", "WARN");  
     # Check for emergency tracing.  
     my $tkey = EmergencyKey($parameter);  
     my $emergencyFile = EmergencyFileName($tkey);  
     if (-e $emergencyFile) {  
         # We have the file. Read in the data.  
         my @tracing = GetFile($emergencyFile);  
         # Pull off the time limit.  
         my $expire = shift @tracing;  
         # Convert it to seconds.  
         $expire *= 3600;  
         # Check the file data.  
         my $stat = stat($emergencyFile);  
         my ($now) = gettimeofday;  
         if ($now - $stat->mtime > $expire) {  
             # Delete the expired file.  
             unlink $emergencyFile;  
2528          } else {          } else {
2529              # Emergency tracing is on. Pull off the destination and              push @retVal, split /\t/,$line;
             # the trace level;  
             $dest = shift @tracing;  
             my $level = shift @tracing;  
             # Convert the destination to a real tracing destination.  
             # temp directory.  
             $dest = EmergencyTracingDest($tkey, $dest);  
             # Insure Tracer is specified.  
             my %moduleHash = map { $_ => 1 } @tracing;  
             $moduleHash{Tracer} = 1;  
             # Set the trace parameter.  
             $tracing = join(" ", $level, sort keys %moduleHash);  
         }  
     } elsif (defined $cgi) {  
         # There's no emergency tracing, but we have a CGI object, so check  
         # for tracing from the form parameters.  
         if ($cgi->param('Trace')) {  
             # Here the user has requested tracing via a form.  
             $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");  
             $tracing = $cgi->param('Trace') . " Tracer";  
         }  
2530      }      }
2531      # Setup the tracing we've determined from all the stuff above.      } else {
2532      TSetup($tracing, $dest);          # Trace the reason the read failed.
2533      # 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);  
2534      }      }
2535        # Return the result.
2536        return @retVal;
2537  }  }
2538    
2539  =head3 EmergencyFileName  =head3 PutLine
2540    
2541  C<< my $fileName = Tracer::EmergencyFileName($tkey); >>      Tracer::PutLine($handle, \@fields, $eol);
2542    
2543  Return the emergency tracing file name. This is the file that specifies  Write a line of data to a tab-delimited file. The specified field values will be
2544  the tracing information.  output in tab-separated form, with a trailing new-line.
2545    
2546  =over 4  =over 4
2547    
2548  =item tkey  =item handle
2549    
2550  Tracing key for the current program.  Output file handle.
2551    
2552  =item RETURN  =item fields
2553    
2554  Returns the name of the file to contain the emergency tracing information.  List of field values.
2555    
2556    =item eol (optional)
2557    
2558    End-of-line character (default is "\n").
2559    
2560  =back  =back
2561    
2562  =cut  =cut
2563    
2564  sub EmergencyFileName {  sub PutLine {
2565      # Get the parameters.      # Get the parameters.
2566      my ($tkey) = @_;      my ($handle, $fields, $eol) = @_;
2567      # Compute the emergency tracing file name.      # Write the data.
2568      return "$FIG_Config::temp/Emergency$tkey.txt";      print $handle join("\t", @{$fields}) . ($eol || "\n");
2569  }  }
2570    
 =head3 EmergencyFileTarget  
   
 C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>  
2571    
2572  Return the emergency tracing target file name. This is the file that receives  =head3 PrintLine
 the tracing output for file-based tracing.  
2573    
2574  =over 4      Tracer::PrintLine($line);
2575    
2576  =item tkey  Print a line of text with a trailing new-line.
2577    
2578  Tracing key for the current program.  =over 4
2579    
2580  =item RETURN  =item line
2581    
2582  Returns the name of the file to contain the trace output.  Line of text to print.
2583    
2584  =back  =back
2585    
2586  =cut  =cut
2587    
2588  sub EmergencyFileTarget {  sub PrintLine {
2589      # Get the parameters.      # Get the parameters.
2590      my ($tkey) = @_;      my ($line) = @_;
2591      # Compute the emergency tracing file name.      # Print the line.
2592      return "$FIG_Config::temp/trace$tkey.log";      print "$line\n";
2593  }  }
2594    
 =head3 EmergencyTracingDest  
2595    
2596  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>  =head2 Other Useful Methods
2597    
2598  This method converts an emergency tracing destination to a real  =head3 ParseParm
 tracing destination. The main difference is that if the  
 destination is C<FILE> or C<APPEND>, we convert it to file  
 output. If the destination is C<DUAL>, we convert it to file  
 and standard output.  
2599    
2600  =over 4      my $listValue = Tracer::ParseParm($string);
2601    
2602  =item tkey  Convert a parameter into a list reference. If the parameter is undefined,
2603    an undefined value will be returned. Otherwise, it will be parsed as a
2604    comma-separated list of values.
2605    
2606  Tracing key for this environment.  =over 4
2607    
2608  =item myDest  =item string
2609    
2610  Destination from the emergency tracing file.  Incoming string.
2611    
2612  =item RETURN  =item RETURN
2613    
2614  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
2615    was undefined.
2616    
2617  =back  =back
2618    
2619  =cut  =cut
2620    
2621  sub EmergencyTracingDest {  sub ParseParm {
2622      # Get the parameters.      # Get the parameters.
2623      my ($tkey, $myDest) = @_;      my ($string) = @_;
2624      # Declare the return variable.      # Declare the return variable.
2625      my $retVal = $myDest;      my $retVal;
2626      # Process according to the destination value.      # Check for data.
2627      if ($myDest eq 'FILE') {      if (defined $string) {
2628          $retVal = ">" . EmergencyFileTarget($tkey);          # We have some, so split it into a list.
2629      } elsif ($myDest eq 'APPEND') {          $retVal = [ split /\s*,\s*/, $string];
2630          $retVal = ">>" . EmergencyFileTarget($tkey);      }
2631      } elsif ($myDest eq 'DUAL') {      # Return the result.
2632          $retVal = "+>" . EmergencyFileTarget($tkey);      return $retVal;
     }  
     # Return the result.  
     return $retVal;  
2633  }  }
2634    
2635  =head3 Emergency  =head3 Now
   
 C<< Emergency($key, $hours, $dest, $level, @modules); >>  
   
 Turn on emergency tracing. This method is normally invoked over the web from  
 a debugging console, but it can also be called by the C<trace.pl> script.  
 The caller specifies the duration of the emergency in hours, the desired tracing  
 destination, the trace level, and a list of the trace modules to activate.  
 For the length of the duration, when a program in an environment with the  
 specified tracing key active invokes a Sprout CGI script, tracing will be  
 turned on automatically. See L</TSetup> for more about tracing setup and  
 L</ETracing> for more about emergency tracing.  
   
 =over 4  
2636    
2637  =item tkey      my $string = Tracer::Now();
2638    
2639  The tracing key. This is used to identify the control file and the trace file.  Return a displayable time stamp containing the local time. Whatever format this
2640    method produces must be parseable by L</ParseDate>.
2641    
2642  =item hours  =cut
2643    
2644  Number of hours to keep emergency tracing alive.  sub Now {
2645        return DisplayTime(time);
2646    }
2647    
2648  =item dest  =head3 DisplayTime
2649    
2650  Tracing destination. If no path information is specified for a file      my $string = Tracer::DisplayTime($time);
 destination, it is put in the FIG temporary directory.  
2651    
2652  =item level  Convert a time value to a displayable time stamp. Whatever format this
2653    method produces must be parseable by L</ParseDate>.
2654    
2655  Tracing level. A higher level means more trace messages.  =over 4
2656    
2657  =item modules  =item time
2658    
2659  A list of the tracing modules to activate.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2660    
2661    =item RETURN
2662    
2663    Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2664    
2665  =back  =back
2666    
2667  =cut  =cut
2668    
2669  sub Emergency {  sub DisplayTime {
2670      # Get the parameters.      my ($time) = @_;
2671      my ($tkey, $hours, $dest, $level, @modules) = @_;      my $retVal = "(n/a)";
2672      # Create the emergency file.      if (defined $time) {
2673      my $specFile = EmergencyFileName($tkey);          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2674      my $outHandle = Open(undef, ">$specFile");          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2675      print $outHandle join("\n", $hours, $dest, $level, @modules, "");                    _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2676        }
2677        return $retVal;
2678  }  }
2679    
2680  =head3 EmergencyKey  # Pad a number to 2 digits.
2681    sub _p2 {
2682        my ($value) = @_;
2683        $value = "0$value" if ($value < 10);
2684        return $value;
2685    }
2686    
2687  C<< my $tkey = EmergencyKey($parameter); >>  =head3 Escape
2688    
2689  Return the Key to be used for emergency tracing. This could be an IP address,      my $codedString = Tracer::Escape($realString);
2690   a session ID, or a user name, depending on the environment.  
2691    Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2692    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2693    result is to reverse the effect of L</UnEscape>.
2694    
2695  =over 4  =over 4
2696    
2697  =item parameter  =item realString
2698    
2699  Parameter defining the method for finding the tracing key. If it is a scalar,  String to escape.
 then it is presumed to be the tracing key itself. If it is a CGI object, then  
 the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is  
 taken from the C<TRACING> environment variable.  
2700    
2701  =item RETURN  =item RETURN
2702    
2703  Returns the key to be used for labels in emergency tracing.  Escaped equivalent of the real string.
2704    
2705  =back  =back
2706    
2707  =cut  =cut
2708    
2709  sub EmergencyKey {  sub Escape {
2710      # Get the parameters.      # Get the parameter.
2711      my ($parameter) = @_;      my ($realString) = @_;
2712      # Declare the return variable.      # Initialize the return variable.
2713      my $retVal;      my $retVal = "";
2714      # Determine the parameter type.      # Loop through the parameter string, looking for sequences to escape.
2715      if (! defined $parameter) {      while (length $realString > 0) {
2716          # Here we're supposed to check the environment.          # Look for the first sequence to escape.
2717          $retVal = $ENV{TRACING};          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2718      } else {              # Here we found it. The text preceding the sequence is in $1. The sequence
2719          my $ptype = ref $parameter;              # itself is in $2. First, move the clear text to the return variable.
2720          if ($ptype eq 'CGI') {              $retVal .= $1;
2721              # Here we were invoked from a web page. Look for a cookie.              # Strip the processed section off the real string.
2722              $retVal = $parameter->cookie('IP');              $realString = substr $realString, (length $2) + (length $1);
2723          } elsif (! $ptype) {              # Get the matched character.
2724              # Here the key was passed in.              my $char = $2;
2725              $retVal = $parameter;              # If we have a CR, we are done.
2726                if ($char ne "\r") {
2727                    # It's not a CR, so encode the escape sequence.
2728                    $char =~ tr/\t\n/tn/;
2729                    $retVal .= "\\" . $char;
2730          }          }
2731            } else {
2732                # Here there are no more escape sequences. The rest of the string is
2733                # transferred unmodified.
2734                $retVal .= $realString;
2735                $realString = "";
2736      }      }
     # If no luck finding a key, use the PID.  
     if (! defined $retVal) {  
         $retVal = $$;  
2737      }      }
2738      # Return the result.      # Return the result.
2739      return $retVal;      return $retVal;
2740  }  }
2741    
2742    =head3 UnEscape
2743    
2744  =head3 TraceParms      my $realString = Tracer::UnEscape($codedString);
   
 C<< Tracer::TraceParms($cgi); >>  
2745    
2746  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2747  at level CGI => 4.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2748    be deleted.
2749    
2750  =over 4  =over 4
2751    
2752  =item cgi  =item codedString
2753    
2754  CGI query object containing the parameters to trace.  String to un-escape.
2755    
2756    =item RETURN
2757    
2758    Returns a copy of the original string with the escape sequences converted to their actual
2759    values.
2760    
2761  =back  =back
2762    
2763  =cut  =cut
2764    
2765  sub TraceParms {  sub UnEscape {
2766      # Get the parameters.      # Get the parameter.
2767      my ($cgi) = @_;      my ($codedString) = @_;
2768      if (T(CGI => 3)) {      # Initialize the return variable.
2769          # Here we want to trace the parameter data.      my $retVal = "";
2770          my @names = $cgi->param;      # Only proceed if the incoming string is nonempty.
2771          for my $parmName (sort @names) {      if (defined $codedString) {
2772              # Note we skip the Trace parameters, which are for our use only.          # Loop through the parameter string, looking for escape sequences. We can't do
2773              if ($parmName ne 'Trace' && $parmName ne 'TF') {          # translating because it causes problems with the escaped slash. ("\\t" becomes
2774                  my @values = $cgi->param($parmName);          # "\<tab>" no matter what we do.)
2775                  Trace("CGI: $parmName = " . join(", ", @values));          while (length $codedString > 0) {
2776              }              # Look for the first escape sequence.
2777                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2778                    # Here we found it. The text preceding the sequence is in $1. The sequence
2779                    # itself is in $2. First, move the clear text to the return variable.
2780                    $retVal .= $1;
2781                    $codedString = substr $codedString, (2 + length $1);
2782                    # Get the escape value.
2783                    my $char = $2;
2784                    # If we have a "\r", we are done.
2785                    if ($char ne 'r') {
2786                        # Here it's not an 'r', so we convert it.
2787                        $char =~ tr/\\tn/\\\t\n/;
2788                        $retVal .= $char;
2789          }          }
2790          # Display the request method.              } else {
2791          my $method = $cgi->request_method();                  # Here there are no more escape sequences. The rest of the string is
2792          Trace("Method: $method");                  # transferred unmodified.
2793                    $retVal .= $codedString;
2794                    $codedString = "";
2795      }      }
     if (T(CGI => 4)) {  
         # Here we want the environment data too.  
         for my $envName (sort keys %ENV) {  
             Trace("ENV: $envName = $ENV{$envName}");  
2796          }          }
2797      }      }
2798        # Return the result.
2799        return $retVal;
2800  }  }
2801    
2802  =head3 ScriptFinish  =head3 Percent
   
 C<< ScriptFinish($webData, $varHash); >>  
   
 Output a web page at the end of a script. Either the string to be output or the  
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
2803    
2804  A typical standard script would loook like the following.      my $percent = Tracer::Percent($number, $base);
2805    
2806      BEGIN {  Returns the percent of the base represented by the given number. If the base
2807          # Print the HTML header.  is zero, returns zero.
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
2808    
2809      my ($cgi, $varHash) = ScriptSetup();  =over 4
     eval {  
         # ... get data from $cgi, put it in $varHash ...  
     };  
     if ($@) {  
         Trace("Script Error: $@") if T(0);  
     }  
     ScriptFinish("Html/MyTemplate.html", $varHash);  
2810    
2811  The idea here is that even if the script fails, you'll see trace messages and  =item number
 useful output.  
2812    
2813  =over 4  Percent numerator.
2814    
2815  =item webData  =item base
2816    
2817  A string containing either the full web page to be written to the output or the  Percent base.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
2818    
2819  =item varHash (optional)  =item RETURN
2820    
2821  If specified, then a reference to a hash mapping variable names for a template  Returns the percentage of the base represented by the numerator.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
2822    
2823  =back  =back
2824    
2825  =cut  =cut
2826    
2827  sub ScriptFinish {  sub Percent {
2828      # Get the parameters.      # Get the parameters.
2829      my ($webData, $varHash) = @_;      my ($number, $base) = @_;
2830      # Check for a template file situation.      # Declare the return variable.
2831      my $outputString;      my $retVal = 0;
2832      if (defined $varHash) {      # Compute the percent.
2833          # Here we have a template file. We need to determine the template type.      if ($base != 0) {
2834          my $template;          $retVal = $number * 100 / $base;
         if ($FIG_Config::template_url && $webData =~ /\.php$/) {  
             $template = "$FIG_Config::template_url/$webData";  
         } else {  
             $template = "<<$webData";  
         }  
         $outputString = PageBuilder::Build($template, $varHash, "Html");  
     } else {  
         # Here the user gave us a raw string.  
         $outputString = $webData;  
     }  
     # Check for trace messages.  
     if ($Destination ne "NONE" && $TraceLevel > 0) {  
         # We have trace messages, so we want to put them at the end of the body. This  
         # is either at the end of the whole string or at the beginning of the BODY  
         # end-tag.  
         my $pos = length $outputString;  
         if ($outputString =~ m#</body>#gi) {  
             $pos = (pos $outputString) - 7;  
         }  
         # If the trace messages were queued, we unroll them. Otherwise, we display the  
         # destination.  
         my $traceHtml;  
         if ($Destination eq "QUEUE") {  
             $traceHtml = QTrace('Html');  
         } elsif ($Destination =~ /^>>(.+)$/) {  
             # Here the tracing output it to a file. We code it as a hyperlink so the user  
             # can copy the file name into the clipboard easily.  
             my $actualDest = $1;  
             $traceHtml = "<p>Tracing output to $actualDest.</p>\n";  
         } else {  
             # Here we have one of the special destinations.  
             $traceHtml = "<P>Tracing output type is $Destination.</p>\n";  
         }  
         substr $outputString, $pos, 0, $traceHtml;  
2835      }      }
2836      # Write the output string.      # Return the result.
2837      print $outputString;      return $retVal;
2838  }  }
2839    
2840  =head3 Insure  =head3 Constrain
2841    
2842  C<< Insure($dirName); >>      my $constrained = Constrain($value, $min, $max);
2843    
2844  Insure a directory is present.  Modify a numeric value to bring it to a point in between a maximum and a minimum.
2845    
2846  =over 4  =over 4
2847    
2848  =item dirName  =item value
2849    
2850  Name of the directory to check. If it does not exist, it will be created.  Value to constrain.
2851    
2852    =item min (optional)
2853    
2854    Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
2855    
2856    =item max (optional)
2857    
2858    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
2859    
2860    =item RETURN
2861    
2862    Returns the incoming value, constrained according to the other parameters.
2863    
2864  =back  =back
2865    
2866  =cut  =cut
2867    
2868  sub Insure {  sub Constrain {
2869      my ($dirName) = @_;      # Get the parameters.
2870      if (! -d $dirName) {      my ($value, $min, $max) = @_;
2871          Trace("Creating $dirName directory.") if T(File => 2);      # Declare the return variable.
2872          eval { mkpath $dirName; };      my $retVal = $value;
2873          if ($@) {      # Apply the minimum constraint.
2874              Confess("Error creating $dirName: $@");      if (defined $min && $retVal < $min) {
2875          }          $retVal = $min;
2876        }
2877        # Apply the maximum constraint.
2878        if (defined $max && $retVal > $max) {
2879            $retVal = $max;
2880      }      }
2881        # Return the result.
2882        return $retVal;
2883  }  }
2884    
2885  =head3 ChDir  =head3 Min
2886    
2887  C<< ChDir($dirName); >>      my $min = Min($value1, $value2, ... $valueN);
2888    
2889  Change to the specified directory.  Return the minimum argument. The arguments are treated as numbers.
2890    
2891  =over 4  =over 4
2892    
2893  =item dirName  =item $value1, $value2, ... $valueN
2894    
2895  Name of the directory to which we want to change.  List of numbers to compare.
2896    
2897    =item RETURN
2898    
2899    Returns the lowest number in the list.
2900    
2901  =back  =back
2902    
2903  =cut  =cut
2904    
2905  sub ChDir {  sub Min {
2906      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
2907      if (! -d $dirName) {      my ($retVal, @values) = @_;
2908          Confess("Cannot change to directory $dirName: no such directory.");      # Loop through the remaining parameters, looking for the lowest.
2909      } else {      for my $value (@values) {
2910          Trace("Changing to directory $dirName.") if T(File => 4);          if ($value < $retVal) {
2911          my $okFlag = chdir $dirName;              $retVal = $value;
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
2912          }          }
2913      }      }
2914        # Return the minimum found.
2915        return $retVal;
2916  }  }
2917    
2918  =head3 SendSMS  =head3 Max
2919    
2920  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>      my $max = Max($value1, $value2, ... $valueN);
2921    
2922  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  Return the maximum argument. The arguments are treated as numbers.
 user name, password, and API ID for the relevant account in the hash reference variable  
 I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For  
 example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID  
 is C<2561022>, then the FIG_Config file must contain  
2923    
2924      $phone =  { user => 'BruceTheHumanPet',  =over 4
                 password => 'silly',  
                 api_id => '2561022' };  
2925    
2926  The original purpose of this method was to insure Bruce would be notified immediately when the  =item $value1, $value2, ... $valueN
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
2927    
2928  The message ID will be returned if successful, and C<undef> if an error occurs.  List of numbers to compare.
2929    
2930  =over 4  =item RETURN
2931    
2932  =item phoneNumber  Returns the highest number in the list.
2933    
2934  Phone number to receive the message, in international format. A United States phone number  =back
 would be prefixed by "1". A British phone number would be prefixed by "44".  
2935    
2936  =item msg  =cut
2937    
2938  Message to send to the specified phone.  sub Max {
2939        # Get the parameters. Note that we prime the return value with the first parameter.
2940        my ($retVal, @values) = @_;
2941        # Loop through the remaining parameters, looking for the highest.
2942        for my $value (@values) {
2943            if ($value > $retVal) {
2944                $retVal = $value;
2945            }
2946        }
2947        # Return the maximum found.
2948        return $retVal;
2949    }
2950    
2951    
2952    =head3 Strip
2953    
2954        my $string = Tracer::Strip($line);
2955    
2956    Strip all line terminators off a string. This is necessary when dealing with files
2957    that may have been transferred back and forth several times among different
2958    operating environments.
2959    
2960    =over 4
2961    
2962    =item line
2963    
2964    Line of text to be stripped.
2965    
2966  =item RETURN  =item RETURN
2967    
2968  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.
2969    
2970  =back  =back
2971    
2972  =cut  =cut
2973    
2974  sub SendSMS {  sub Strip {
2975      # Get the parameters.      # Get a copy of the parameter string.
2976      my ($phoneNumber, $msg) = @_;      my ($string) = @_;
2977      # Declare the return variable. If we do not change it, C<undef> will be returned.      my $retVal = (defined $string ? $string : "");
2978      my $retVal;      # Strip the line terminator characters.
2979      # 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);  
             }  
         }  
     }  
2980      # Return the result.      # Return the result.
2981      return $retVal;      return $retVal;
2982  }  }
2983    
2984  =head3 CommaFormat  =head3 Pad
2985    
2986  C<< my $formatted = Tracer::CommaFormat($number); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
2987    
2988  Insert commas into a number.  Pad a string to a specified length. The pad character will be a
2989    space, and the padding will be on the right side unless specified
2990    in the third parameter.
2991    
2992  =over 4  =over 4
2993    
2994  =item number  =item string
2995    
2996  A sequence of digits.  String to be padded.
2997    
2998    =item len
2999    
3000    Desired length of the padded string.
3001    
3002    =item left (optional)
3003    
3004    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3005    
3006    =item padChar (optional)
3007    
3008    Character to use for padding. The default is a space.
3009    
3010  =item RETURN  =item RETURN
3011    
3012  Returns the same digits with commas strategically inserted.  Returns a copy of the original string with the pad character added to the
3013    specified end so that it achieves the desired length.
3014    
3015  =back  =back
3016    
3017  =cut  =cut
3018    
3019  sub CommaFormat {  sub Pad {
3020      # Get the parameters.      # Get the parameters.
3021      my ($number) = @_;      my ($string, $len, $left, $padChar) = @_;
3022      # Pad the length up to a multiple of three.      # Compute the padding character.
3023      my $padded = "$number";      if (! defined $padChar) {
3024      $padded = " " . $padded while length($padded) % 3 != 0;          $padChar = " ";
3025      # This is a fancy PERL trick. The parentheses in the SPLIT pattern      }
3026      # cause the delimiters to be included in the output stream. The      # Compute the number of spaces needed.
3027      # GREP removes the empty strings in between the delimiters.      my $needed = $len - length $string;
3028      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));      # Copy the string into the return variable.
3029      # Clean out the spaces.      my $retVal = $string;
3030      $retVal =~ s/ //g;      # Only proceed if padding is needed.
3031        if ($needed > 0) {
3032            # Create the pad string.
3033            my $pad = $padChar x $needed;
3034            # Affix it to the return value.
3035            if ($left) {
3036                $retVal = $pad . $retVal;
3037            } else {
3038                $retVal .= $pad;
3039            }
3040        }
3041      # Return the result.      # Return the result.
3042      return $retVal;      return $retVal;
3043  }  }
 =head3 SetPermissions  
3044    
3045  C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  =head3 EOF
3046    
3047    This is a constant that is lexically greater than any useful string.
3048    
3049  Set the permissions for a directory and all the files and folders inside it.  =cut
 In addition, the group ownership will be changed to the specified value.  
3050    
3051  This method is more vulnerable than most to permission and compatability  sub EOF {
3052  problems, so it does internal error recovery.      return "\xFF\xFF\xFF\xFF\xFF";
3053    }
3054    
3055    =head3 TICK
3056    
3057        my @results = TICK($commandString);
3058    
3059    Perform a back-tick operation on a command. If this is a Windows environment, any leading
3060    dot-slash (C<./> will be removed. So, for example, if you were doing
3061    
3062        `./protein.cgi`
3063    
3064    from inside a CGI script, it would work fine in Unix, but would issue an error message
3065    in Windows complaining that C<'.'> is not a valid command. If instead you code
3066    
3067        TICK("./protein.cgi")
3068    
3069    it will work correctly in both environments.
3070    
3071  =over 4  =over 4
3072    
3073  =item dirName  =item commandString
3074    
3075  Name of the directory to process.  The command string to pass to the system.
3076    
3077  =item group  =item RETURN
3078    
3079    Returns the standard output from the specified command, as a list.
3080    
3081    =back
3082    
3083    =cut
3084    #: Return Type @;
3085    sub TICK {
3086        # Get the parameters.
3087        my ($commandString) = @_;
3088        # Chop off the dot-slash if this is Windows.
3089        if ($FIG_Config::win_mode) {
3090            $commandString =~ s!^\./!!;
3091        }
3092        # Activate the command and return the result.
3093        return `$commandString`;
3094    }
3095    
 Name of the group to be assigned.  
3096    
3097  =item mask  =head3 CommaFormat
3098    
3099  Permission mask. Bits that are C<1> in this mask will be ORed into the      my $formatted = Tracer::CommaFormat($number);
 permission bits of any file or directory that does not already have them  
 set to 1.  
3100    
3101  =item otherMasks  Insert commas into a number.
3102    
3103  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>.  
3104    
3105      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  =item number
3106    
3107  The list is ordered, so the following would use 0777 for C<tmp1> and  A sequence of digits.
 0666 for C<tmp>, C<tmp2>, or C<tmp3>.  
3108    
3109      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  =item RETURN
                                                    '^tmp' => 0666);  
3110    
3111  Note that the pattern matches are all case-insensitive, and only directory  Returns the same digits with commas strategically inserted.
 names are matched, not file names.  
3112    
3113  =back  =back
3114    
3115  =cut  =cut
3116    
3117  sub SetPermissions {  sub CommaFormat {
3118      # Get the parameters.      # Get the parameters.
3119      my ($dirName, $group, $mask, @otherMasks) = @_;      my ($number) = @_;
3120      # Set up for error recovery.      # Pad the length up to a multiple of three.
3121      eval {      my $padded = "$number";
3122          # Switch to the specified directory.      $padded = " " . $padded while length($padded) % 3 != 0;
3123          ChDir($dirName);      # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3124          # Get the group ID.      # cause the delimiters to be included in the output stream. The
3125          my $gid = getgrnam($group);      # GREP removes the empty strings in between the delimiters.
3126          # Get the mask for tracing.      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3127          my $traceMask = sprintf("%04o", $mask) . "($mask)";      # Clean out the spaces.
3128          Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);      $retVal =~ s/ //g;
3129          my $fixCount = 0;      # Return the result.
3130          my $lookCount = 0;      return $retVal;
         # @dirs will be a stack of directories to be processed.  
         my @dirs = (getcwd());  
         while (scalar(@dirs) > 0) {  
             # Get the current directory.  
             my $dir = pop @dirs;  
             # Check for a match to one of the specified directory names. To do  
             # that, we need to pull the individual part of the name off of the  
             # whole path.  
             my $simpleName = $dir;  
             if ($dir =~ m!/([^/]+)$!) {  
                 $simpleName = $1;  
             }  
             Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);  
             # Search for a match.  
             my $match = 0;  
             my $i;  
             for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {  
                 my $pattern = $otherMasks[$i];  
                 if ($simpleName =~ /$pattern/i) {  
                     $match = 1;  
                 }  
             }  
             # Check for a match. Note we use $i-1 because the loop added 2  
             # before terminating due to the match.  
             if ($match && $otherMasks[$i-1] != $mask) {  
                 # This directory matches one of the incoming patterns, and it's  
                 # a different mask, so we process it recursively with that mask.  
                 SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);  
             } else {  
                 # Here we can process normally. Get all of the non-hidden members.  
                 my @submems = OpenDir($dir, 1);  
                 for my $submem (@submems) {  
                     # Get the full name.  
                     my $thisMem = "$dir/$submem";  
                     Trace("Checking member $thisMem.") if T(4);  
                     $lookCount++;  
                     if ($lookCount % 1000 == 0) {  
                         Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);  
                     }  
                     # Fix the group.  
                     chown -1, $gid, $thisMem;  
                     # Insure this member is not a symlink.  
                     if (! -l $thisMem) {  
                         # Get its info.  
                         my $fileInfo = stat $thisMem;  
                         # Only proceed if we got the info. Otherwise, it's a hard link  
                         # and we want to skip it anyway.  
                         if ($fileInfo) {  
                             my $fileMode = $fileInfo->mode;  
                             if (($fileMode & $mask) != $mask) {  
                                 # Fix this member.  
                                 $fileMode |= $mask;  
                                 chmod $fileMode, $thisMem;  
                                 $fixCount++;  
                             }  
                             # If it's a subdirectory, stack it.  
                             if (-d $thisMem) {  
                                 push @dirs, $thisMem;  
                             }  
                         }  
                     }  
                 }  
             }  
         }  
         Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);  
     };  
     # Check for an error.  
     if ($@) {  
         Confess("SetPermissions error: $@");  
     }  
3131  }  }
3132    
3133    
3134  =head3 CompareLists  =head3 CompareLists
3135    
3136  C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3137    
3138  Compare two lists of tuples, and return a hash analyzing the differences. The lists  Compare two lists of tuples, and return a hash analyzing the differences. The lists
3139  are presumed to be sorted alphabetically by the value in the $keyIndex column.  are presumed to be sorted alphabetically by the value in the $keyIndex column.
# Line 2950  Line 3198 
3198      return ($inserted, $deleted);      return ($inserted, $deleted);
3199  }  }
3200    
 =head3 GetLine  
   
 C<< my @data = Tracer::GetLine($handle); >>  
   
 Read a line of data from a tab-delimited file.  
   
 =over 4  
   
 =item handle  
   
 Open file handle from which to read.  
   
 =item RETURN  
   
 Returns a list of the fields in the record read. The fields are presumed to be  
 tab-delimited. If we are at the end of the file, then an empty list will be  
 returned. If an empty line is read, a single list item consisting of a null  
 string will be returned.  
   
 =back  
   
 =cut  
   
 sub GetLine {  
     # Get the parameters.  
     my ($handle) = @_;  
     # Declare the return variable.  
     my @retVal = ();  
     Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);  
     # Read from the file.  
     my $line = <$handle>;  
     # Only proceed if we found something.  
     if (defined $line) {  
         # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an  
         # upload control and have a nonstandard EOL combination.  
         $line =~ s/(\r|\n)+$//;  
         # Here we do some fancy tracing to help in debugging complicated EOL marks.  
         if (T(File => 4)) {  
             my $escapedLine = $line;  
             $escapedLine =~ s/\n/\\n/g;  
             $escapedLine =~ s/\r/\\r/g;  
             $escapedLine =~ s/\t/\\t/g;  
             Trace("Line read: -->$escapedLine<--");  
         }  
         # If the line is empty, return a single empty string; otherwise, parse  
         # it into fields.  
         if ($line eq "") {  
             push @retVal, "";  
         } else {  
             push @retVal, split /\t/,$line;  
         }  
     } else {  
         # Trace the reason the read failed.  
         Trace("End of file: $!") if T(File => 3);  
     }  
     # Return the result.  
     return @retVal;  
 }  
   
 =head3 PutLine  
   
 C<< Tracer::PutLine($handle, \@fields, $eol); >>  
   
 Write a line of data to a tab-delimited file. The specified field values will be  
 output in tab-separated form, with a trailing new-line.  
   
 =over 4  
   
 =item handle  
   
 Output file handle.  
   
 =item fields  
   
 List of field values.  
   
 =item eol (optional)  
   
 End-of-line character (default is "\n").  
   
 =back  
   
 =cut  
   
 sub PutLine {  
     # Get the parameters.  
     my ($handle, $fields, $eol) = @_;  
     # Write the data.  
     print $handle join("\t", @{$fields}) . ($eol || "\n");  
 }  
   
3201  =head3 GenerateURL  =head3 GenerateURL
3202    
3203  C<< my $queryUrl = Tracer::GenerateURL($page, %parameters); >>      my $queryUrl = Tracer::GenerateURL($page, %parameters);
3204    
3205  Generate a GET-style URL for the specified page with the specified parameter  Generate a GET-style URL for the specified page with the specified parameter
3206  names and values. The values will be URL-escaped automatically. So, for  names and values. The values will be URL-escaped automatically. So, for
# Line 3091  Line 3248 
3248    
3249  =head3 ApplyURL  =head3 ApplyURL
3250    
3251  C<< Tracer::ApplyURL($table, $target, $url); >>      Tracer::ApplyURL($table, $target, $url);
3252    
3253  Run through a two-dimensional table (or more accurately, a list of lists), converting the  Run through a two-dimensional table (or more accurately, a list of lists), converting the
3254  I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The  I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
# Line 3134  Line 3291 
3291    
3292  =head3 CombineURL  =head3 CombineURL
3293    
3294  C<< my $combinedHtml = Tracer::CombineURL($text, $url); >>      my $combinedHtml = Tracer::CombineURL($text, $url);
3295    
3296  This method will convert the specified text into HTML hyperlinked to the specified  This method will convert the specified text into HTML hyperlinked to the specified
3297  URL. The hyperlinking will only take place if the URL looks legitimate: that is, it  URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
# Line 3175  Line 3332 
3332      return $retVal;      return $retVal;
3333  }  }
3334    
3335    =head3 Cmp
3336    
3337        my $cmp = Tracer::Cmp($a, $b);
3338    
3339    This method performs a universal sort comparison. Each value coming in is
3340    separated into a leading text part and a trailing number part. The text
3341    part is string compared, and if both parts are equal, then the number
3342    parts are compared numerically. A stream of just numbers or a stream of
3343    just strings will sort correctly, and a mixed stream will sort with the
3344    numbers first. Strings with a label and a number will sort in the
3345    expected manner instead of lexically.
3346    
3347    =over 4
3348    
3349    =item a
3350    
3351    First item to compare.
3352    
3353    =item b
3354    
3355    Second item to compare.
3356    
3357    =item RETURN
3358    
3359    Returns a negative number if the first item should sort first (is less), a positive
3360    number if the first item should sort second (is greater), and a zero if the items are
3361    equal.
3362    
3363    =back
3364    
3365    =cut
3366    
3367    sub Cmp {
3368        # Get the parameters.
3369        my ($a, $b) = @_;
3370        # Declare the return value.
3371        my $retVal;
3372        # Check for nulls.
3373        if (! defined($a)) {
3374            $retVal = (! defined($b) ? 0 : -1);
3375        } elsif (! defined($b)) {
3376            $retVal = 1;
3377        } else {
3378            # Here we have two real values. Parse the two strings.
3379            $a =~ /^(\D*)(\d*)$/;
3380            my $aParsed = [$1, $2];
3381            $b =~ /^(\D*)(\d*)$/;
3382            my $bParsed = [$1, $2];
3383            # Compare the string parts.
3384            $retVal = $aParsed->[0] cmp $bParsed->[0];
3385            if (! $retVal) {
3386                $retVal = $aParsed->[1] <=> $bParsed->[1];
3387            }
3388        }
3389        # Return the result.
3390        return $retVal;
3391    }
3392    
3393    
3394    =head3 TrackingCode
3395    
3396        my $html = Tracer::TrackingCode();
3397    
3398    Returns the HTML code for doing web page traffic monitoring. If the
3399    current environment is a test system, then it returns a null string;
3400    otherwise, it returns a bunch of javascript containing code for turning
3401    on SiteMeter and Google Analytics.
3402    
3403    =cut
3404    
3405    sub TrackingCode {
3406        # Declare the return variable.
3407        my $retVal = "<!-- tracking off -->";
3408        # Determine if we're in production.
3409        if ($FIG_Config::site_meter) {
3410            $retVal = <<END_HTML
3411            <!-- Site Meter -->
3412            <script type="text/javascript" src="http://s20.sitemeter.com/js/counter.js?site=s20nmpdr">
3413            </script>
3414            <noscript>
3415            <a href="http://s20.sitemeter.com/stats.asp?site=s20nmpdr" target="_top">
3416            <img src="http://s20.sitemeter.com/meter.asp?site=s20nmpdr" alt="Site Meter" border="0"/></a>
3417            </noscript>
3418            <!-- Copyright (c)2006 Site Meter -->
3419    END_HTML
3420        }
3421        return $retVal;
3422    }
3423    
3424    
3425  1;  1;

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