[Bio] / FigKernelPackages / Tracer.pm Repository:
ViewVC logotype

Diff of /FigKernelPackages/Tracer.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.73, Tue Oct 3 12:04:50 2006 UTC revision 1.105, Wed May 14 09:09:25 2008 UTC
# Line 1  Line 1 
1  #  # -*- perl -*-
2    ########################################################################
3  # Copyright (c) 2003-2006 University of Chicago and Fellowship  # Copyright (c) 2003-2006 University of Chicago and Fellowship
4  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
5  #  #
# Line 13  Line 14 
14  # at info@ci.uchicago.edu or the Fellowship for Interpretation of  # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15  # Genomes at veronika@thefig.info or download a copy from  # Genomes at veronika@thefig.info or download a copy from
16  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
17  #  ########################################################################
18    
19  package Tracer;  package Tracer;
20    
21      require Exporter;      require Exporter;
22      @ISA = ('Exporter');      @ISA = ('Exporter');
23      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn);
24      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
25      use strict;      use strict;
26      use Carp qw(longmess croak);      use Carp qw(longmess croak carp);
27      use CGI;      use CGI;
28      use Cwd;      use Cwd;
29      use FIG_Config;      use FIG_Config;
# Line 34  Line 35 
35      use LWP::UserAgent;      use LWP::UserAgent;
36      use Time::HiRes 'gettimeofday';      use Time::HiRes 'gettimeofday';
37      use URI::Escape;      use URI::Escape;
38        use Time::Local;
39        use POSIX qw(strftime);
40        use Time::Zone;
41    
42    
43  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
44    
# Line 158  Line 163 
163    
164  Sometimes, you need a way for tracing to happen automatically without putting parameters  Sometimes, you need a way for tracing to happen automatically without putting parameters
165  in a form or on the command line. Emergency tracing does this. You invoke emergency tracing  in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
166  from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.  from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
167  Emergency tracing requires you specify a tracing key. For command-line tools, the key is  that you specify a tracing key. For command-line tools, the key is
168  taken from the C<TRACING> environment variable. For web services, the key is taken from  taken from the C<TRACING> environment variable. For web services, the key is taken from
169  a cookie. Either way, the key tells the tracing facility who you are, so that you control  a cookie. Either way, the key tells the tracing facility who you are, so that you control
170  the tracing in your environment without stepping on other users.  the tracing in your environment without stepping on other users.
# Line 182  Line 187 
187    
188  The web script will look for the tracing key in the cookies, and the command-line  The web script will look for the tracing key in the cookies, and the command-line
189  script will look for it in the C<TRACING> environment variable. If you are  script will look for it in the C<TRACING> environment variable. If you are
190  using the L</StandardScript> or L</StandardSetup> methods, emergency tracing  using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
191  will be configured automatically.  will be configured automatically.
192    
 =head3 Debugging Control Panel  
   
 The debugging control panel provides several tools to assist in development of  
 SEED and Sprout software. You access the debugging control panel from the URL  
 C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,  
 for example, the panel access point for the development NMPDR system is  
 C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to  
 find out what the password is. From this page, you can also specify a tracing  
 key. If you don't specify a key, one will be generated for you.  
   
 =head4 Emergency Tracing Form  
   
 At the bottom of the debugging control panel is a form that allows you to  
 specify a trace level and tracing categories. Special and common categories  
 are listed with check boxes. You can hold your mouse over a check box to see  
 what its category does. In general, however, a category name is the same as  
 the name of the package in which the trace message occurs.  
   
 Additional categories can be entered in an input box, delimited by spaces or commas.  
   
 The B<Activate> button turns on Emergency tracing at the level you specify with the  
 specified categories active. The B<Terminate> button turns tracing off. The  
 B<Show File> button displays the current contents of the trace file. The tracing  
 form at the bottom of the control panel is designed for emergency tracing, so it  
 will only affect programs that call L</ETracing>, L</StandardScript>,  
 or L</StandardSetup>.  
   
 =head4 Script Form  
   
 The top form of the debugging control panel allows you to enter a tiny script and  
 have the output generated in a formatted table. Certain object variables are  
 predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),  
 and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.  
   
 The last line of the script must be a scalar, but it can be a reference to a hash,  
 a list, a list of lists, and various other combinations. If you select the appropriate  
 data type in the dropdown box, the output will be formatted accordingly. The form  
 also has controls for specifying tracing. These controls override any emergency  
 tracing in effect.  
   
 =head4 Database Query Forms  
   
 The forms between the script form and the emergency tracing form allow you to  
 make queries against the database. The FIG query form allows simple queries against  
 a single FIG table. The Sprout query form uses the B<GetAll> method to do a  
 multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>  
 package, and it takes five parameters.  
   
     GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);  
   
 Each of the five parameters corresponds to a text box on the query form:  
   
 =over 4  
   
 =item Objects  
   
 Comma-separated list containing the names of the entity and relationship objects to be retrieved.  
   
 =item Filter  
   
 WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  
 be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form  
 B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a  
 field, I<objectName> is the name of the entity or relationship object containing the field, and  
 I<number> is the 1-based position of the object in the object list. Any parameters  
 specified in the filter clause should be specified in the B<Params> field.  
 The fields in a filter clause can come from primary entity relations,  
 relationship relations, or secondary entity relations; however, all of the  
 entities and relationships involved must be included in the list of object names.  
   
 =item Params  
   
 List of the parameters to be substituted in for the parameters marks in the filter clause. This  
 is a comma-separated list without any quoting or escaping.  
   
 =item fields  
   
 Comma-separated list of the fields to be returned in each element of the list returned. Fields  
 are specified in the same manner as in the filter clause.  
   
 =item count  
   
 Maximum number of records to return. If omitted or 0, all available records will be returned.  
   
 =back  
   
 B<GetAll> automatically joins together the entities and relationships listed in the object  
 names. This simplifies the coding of the filter clause, but it means that some queries are  
 not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation  
 that has yet to be addressed.  
   
193  =cut  =cut
194    
195  # Declare the configuration variables.  # Declare the configuration variables.
196    
197  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
198  my $TeeFlag = 0;            # TRUE if output is going to a file and to the  my $TeeFlag = 0;            # TRUE if output is going to a file and to the
199                              # standard output                              # standard output
200  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
201                              # hash of active category names                              # hash of active category names
202    my @LevelNames = qw(error warn notice info detail);
203  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
204                              # messages                              # messages
205  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
206  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
207    my $LastLevel = 0;          # level of the last test call
208  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
209  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
210    my $SavedCGI;               # CGI object passed to ETracing
211    my $CommandLine;            # Command line passed to StandardSetup
212    umask 2;                    # Fix the damn umask so everything is group-writable.
213    
214  =head2 Public Methods  =head2 Tracing Methods
215    
216    =head3 Setups
217    
218        my $count = Tracer::Setups();
219    
220    Return the number of times L</TSetup> has been called.
221    
222    This method allows for the creation of conditional tracing setups where, for example, we
223    may want to set up tracing if nobody else has done it before us.
224    
225    =cut
226    
227    sub Setups {
228        return $SetupCount;
229    }
230    
231  =head3 TSetup  =head3 TSetup
232    
233  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
234    
235  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
236  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 346  Line 280 
280          }          }
281      }      }
282      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
283      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
284      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
285        # the standard output (tee mode).
286      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
287          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
288              $TeeFlag = 1;              $TeeFlag = 1;
289              $target = substr($target, 1);              $target = substr($target, 1);
290          }          }
291          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
292                # We need to initialize the file (which clears it).
293              open TRACEFILE, $target;              open TRACEFILE, $target;
294              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
295              close TRACEFILE;              close TRACEFILE;
296                # Set to append mode now that the file has been cleared.
297              $Destination = ">$target";              $Destination = ">$target";
298          } else {          } else {
299              $Destination = $target;              $Destination = $target;
# Line 368  Line 305 
305      $SetupCount++;      $SetupCount++;
306  }  }
307    
308  =head3 StandardSetup  =head3 SetLevel
309    
310  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
311    
312  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.  
313    
314  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.  
315    
316  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  
317    
318      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
319    
320  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.  
321    
322  =over 4  =cut
323    
324  =item SQL  sub SetLevel {
325        $TraceLevel = $_[0];
326    }
327    
328  Traces SQL commands and activity.  =head3 ParseDate
329    
330  =item Tracer      my $time = Tracer::ParseDate($dateString);
331    
332  Traces error messages and call stacks.  Convert a date into a PERL time number. This method expects a date-like string
333    and parses it into a number. The string must be vaguely date-like or it will
334    return an undefined value. Our requirement is that a month and day be
335    present and that three pieces of the date string (time of day, month and day,
336    year) be separated by likely delimiters, such as spaces, commas, and such-like.
337    
338  =back  If a time of day is present, it must be in military time with two digits for
339    everything but the hour.
340    
341  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.  
342    
343      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
344    equally innocuous. This means, however, that a sufficiently long sentence with date-like
345    parts in it may be interpreted as a date. Hopefully this will not be a problem.
346    
347  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  
348    
349  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.  
350    
351      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  =over 4
352    
353  would send the trace output to C<traceBruce.log> in the temporary directory.  =item dateString
354    
355  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.  
356    
357  You can specify a different default trace level by setting C<$options->{trace}>  =item RETURN
 prior to calling this method.  
358    
359  An example at this point would help. Consider, for example, the command-line utility  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
360  C<TransactFeatures>. It accepts a list of positional parameters plus the options  the date string is invalid. A valid date string must contain a month and day.
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
361    
362      my ($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);  
363    
364    =cut
365    
366  The call to C<ParseCommand> specifies the default values for the options and  # Universal month conversion table.
367  stores the actual options in a hash that is returned as C<$options>. The  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
368  positional parameters are returned in C<@parameters>.                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
369                                Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
370                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
371                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
372                                Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
373                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
374                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
375                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
376                                Oct =>  9, October  =>   9, '10' =>  9,
377                                Nov => 10, November =>  10, '11' => 10,
378                                Dec => 11, December =>  11, '12' => 11
379                            };
380    
381  The following is a sample command line for C<TransactFeatures>.  sub ParseDate {
382        # Get the parameters.
383        my ($dateString) = @_;
384        # Declare the return variable.
385        my $retVal;
386        # Find the month and day of month. There are two ways that can happen. We check for the
387        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
388        # won't be fooled into thinking the month is Sunday.
389        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
390            my ($mon, $mday) = (MONTHS->{$1}, $2);
391            # Insist that the month and day are valid.
392            if (defined($mon) && $2 >= 1 && $2 <= 31) {
393                # Find the time.
394                my ($hour, $min, $sec) = (0, 0, 0);
395                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
396                    ($hour, $min, $sec) = ($1, $2, $3);
397                }
398                # Find the year.
399                my $year;
400                if ($dateString =~ /\b(\d{4})\b/) {
401                    $year = $1;
402                } else {
403                    # Get the default year, which is this one. Note we must convert it to
404                    # the four-digit value expected by "timelocal".
405                    (undef, undef, undef, undef, undef, $year) = localtime();
406                    $year += 1900;
407                }
408                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
409            }
410        }
411        # Return the result.
412        return $retVal;
413    }
414    
415      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  =head3 LogErrors
416    
417  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional      Tracer::LogErrors($fileName);
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
418    
419      { trace => 2, sql => 0, safe => 0,  Route the standard error output to a log file.
       noAlias => 1, start => ' ', tblFiles => 0 }  
420    
421  Use of C<StandardSetup> in this way provides a simple way of performing  =over 4
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
422    
423  If the C<background> option is specified on the command line, then the  =item fileName
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
424    
425      -user=Bruce -background  Name of the file to receive the error output.
426    
427  then the trace output would go to C<traceBruce.log>, the standard output to  =back
 C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to  
 simplify starting a command in the background.  
428    
429  The user name is also used as the tracing key for L</Emergency Tracing>.  =cut
 Specifying a value of C<E> for the trace level causes emergency tracing to  
 be used instead of custom tracing. If the user name is not specified,  
 the tracing key is taken from the C<Tracing> environment variable. If there  
 is no value for that variable, the tracing key will be computed from the PID.  
430    
431  Finally, if the special option C<-h> is specified, the option names will  sub LogErrors {
432  be traced at level 0 and the program will exit without processing.      # Get the file name.
433  This provides a limited help capability. For example, if the user enters      my ($fileName) = @_;
434        # Open the file as the standard error output.
435        open STDERR, '>', $fileName;
436    }
437    
438      TransactFeatures -h  =head3 Trace
439    
440  he would see the following output.      Trace($message);
441    
442      TransactFeatures [options] command transactionDirectory IDfile  Write a trace message to the target location specified in L</TSetup>. If there has not been
443          -trace    tracing level (default E)  any prior call to B<TSetup>.
         -sql      trace SQL commands  
         -safe     use database transactions  
         -noAlias  do not expect aliases in CHANGE transactions  
         -start    start with this genome  
         -tblFiles output TBL files containing the corrected IDs  
444    
445  The caller has the option of modifying the tracing scheme by placing a value  =over 4
 for C<trace> in the incoming options hash. The default value can be overridden,  
 or the tracing to the standard output can be turned off by suffixing a minus  
 sign to the trace level. So, for example,  
446    
447      { trace => [0, "tracing level (default 0)"],  =item message
        ...  
448    
449  would set the default trace level to 0 instead of E, while  Message to write.
450    
451      { trace => ["2-", "tracing level (default 2)"],  =back
        ...  
452    
453  would set the default to 2, but trace only to the log file, not to the  =cut
 standard output.  
454    
455  The parameters to this method are as follows.  sub Trace {
456        # Get the parameters.
457        my ($message) = @_;
458        # Strip off any line terminators at the end of the message. We will add
459        # new-line stuff ourselves.
460        my $stripped = Strip($message);
461        # Compute the caller information.
462        my ($callPackage, $callFile, $callLine) = caller();
463        my $callFileTitle = basename($callFile);
464        # Check the caller.
465        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
466        # Get the timestamp.
467        my $timeStamp = Now();
468        # Build the prefix.
469        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
470        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
471        # Format the message.
472        my $formatted = "$prefix $stripped";
473        # Process according to the destination.
474        if ($Destination eq "TEXT") {
475            # Write the message to the standard output.
476            print "$formatted\n";
477        } elsif ($Destination eq "ERROR") {
478            # Write the message to the error output. Here, we want our prefix fields.
479            print STDERR "$formatted\n";
480        } elsif ($Destination eq "WARN") {
481            # Emit the message to the standard error output. It is presumed that the
482            # error logger will add its own prefix fields, the notable exception being
483            # the caller info.
484            print STDERR "$callerInfo$stripped\n";
485        } elsif ($Destination eq "QUEUE") {
486            # Push the message into the queue.
487            push @Queue, "$formatted";
488        } elsif ($Destination eq "HTML") {
489            # Convert the message to HTML and write it to the standard output.
490            my $escapedMessage = CGI::escapeHTML($stripped);
491            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
492        } elsif ($Destination =~ m/^>>/) {
493            # Write the trace message to an output file.
494            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
495            print TRACING "$formatted\n";
496            close TRACING;
497            # If the Tee flag is on, echo it to the standard output.
498            if ($TeeFlag) {
499                print "$formatted\n";
500            }
501        }
502    }
503    
504  =over 4  =head3 T
505    
506  =item categories      my $switch = T($category, $traceLevel);
507    
508  Reference to a list of tracing category names. These should be names of      or
 packages whose internal workings will need to be debugged to get the  
 command working.  
509    
510  =item options      my $switch = T($traceLevel);
511    
512  Reference to a hash containing the legal options for the current command mapped  Return TRUE if the trace level is at or above a specified value and the specified category
513  to their default values and descriptions. The user can override the defaults  is active, else FALSE. If no category is specified, the caller's package name is used.
 by specifying the options as command-line switches prefixed by a hyphen.  
 Tracing-related options may be added to this hash. If the C<-h> option is  
 specified on the command line, the option descriptions will be used to  
 explain the options. To turn off tracing to the standard output, add a  
 minus sign to the value for C<trace> (see above).  
514    
515  =item parmHelp  =over 4
516    
517  A string that vaguely describes the positional parameters. This is used  =item category
 if the user specifies the C<-h> option.  
518    
519  =item argv  Category to which the message belongs. If not specified, the caller's package name is
520    used.
521    
522  List of command line parameters, including the option switches, which must  =item traceLevel
523  precede the positional parameters and be prefixed by a hyphen.  
524    Relevant tracing level.
525    
526  =item RETURN  =item RETURN
527    
528  Returns a list. The first element of the list is the reference to a hash that  TRUE if a message at the specified trace level would appear in the trace, else FALSE.
 maps the command-line option switches to their values. These will either be the  
 default values or overrides specified on the command line. The remaining  
 elements of the list are the position parameters, in order.  
529    
530  =back  =back
531    
532  =cut  =cut
533    
534  sub StandardSetup {  sub T {
535        # Declare the return variable.
536        my $retVal = 0;
537        # Only proceed if tracing is turned on.
538        if ($Destination ne "NONE") {
539      # Get the parameters.      # Get the parameters.
540      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
541      # Get the default tracing key.          if (!defined $traceLevel) {
542      my $tkey = EmergencyKey();              # Here we have no category, so we need to get the calling package.
543      # Add the tracing options.              # The calling package is normally the first parameter. If it is
544      if (! exists $options->{trace}) {              # omitted, the first parameter will be the tracelevel. So, the
545          $options->{trace} = ['E', "tracing level (E for emergency tracing)"];              # first thing we do is shift the so-called category into the
546      }              # $traceLevel variable where it belongs.
547      $options->{sql} = [0, "turn on SQL tracing"];              $traceLevel = $category;
548      $options->{h} = [0, "display command-line options"];              my ($package, $fileName, $line) = caller;
549      $options->{user} = [$tkey, "tracing key"];              # If there is no calling package, we default to "main".
550      $options->{background} = [0, "spool standard and error output"];              if (!$package) {
551      # Create a parsing hash from the options hash. The parsing hash                  $category = "main";
     # contains the default values rather than the default value  
     # and the description. While we're at it, we'll memorize the  
     # length of the longest option name.  
     my $longestName = 0;  
     my %parseOptions = ();  
     for my $key (keys %{$options}) {  
         if (length $key > $longestName) {  
             $longestName = length $key;  
         }  
         $parseOptions{$key} = $options->{$key}->[0];  
     }  
     # Parse the command line.  
     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);  
     # Get the logfile suffix.  
     my $suffix = $retOptions->{user};  
     # Check for background mode.  
     if ($retOptions->{background}) {  
         my $outFileName = "$FIG_Config::temp/out$suffix.log";  
         my $errFileName = "$FIG_Config::temp/err$suffix.log";  
         open STDOUT, ">$outFileName";  
         open STDERR, ">$errFileName";  
     }  
     # Now we want to set up tracing. First, we need to know if the user  
     # wants emergency tracing.  
     if ($retOptions->{trace} eq 'E') {  
         ETracing($retOptions->{user});  
     } else {  
         # Here the tracing is controlled from the command line.  
         my @cats = @{$categories};  
         if ($retOptions->{sql}) {  
             push @cats, "SQL";  
         }  
         # Add the default categories.  
         push @cats, "Tracer";  
         # Next, we create the category string by joining the categories.  
         my $cats = join(" ", @cats);  
         # Check to determine whether or not the caller wants to turn off tracing  
         # to the standard output.  
         my $traceLevel = $retOptions->{trace};  
         my $textOKFlag = 1;  
         if ($traceLevel =~ /^(.)-/) {  
             $traceLevel = $1;  
             $textOKFlag = 0;  
         }  
         # Now we set up the trace mode.  
         my $traceMode;  
         # Verify that we can open a file in the FIG temporary directory.  
         my $traceFileName = "$FIG_Config::temp/trace$suffix.log";  
         if (open TESTTRACE, ">$traceFileName") {  
             # Here we can trace to a file.  
             $traceMode = ">$traceFileName";  
             if ($textOKFlag) {  
                 # Echo to standard output if the text-OK flag is set.  
                 $traceMode = "+$traceMode";  
             }  
             # Close the test file.  
             close TESTTRACE;  
         } else {  
             # Here we can't trace to a file. We trace to the standard output if it's  
             # okay, and the error log otherwise.  
             if ($textOKFlag) {  
                 $traceMode = "TEXT";  
552              } else {              } else {
553                  $traceMode = "WARN";                  my @cats = split /::/, $package;
554              }                  $category = $cats[$#cats];
         }  
         # Now set up the tracing.  
         TSetup("$traceLevel $cats", $traceMode);  
555      }      }
     # Check for the "h" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($retOptions->{h}) {  
         $0 =~ m#[/\\](\w+)(\.pl)?$#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] . ")";  
556              }              }
557              print "  $name $desc\n";          # Save the category name and level.
558            $LastCategory = $category;
559            $LastLevel = $traceLevel;
560            # Convert it to lower case before we hash it.
561            $category = lc $category;
562            # Validate the trace level.
563            if (ref $traceLevel) {
564                Confess("Bad trace level.");
565            } elsif (ref $TraceLevel) {
566                Confess("Bad trace config.");
567          }          }
568          exit(0);          # Make the check. Note that level 0 shows even if the category is turned off.
569            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
570      }      }
571      # Return the parsed parameters.      # Return the computed result.
572      return ($retOptions, @retParameters);      return $retVal;
573  }  }
574    
575  =head3 Setups  =head3 QTrace
   
 C<< my $count = Tracer::Setups(); >>  
   
 Return the number of times L</TSetup> has been called.  
   
 This method allows for the creation of conditional tracing setups where, for example, we  
 may want to set up tracing if nobody else has done it before us.  
   
 =cut  
576    
577  sub Setups {      my $data = QTrace($format);
     return $SetupCount;  
 }  
578    
579  =head3 Open  Return the queued trace data in the specified format.
580    
581  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  =over 4
582    
583  Open a file.  =item format
584    
585  The I<$fileSpec> is essentially the second argument of the PERL C<open>  C<html> to format the data as an HTML list, C<text> to format it as straight text.
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
586    
587      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =back
588    
589  would open for output appended to the specified file, and  =cut
590    
591      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  sub QTrace {
592        # Get the parameter.
593        my ($format) = @_;
594        # Create the return variable.
595        my $retVal = "";
596        # Only proceed if there is an actual queue.
597        if (@Queue) {
598            # Process according to the format.
599            if ($format =~ m/^HTML$/i) {
600                # Convert the queue into an HTML list.
601                $retVal = "<ul>\n";
602                for my $line (@Queue) {
603                    my $escapedLine = CGI::escapeHTML($line);
604                    $retVal .= "<li>$escapedLine</li>\n";
605                }
606                $retVal .= "</ul>\n";
607            } elsif ($format =~ m/^TEXT$/i) {
608                # Convert the queue into a list of text lines.
609                $retVal = join("\n", @Queue) . "\n";
610            }
611            # Clear the queue.
612            @Queue = ();
613        }
614        # Return the formatted list.
615        return $retVal;
616    }
617    
618  would open a pipe that sorts the records written and removes duplicates. Note  =head3 Confess
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
619    
620      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");      Confess($message);
621    
622  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  Trace the call stack and abort the program with the specified message. When used with
623  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
624  failed open will throw an exception and the third parameter will be used to construct  So, for example
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
625    
626      Could not open "/usr/spool/news/twitlog"      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
627    
628  Note that the mode characters are automatically cleaned from the file name.  Will abort the program with a stack trace if the value of C<$recNum> is negative.
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
629    
630      Could not open "/usr/spool/news/twitlog": file not found.  =over 4
631    
632  In some versions of PERL the only error message we get is a number, which  =item message
 corresponds to the C++ C<errno> value.  
633    
634      Could not open "/usr/spool/news/twitlog": 6.  Message to include in the trace.
635    
636  =over 4  =back
637    
638  =item fileHandle  =cut
639    
640  File handle. If this parameter is C<undef>, a file handle will be generated  sub Confess {
641  and returned as the value of this method.      # Get the parameters.
642        my ($message) = @_;
643        # Set up the category and level.
644        $LastCategory = "(confess)";
645        $LastLevel = 0;
646        if (! defined($FIG_Config::no_tool_hdr)) {
647            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
648            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
649            # Only proceed if the tool header file is actually present.
650            if (-f $toolHeaderFile) {
651                my $fh;
652                if (open $fh, "<$toolHeaderFile") {
653                    my @lines = <$fh>;
654                    Trace("Tool header has " . scalar(@lines) . " lines.");
655                }
656            }
657        }
658        # Trace the call stack.
659        Cluck($message);
660        # Abort the program.
661        croak(">>> $message");
662    }
663    
664  =item fileSpec  =head3 Warn
665    
666  File name and mode, as per the PERL C<open> function.      Warn($message);
667    
668  =item message (optional)  This method traces an important message. If an RSS feed is configured
669    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
670    then the message will be echoed to the feed. In general, a tracing
671    destination of C<WARN> indicates that the caller is running as a web
672    service in a production environment; however, this is not a requirement.
673    
674    To force warnings into the RSS feed even when the tracing destination
675    is not C<WARN>, simply specify the C<Feed> tracing module. This can be
676    configured automatically when L</StandardSetup> is used.
677    
678    The L</Cluck> method calls this one for its final message. Since
679    L</Confess> calls L</Cluck>, this means that any error which is caught
680    and confessed will put something in the feed. This insures that someone
681    will be alerted relatively quickly when a failure occurs.
682    
683  Error message to use if the open fails. If omitted, a standard error message  =over 4
 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>.  
684    
685  =item RETURN  =item message
686    
687  Returns the name of the file handle assigned to the file, or C<undef> if the  Message to be traced.
 open failed.  
688    
689  =back  =back
690    
691  =cut  =cut
692    
693  sub Open {  sub Warn {
694      # Get the parameters.      # Get the parameters.
695      my ($fileHandle, $fileSpec, $message) = @_;      my ($message) = @_;
696      # Attempt to open the file.      # Trace the message.
697      my $rv = open $fileHandle, $fileSpec;      Trace($message);
698      # If the open failed, generate an error message.      # Check for feed forcing.
699      if (! $rv) {      my $forceFeed = exists $Categories{feed};
700          # Save the system error message.      # An error here would be disastrous. Note, however, that we aren't too worried
701          my $sysMessage = $!;      # about losing events. The error log is always available for the occasions where
702          # See if we need a default message.      # we mess up. Note that if debug mode is specified, we do this stuff even in a
703          if (!$message) {      # test environment.
704              # Clean any obvious mode characters and leading spaces from the      eval {
705              # filename.          # Do we need to put this in the RSS feed?
706              my ($fileName) = FindNamePart($fileSpec);          if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
707              $message = "Could not open \"$fileName\"";              # Yes. We now need to compute the date, the link, and the title.
708                # First, the date, in a very specific format.
709                my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
710                    (tz_local_offset() / 30);
711                # Environment data goes in here. We start with the date.
712                my $environment = "$date.  ";
713                # If we need to recap the message (because it's too long to be a title), we'll
714                # put it in here.
715                my $recap;
716                # Copy the message and remove excess space.
717                my $title = $message;
718                $title =~ s/\s+/ /gs;
719                # If it's too long, we have to split it up.
720                if (length $title > 60) {
721                    # Put the full message in the environment string.
722                    $recap = $title;
723                    # Excerpt it as the title.
724                    $title = substr($title, 0, 50) . "...";
725                }
726                # If we have a CGI object, then this is a web error. Otherwise, it's
727                # command-line.
728                if (defined $SavedCGI) {
729                    # We're in a web service. The environment is the user's IP, and the link
730                    # is the URL that got us here.
731                    my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
732                    $environment .= "Event Reported at IP address $key.";
733                    my $url = $SavedCGI->url(-full => 1, -query => 1);
734                    # We need the user agent string and (if available) the referrer.
735                    # The referrer will be the link.
736                    $environment .= "User Agent $ENV{HTTP_USER_AGENT}";
737                    if ($ENV{HTTP_REFERER}) {
738                        my $link = $ENV{HTTP_REFERER};
739                        $environment .= " referred from <a href=\"$link\">$link</a>.";
740                    } else {
741                        $environment .= " referrer unknown.";
742                    }
743                    # Close off the sentence with the original link.
744                    $environment .= " URL of error is <a href=\"$url\">$url</a>.";
745                } else {
746                    # No CGI object, so we're a command-line tool. Use the tracing
747                    # key and the PID as the user identifier, and add the command.
748                    my $key = EmergencyKey();
749                    $environment .= "Event Reported by $key Process $$.";
750                    if ($CommandLine) {
751                        # We're in a StandardSetup script, so we have the real command line.
752                        $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
753                    } elsif ($ENV{_}) {
754                        # We're in a BASH script, so the command has been stored in the _ variable.
755                        $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
756                    }
757                }
758                # Build a GUID. We use the current time, the title, and the process ID,
759                # then digest the result.
760                my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
761                # Finally, the description. This is a stack trace plus various environmental stuff.
762                my $stackTrace = "";
763                my @trace = LongMess();
764                # Only proceed if we got something back.
765                if (scalar(@trace) > 0) {
766                    $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
767                    $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
768                }
769                # We got the stack trace. Now it's time to put it all together.
770                # We have a goofy thing here in that we need to HTML-escape some sections of the description
771                # twice. They will be escaped once here, and then once when written by XML::Simple. They are
772                # unescaped once when processed by the RSS reader, and stuff in the description is treated as
773                # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
774                # our <br>s and <pre>s are used to format the description.
775                $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
776                my $description = "$recap$environment  $stackTrace";
777                # Okay, we have all the pieces. Create a hash of the new event.
778                my $newItem = { title => $title,
779                                description => $description,
780                                category => $LastCategory,
781                                pubDate => $date,
782                                guid => $guid,
783                               };
784                # We need XML capability for this.
785                require XML::Simple;
786                # The RSS document goes in here.
787                my $rss;
788                # Get the name of the RSS file. It's in the FIG temporary directory.
789                my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
790                # Does it exist?
791                if (-s $fileName) {
792                    # Slurp it in.
793                    $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
794                } else {
795                    my $size = -s $fileName;
796                    # Create an empty channel.
797                    $rss = {
798                        channel => {
799                            title => 'NMPDR Warning Feed',
800                            link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
801                            description => "Important messages regarding the status of the NMPDR.",
802                            generator => "NMPDR Trace Facility",
803                            docs => "http://blogs.law.harvard.edu/tech/rss",
804                            item => []
805                        },
806                    };
807          }          }
808          # Terminate with an error using the supplied message and the              # Get the channel object.
809          # error message from the file system.              my $channel = $rss->{channel};
810          Confess("$message: $!");              # Update the last-build date.
811                $channel->{lastBuildDate} = $date;
812                # Get the item array.
813                my $items = $channel->{item};
814                # Insure it has only 100 entries.
815                while (scalar @{$items} > 100) {
816                    pop @{$items};
817                }
818                # Add our new item at the front.
819                unshift @{$items}, $newItem;
820                # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
821                # the requirements for those.
822                my $xml = XML::Simple::XMLout($rss, NoAttr => 1, RootName => undef, XmlDecl => '');
823                # Here we put in the root and declaration. The problem is that the root has to have the version attribute
824                # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
825                $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
826                # We don't use Open here because we can't afford an error.
827                if (open XMLOUT, ">$fileName") {
828                    print XMLOUT $xml;
829                    close XMLOUT;
830                }
831            }
832        };
833        if ($@) {
834            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
835            # (which is a good thing).
836            my $error = $@;
837            Trace("Feed Error: $error") if T(Feed => 0);
838      }      }
     # Return the file handle.  
     return $fileHandle;  
839  }  }
840    
841  =head3 FindNamePart  =head3 Assert
   
 C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>  
842    
843  Extract the portion of a file specification that contains the file name.      Assert($condition1, $condition2, ... $conditionN);
844    
845  A file specification is the string passed to an C<open> call. It specifies the file  Return TRUE if all the conditions are true. This method can be used in conjunction with
846  mode and name. In a truly complex situation, it can specify a pipe sequence. This  the OR operator and the L</Confess> method as a debugging assert.
847  method assumes that the file name is whatever follows the first angle bracket  So, for example
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
   
     >>/usr/fig/myfile.txt  
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
   
 If the method cannot find a file name using its normal methods, it will return the  
 whole incoming string.  
   
 =over 4  
   
 =item fileSpec  
   
 File specification string from which the file name is to be extracted.  
   
 =item RETURN  
848    
849  Returns a three-element list. The first element contains the file name portion of      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
 the specified string, or the whole string if a file name cannot be found via normal  
 methods. The second element contains the start position of the file name portion and  
 the third element contains the length.  
850    
851  =back  Will abort the program with a stack trace if the value of C<$recNum> is negative.
852    
853  =cut  =cut
854  #: Return Type $;  sub Assert {
855  sub FindNamePart {      my $retVal = 1;
856      # Get the parameters.      LOOP: for my $condition (@_) {
857      my ($fileSpec) = @_;          if (! $condition) {
858      # Default to the whole input string.              $retVal = 0;
859      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);              last LOOP;
     # Parse out the file name if we can.  
     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {  
         $retVal = $2;  
         $len = length $retVal;  
         $pos = (length $fileSpec) - (length $3) - $len;  
860      }      }
861      # Return the result.      }
862      return ($retVal, $pos, $len);      return $retVal;
863  }  }
864    
865  =head3 OpenDir  =head3 Cluck
   
 C<< my @files = OpenDir($dirName, $filtered, $flag); >>  
   
 Open a directory and return all the file names. This function essentially performs  
 the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  
 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  
 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be  
 filtered out of the return list. If the directory does not open and I<$flag> is not  
 set, an exception is thrown. So, for example,  
   
     my @files = OpenDir("/Volumes/fig/contigs", 1);  
   
 is effectively the same as  
866    
867      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");      Cluck($message);
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
868    
869  Similarly, the following code  Trace the call stack. Note that for best results, you should qualify the call with a
870    trace condition. For example,
871    
872      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);      Cluck("Starting record parse.") if T(3);
873    
874  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  will only trace the stack if the trace level for the package is 3 or more.
 automatically returns an empty list if the directory fails to open.  
875    
876  =over 4  =over 4
877    
878  =item dirName  =item message
879    
880  Name of the directory to open.  Message to include in the trace.
881    
882  =item filtered  =back
883    
884  TRUE if files whose names begin with a period (C<.>) should be automatically removed  =cut
 from the list, else FALSE.  
885    
886  =item flag  sub Cluck {
887        # Get the parameters.
888        my ($message) = @_;
889        # Trace what's happening.
890        Trace("Stack trace for event: $message");
891        # Get the stack trace.
892        my @trace = LongMess();
893        # Convert the trace to a series of messages.
894        for my $line (@trace) {
895            # Replace the tab at the beginning with spaces.
896            $line =~ s/^\t/    /;
897            # Trace the line.
898            Trace($line);
899        }
900        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
901        Warn($message);
902    }
903    
904  TRUE if a failure to open is okay, else FALSE  =head3 LongMess
905    
906  =back      my @lines = Tracer::LongMess();
907    
908    Return a stack trace with all tracing methods removed. The return will be in the form of a list
909    of message strings.
910    
911  =cut  =cut
912  #: Return Type @;  
913  sub OpenDir {  sub LongMess {
     # Get the parameters.  
     my ($dirName, $filtered, $flag) = @_;  
914      # Declare the return variable.      # Declare the return variable.
915      my @retVal = ();      my @retVal = ();
916      # Open the directory.      my $confession = longmess("");
917      if (opendir(my $dirHandle, $dirName)) {      for my $line (split /\s*\n/, $confession) {
918          # The directory opened successfully. Get the appropriate list according to the          unless ($line =~ /Tracer\.pm/) {
919          # strictures of the filter parameter.              # Here we have a line worth keeping. Push it onto the result list.
920          if ($filtered) {              push @retVal, $line;
             @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;  
         } else {  
             @retVal = readdir $dirHandle;  
921          }          }
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
922      }      }
923      # Return the result.      # Return the result.
924      return @retVal;      return @retVal;
925  }  }
926    
927  =head3 SetLevel  =head3 ETracing
928    
929  C<< Tracer::SetLevel($newLevel); >>      ETracing($parameter);
930    
931  Modify the trace level. A higher trace level will cause more messages to appear.  Set up emergency tracing. Emergency tracing is tracing that is turned
932    on automatically for any program that calls this method. The emergency
933    tracing parameters are stored in a a file identified by a tracing key.
934    If this method is called with a CGI object, then the tracing key is
935    taken from a cookie. If it is called with no parameters, then the tracing
936    key is taken from an environment variable. If it is called with a string,
937    the tracing key is that string.
938    
939  =over 4  =over 4
940    
941  =item newLevel  =item parameter
942    
943  Proposed new trace level.  A parameter from which the tracing key is computed. If it is a scalar,
944    that scalar is used as the tracing key. If it is a CGI object, the
945    tracing key is taken from the C<IP> cookie. If it is omitted, the
946    tracing key is taken from the C<TRACING> environment variable. If it
947    is a CGI object and emergency tracing is not on, the C<Trace> and
948    C<TF> parameters will be used to determine the type of tracing.
949    
950  =back  =back
951    
952  =cut  =cut
953    
954  sub SetLevel {  sub ETracing {
955      $TraceLevel = $_[0];      # Get the parameter.
956        my ($parameter) = @_;
957        # Check for CGI mode.
958        if (defined $parameter && ref $parameter eq 'CGI') {
959            $SavedCGI = $parameter;
960        } else {
961            $SavedCGI = undef;
962        }
963        # Default to no tracing except errors.
964        my ($tracing, $dest) = ("0", "WARN");
965        # Check for emergency tracing.
966        my $tkey = EmergencyKey($parameter);
967        my $emergencyFile = EmergencyFileName($tkey);
968        if (-e $emergencyFile) {
969            # We have the file. Read in the data.
970            my @tracing = GetFile($emergencyFile);
971            # Pull off the time limit.
972            my $expire = shift @tracing;
973            # Convert it to seconds.
974            $expire *= 3600;
975            # Check the file data.
976            my $stat = stat($emergencyFile);
977            my ($now) = gettimeofday;
978            if ($now - $stat->mtime > $expire) {
979                # Delete the expired file.
980                unlink $emergencyFile;
981            } else {
982                # Emergency tracing is on. Pull off the destination and
983                # the trace level;
984                $dest = shift @tracing;
985                my $level = shift @tracing;
986                # Convert the destination to a real tracing destination.
987                # temp directory.
988                $dest = EmergencyTracingDest($tkey, $dest);
989                # Insure Tracer is specified.
990                my %moduleHash = map { $_ => 1 } @tracing;
991                $moduleHash{Tracer} = 1;
992                # Set the trace parameter.
993                $tracing = join(" ", $level, sort keys %moduleHash);
994            }
995        } elsif (defined $SavedCGI) {
996            # There's no emergency tracing, but we have a CGI object, so check
997            # for tracing from the form parameters.
998            if ($SavedCGI->param('Trace')) {
999                # Here the user has requested tracing via a form.
1000                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1001                $tracing = $SavedCGI->param('Trace') . " Tracer";
1002            }
1003        }
1004        # Setup the tracing we've determined from all the stuff above.
1005        TSetup($tracing, $dest);
1006        # Check to see if we're a web script.
1007        if (defined $SavedCGI) {
1008            # Yes we are. Trace the form and environment data.
1009            TraceParms($SavedCGI);
1010            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1011            # emitted by the script in its raw form.
1012            if (T(Raw => 3)) {
1013                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1014            }
1015        }
1016  }  }
1017    
1018  =head3 Now  =head3 EmergencyFileName
1019    
1020  C<< my $string = Tracer::Now(); >>      my $fileName = Tracer::EmergencyFileName($tkey);
1021    
1022  Return a displayable time stamp containing the local time.  Return the emergency tracing file name. This is the file that specifies
1023    the tracing information.
1024    
1025  =cut  =over 4
1026    
1027  sub Now {  =item tkey
     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 $retVal;  
 }  
1028    
1029  # Pad a number to 2 digits.  Tracing key for the current program.
1030  sub _p2 {  
1031      my ($value) = @_;  =item RETURN
1032      $value = "0$value" if ($value < 10);  
1033      return $value;  Returns the name of the file to contain the emergency tracing information.
1034    
1035    =back
1036    
1037    =cut
1038    
1039    sub EmergencyFileName {
1040        # Get the parameters.
1041        my ($tkey) = @_;
1042        # Compute the emergency tracing file name.
1043        return "$FIG_Config::temp/Emergency$tkey.txt";
1044  }  }
1045    
1046  =head3 LogErrors  =head3 EmergencyFileTarget
1047    
1048  C<< Tracer::LogErrors($fileName); >>      my $fileName = Tracer::EmergencyFileTarget($tkey);
1049    
1050  Route the standard error output to a log file.  Return the emergency tracing target file name. This is the file that receives
1051    the tracing output for file-based tracing.
1052    
1053  =over 4  =over 4
1054    
1055  =item fileName  =item tkey
1056    
1057  Name of the file to receive the error output.  Tracing key for the current program.
1058    
1059    =item RETURN
1060    
1061    Returns the name of the file to contain the trace output.
1062    
1063  =back  =back
1064    
1065  =cut  =cut
1066    
1067  sub LogErrors {  sub EmergencyFileTarget {
1068      # Get the file name.      # Get the parameters.
1069      my ($fileName) = @_;      my ($tkey) = @_;
1070      # Open the file as the standard error output.      # Compute the emergency tracing file name.
1071      open STDERR, '>', $fileName;      return "$FIG_Config::temp/trace$tkey.log";
1072  }  }
1073    
1074  =head3 ReadOptions  =head3 EmergencyTracingDest
1075    
1076  C<< my %options = Tracer::ReadOptions($fileName); >>      my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1077    
1078  Read a set of options from a file. Each option is encoded in a line of text that has the  This method converts an emergency tracing destination to a real
1079  format  tracing destination. The main difference is that if the
1080    destination is C<FILE> or C<APPEND>, we convert it to file
1081    output. If the destination is C<DUAL>, we convert it to file
1082    and standard output.
1083    
1084  I<optionName>C<=>I<optionValue>C<; >I<comment>  =over 4
1085    
1086  The option name must consist entirely of letters, digits, and the punctuation characters  =item tkey
 C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  
 character is a semi-colon will be ignored. The return hash will map each option name to  
 the corresponding option value.  
1087    
1088  =over 4  Tracing key for this environment.
1089    
1090  =item fileName  =item myDest
1091    
1092  Name of the file containing the option data.  Destination from the emergency tracing file.
1093    
1094  =item RETURN  =item RETURN
1095    
1096  Returns a hash mapping the option names specified in the file to their corresponding option  Returns a destination that can be passed into L</TSetup>.
 value.  
1097    
1098  =back  =back
1099    
1100  =cut  =cut
1101    
1102  sub ReadOptions {  sub EmergencyTracingDest {
1103      # Get the parameters.      # Get the parameters.
1104      my ($fileName) = @_;      my ($tkey, $myDest) = @_;
1105      # Open the file.      # Declare the return variable.
1106      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");      my $retVal = $myDest;
1107      # Count the number of records read.      # Process according to the destination value.
1108      my ($records, $comments) = 0;      if ($myDest eq 'FILE') {
1109      # Create the return hash.          $retVal = ">" . EmergencyFileTarget($tkey);
1110      my %retVal = ();      } elsif ($myDest eq 'APPEND') {
1111      # Loop through the file, accumulating key-value pairs.          $retVal = ">>" . EmergencyFileTarget($tkey);
1112      while (my $line = <CONFIGFILE>) {      } elsif ($myDest eq 'DUAL') {
1113          # Denote we've read a line.          $retVal = "+>" . EmergencyFileTarget($tkey);
1114          $records++;      } elsif ($myDest eq 'WARN') {
1115          # Determine the line type.          $retVal = "WARN";
         if ($line =~ /^\s*[\n\r]/) {  
             # A blank line is a comment.  
             $comments++;  
         } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {  
             # Here we have an option assignment.  
             retVal{$1} = $2;  
         } elsif ($line =~ /^\s*;/) {  
             # Here we have a text comment.  
             $comments++;  
         } else {  
             # Here we have an invalid line.  
             Trace("Invalid option statement in record $records.") if T(0);  
         }  
1116      }      }
1117      # Return the hash created.      # Return the result.
1118      return %retVal;      return $retVal;
1119  }  }
1120    
1121  =head3 GetOptions  =head3 Emergency
   
 C<< Tracer::GetOptions(\%defaults, \%options); >>  
1122    
1123  Merge a specified set of options into a table of defaults. This method takes two hash references      Emergency($key, $hours, $dest, $level, @modules);
 as input and uses the data from the second to update the first. If the second does not exist,  
 there will be no effect. An error will be thrown if one of the entries in the second hash does not  
 exist in the first.  
1124    
1125  Consider the following example.  Turn on emergency tracing. This method is normally invoked over the web from
1126    a debugging console, but it can also be called by the C<trace.pl> script.
1127    The caller specifies the duration of the emergency in hours, the desired tracing
1128    destination, the trace level, and a list of the trace modules to activate.
1129    For the length of the duration, when a program in an environment with the
1130    specified tracing key active invokes a Sprout CGI script, tracing will be
1131    turned on automatically. See L</TSetup> for more about tracing setup and
1132    L</ETracing> for more about emergency tracing.
1133    
1134  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  =over 4
1135    
1136  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  =item tkey
 B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  
 B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and  
 the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  
 will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  
1137    
1138  C<< {databaseType => 'Oracle'} >>  The tracing key. This is used to identify the control file and the trace file.
1139    
1140  an error will occur because the B<databaseType> option does not exist.  =item hours
1141    
1142  =over 4  Number of hours to keep emergency tracing alive.
1143    
1144  =item defaults  =item dest
1145    
1146  Table of default option values.  Tracing destination. If no path information is specified for a file
1147    destination, it is put in the FIG temporary directory.
1148    
1149  =item options  =item level
1150    
1151  Table of overrides, if any.  Tracing level. A higher level means more trace messages.
1152    
1153  =item RETURN  =item modules
1154    
1155  Returns a reference to the default table passed in as the first parameter.  A list of the tracing modules to activate.
1156    
1157  =back  =back
1158    
1159  =cut  =cut
1160    
1161  sub GetOptions {  sub Emergency {
1162      # Get the parameters.      # Get the parameters.
1163      my ($defaults, $options) = @_;      my ($tkey, $hours, $dest, $level, @modules) = @_;
1164      # Check for overrides.      # Create the emergency file.
1165      if ($options) {      my $specFile = EmergencyFileName($tkey);
1166          # Loop through the overrides.      my $outHandle = Open(undef, ">$specFile");
1167          while (my ($option, $setting) = each %{$options}) {      print $outHandle join("\n", $hours, $dest, $level, @modules, "");
             # Insure this override exists.  
             if (!exists $defaults->{$option}) {  
                 croak "Unrecognized option $option encountered.";  
             } else {  
                 # Apply the override.  
                 $defaults->{$option} = $setting;  
             }  
         }  
     }  
     # Return the merged table.  
     return $defaults;  
1168  }  }
1169    
1170  =head3 MergeOptions  =head3 EmergencyKey
1171    
1172  C<< Tracer::MergeOptions(\%table, \%defaults); >>      my $tkey = EmergencyKey($parameter);
1173    
1174  Merge default values into a hash table. This method looks at the key-value pairs in the  Return the Key to be used for emergency tracing. This could be an IP address,
1175  second (default) hash, and if a matching key is not found in the first hash, the default   a session ID, or a user name, depending on the environment.
 pair is copied in. The process is similar to L</GetOptions>, but there is no error-  
 checking and no return value.  
1176    
1177  =over 4  =over 4
1178    
1179  =item table  =item parameter
1180    
1181  Hash table to be updated with the default values.  Parameter defining the method for finding the tracing key. If it is a scalar,
1182    then it is presumed to be the tracing key itself. If it is a CGI object, then
1183    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1184    taken from the C<TRACING> environment variable.
1185    
1186  =item defaults  =item RETURN
1187    
1188  Default values to be merged into the first hash table if they are not already present.  Returns the key to be used for labels in emergency tracing.
1189    
1190  =back  =back
1191    
1192  =cut  =cut
1193    
1194  sub MergeOptions {  sub EmergencyKey {
1195      # Get the parameters.      # Get the parameters.
1196      my ($table, $defaults) = @_;      my ($parameter) = @_;
1197      # Loop through the defaults.      # Declare the return variable.
1198      while (my ($key, $value) = each %{$defaults}) {      my $retVal;
1199          if (!exists $table->{$key}) {      # Determine the parameter type.
1200              $table->{$key} = $value;      if (! defined $parameter) {
1201            # Here we're supposed to check the environment. If that fails, we
1202            # get the effective login ID.
1203            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1204        } else {
1205            my $ptype = ref $parameter;
1206            if ($ptype eq 'CGI') {
1207                # Here we were invoked from a web page. Look for a cookie.
1208                $retVal = $parameter->cookie('IP');
1209            } elsif (! $ptype) {
1210                # Here the key was passed in.
1211                $retVal = $parameter;
1212          }          }
1213      }      }
1214        # If no luck finding a key, use the PID.
1215        if (! defined $retVal) {
1216            $retVal = $$;
1217        }
1218        # Return the result.
1219        return $retVal;
1220  }  }
1221    
 =head3 Trace  
1222    
1223  C<< Trace($message); >>  =head3 TraceParms
1224    
1225  Write a trace message to the target location specified in L</TSetup>. If there has not been      Tracer::TraceParms($cgi);
1226  any prior call to B<TSetup>.  
1227    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1228    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1229    
1230  =over 4  =over 4
1231    
1232  =item message  =item cgi
1233    
1234  Message to write.  CGI query object containing the parameters to trace.
1235    
1236  =back  =back
1237    
1238  =cut  =cut
1239    
1240  sub Trace {  sub TraceParms {
1241      # Get the parameters.      # Get the parameters.
1242      my ($message) = @_;      my ($cgi) = @_;
1243      # Get the timestamp.      if (T(CGI => 2)) {
1244      my $timeStamp = Now();          # Here we trace the GET-style URL for the script.
1245      # Format the message. Note we strip off any line terminators at the end.          Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1246      my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);      }
1247      # Process according to the destination.      if (T(CGI => 3)) {
1248      if ($Destination eq "TEXT") {          # Here we want to trace the parameter data.
1249          # Write the message to the standard output.          my @names = $cgi->param;
1250          print "$formatted\n";          for my $parmName (sort @names) {
1251      } elsif ($Destination eq "ERROR") {              # Note we skip the Trace parameters, which are for our use only.
1252          # Write the message to the error output.              if ($parmName ne 'Trace' && $parmName ne 'TF') {
1253          print STDERR "$formatted\n";                  my @values = $cgi->param($parmName);
1254      } elsif ($Destination eq "QUEUE") {                  Trace("[CGI] $parmName = " . join(", ", @values));
1255          # Push the message into the queue.              }
1256          push @Queue, "$formatted";          }
1257      } elsif ($Destination eq "HTML") {          # Display the request method.
1258          # Convert the message to HTML and write it to the standard output.          my $method = $cgi->request_method();
1259          my $escapedMessage = CGI::escapeHTML($message);          Trace("Method: $method");
1260          print "<p>$formatted</p>\n";      }
1261      } elsif ($Destination eq "WARN") {      if (T(CGI => 4)) {
1262         # Emit the message as a warning.          # Here we want the environment data too.
1263         warn $message;          for my $envName (sort keys %ENV) {
1264      } elsif ($Destination =~ m/^>>/) {              Trace("[ENV] $envName = $ENV{$envName}");
         # Write the trace message to an output file.  
         (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";  
         print TRACING "$formatted\n";  
         close TRACING;  
         # If the Tee flag is on, echo it to the standard output.  
         if ($TeeFlag) {  
             print "$formatted\n";  
1265          }          }
1266      }      }
1267  }  }
1268    
1269  =head3 T  =head3 TraceImages
   
 C<< my $switch = T($category, $traceLevel); >>  
   
     or  
1270    
1271  C<< my $switch = T($traceLevel); >>      Tracer::TraceImages($htmlString);
1272    
1273  Return TRUE if the trace level is at or above a specified value and the specified category  Trace information about all of an html document's images. The tracing
1274  is active, else FALSE. If no category is specified, the caller's package name is used.  will be for type "IMG" at level 3. The image's source string
1275    will be displayed. This is generally either the URL of the image or
1276    raw data for the image itself. If the source is too long, only the first 300
1277    characters will be shown at trace level 3. The entire source will be shown,
1278    however, at trace level 4. This method is not very smart, and might catch
1279    Javascript code, but it is still useful when debugging the arcane
1280    behavior of images in multiple browser environments.
1281    
1282  =over 4  =over 4
1283    
1284  =item category  =item htmlString
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
   
 Relevant tracing level.  
   
 =item RETURN  
1285    
1286  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  HTML text for an outgoing web page.
1287    
1288  =back  =back
1289    
1290  =cut  =cut
1291    
1292  sub T {  sub TraceImages {
1293      # Declare the return variable.      # Only proceed if we're at the proper trace level.
1294      my $retVal = 0;      if (T(IMG => 3)) {
1295      # Only proceed if tracing is turned on.          # For performance reasons we're manipulating $_[0] instead of retrieving the string
1296      if ($Destination ne "NONE") {          # into a variable called "$htmlString". This is because we expect html strings to be
1297          # Get the parameters.          # long, and don't want to copy them any more than we have to.
1298          my ($category, $traceLevel) = @_;          Trace(length($_[0]) . " characters in web page.");
1299          if (!defined $traceLevel) {          # Loop through the HTML, culling image tags.
1300              # Here we have no category, so we need to get the calling package.          while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1301              # The calling package is normally the first parameter. If it is              # Extract the source string and determine whether or not it's too long.
1302              # omitted, the first parameter will be the tracelevel. So, the              my $srcString = $1;
1303              # first thing we do is shift the so-called category into the              my $pos = pos($_[0]) - length($srcString);
1304              # $traceLevel variable where it belongs.              my $excess = length($srcString) - 300;
1305              $traceLevel = $category;              # We'll put the display string in here.
1306              my ($package, $fileName, $line) = caller;              my $srcDisplay = $srcString;
1307              # If there is no calling package, we default to "main".              # If it's a data string, split it at the comma.
1308              if (!$package) {              $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1309                  $category = "main";              # If there's no excess or we're at trace level 4, we're done. At level 3 with
1310              } else {              # a long string, however, we only show the first 300 characters.
1311                  $category = $package;              if ($excess > 0 && ! T(IMG => 4)) {
1312                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1313              }              }
1314                # Output the trace message.
1315                Trace("Image tag at position $pos:\n$srcDisplay");
1316          }          }
         # 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.");  
         }  
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
1317      }      }
     # Return the computed result.  
     return $retVal;  
1318  }  }
1319    
1320  =head3 ParseCommand  =head2 Command-Line Utility Methods
1321    
1322  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  =head3 SendSMS
1323    
1324  Parse a command line consisting of a list of parameters. The initial parameters may be option      my $msgID = Tracer::SendSMS($phoneNumber, $msg);
 specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  
 off and merged into a table of default options. The remainder of the command line is  
 returned as a list of positional arguments. For example, consider the following invocation.  
1325    
1326  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1327    user name, password, and API ID for the relevant account in the hash reference variable
1328    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1329    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1330    is C<2561022>, then the FIG_Config file must contain
1331    
1332  In this case, the list @words will be treated as a command line. There are two options available,      $phone =  { user => 'BruceTheHumanPet',
1333  B<errors> and B<logFile>. If @words has the following format                  password => 'silly',
1334                    api_id => '2561022' };
1335    
1336  C<< -logFile=error.log apple orange rutabaga >>  The original purpose of this method was to insure Bruce would be notified immediately when the
1337    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1338    when you call this method.
1339    
1340  then at the end of the invocation, C<$options> will be  The message ID will be returned if successful, and C<undef> if an error occurs.
   
 C<< { errors => 0, logFile => 'error.log' } >>  
   
 and C<@arguments> will contain  
   
 C<< apple orange rutabaga >>  
   
 The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  
 support for quote characters.  
1341    
1342  =over 4  =over 4
1343    
1344  =item optionTable  =item phoneNumber
1345    
1346  Table of default options.  Phone number to receive the message, in international format. A United States phone number
1347    would be prefixed by "1". A British phone number would be prefixed by "44".
1348    
1349  =item inputList  =item msg
1350    
1351  List of words on the command line.  Message to send to the specified phone.
1352    
1353  =item RETURN  =item RETURN
1354    
1355  Returns a reference to the option table and a list of the positional arguments.  Returns the message ID if successful, and C<undef> if the message could not be sent.
1356    
1357  =back  =back
1358    
1359  =cut  =cut
1360    
1361  sub ParseCommand {  sub SendSMS {
1362      # Get the parameters.      # Get the parameters.
1363      my ($optionTable, @inputList) = @_;      my ($phoneNumber, $msg) = @_;
1364      # Process any options in the input list.      # Declare the return variable. If we do not change it, C<undef> will be returned.
1365      my %overrides = ();      my $retVal;
1366      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      # Only proceed if we have phone support.
1367          # Get the current option.      if (! defined $FIG_Config::phone) {
1368          my $arg = shift @inputList;          Trace("Phone support not present in FIG_Config.") if T(1);
         # Pull out the option name.  
         $arg =~ /^-([^=]*)/g;  
         my $name = $1;  
         # Check for an option value.  
         if ($arg =~ /\G=(.*)$/g) {  
             # Here we have a value for the option.  
             $overrides{$name} = UnEscape($1);  
1369          } else {          } else {
1370              # Here there is no value, so we use 1.          # Get the phone data.
1371              $overrides{$name} = 1;          my $parms = $FIG_Config::phone;
1372            # Get the Clickatell URL.
1373            my $url = "http://api.clickatell.com/http/";
1374            # Create the user agent.
1375            my $ua = LWP::UserAgent->new;
1376            # Request a Clickatell session.
1377            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1378                                         password => $parms->{password},
1379                                         api_id => $parms->{api_id},
1380                                         to => $phoneNumber,
1381                                         text => $msg});
1382            # Check for an error.
1383            if (! $resp->is_success) {
1384                Trace("Alert failed.") if T(1);
1385            } else {
1386                # Get the message ID.
1387                my $rstring = $resp->content;
1388                if ($rstring =~ /^ID:\s+(.*)$/) {
1389                    $retVal = $1;
1390                } else {
1391                    Trace("Phone attempt failed with $rstring") if T(1);
1392          }          }
1393      }      }
     # Merge the options into the defaults.  
     GetOptions($optionTable, \%overrides);  
     # Translate the remaining parameters.  
     my @retVal = ();  
     for my $inputParm (@inputList) {  
         push @retVal, UnEscape($inputParm);  
1394      }      }
1395      # Return the results.      # Return the result.
1396      return ($optionTable, @retVal);      return $retVal;
1397  }  }
1398    
1399  =head3 Escape  =head3 StandardSetup
1400    
1401  C<< my $codedString = Tracer::Escape($realString); >>      my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1402    
1403  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  This method performs standard command-line parsing and tracing setup. The return
1404  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  values are a hash of the command-line options and a list of the positional
1405  result is to reverse the effect of L</UnEscape>.  parameters. Tracing is automatically set up and the command-line options are
1406    validated.
1407    
1408    This is a complex method that does a lot of grunt work. The parameters can
1409    be more easily understood, however, once they are examined individually.
1410    
1411    The I<categories> parameter is the most obtuse. It is a reference to a list of
1412    special-purpose tracing categories. Most tracing categories are PERL package
1413    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1414    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1415    
1416        ["Sprout", "SproutLoad", "ERDB"]
1417    
1418    This would cause trace messages in the specified three packages to appear in
1419    the output. There are two special tracing categories that are automatically
1420    handled by this method. In other words, if you used L</TSetup> you would need
1421    to include these categories manually, but if you use this method they are turned
1422    on automatically.
1423    
1424  =over 4  =over 4
1425    
1426  =item realString  =item SQL
1427    
1428  String to escape.  Traces SQL commands and activity.
1429    
1430    =item Tracer
1431    
1432    Traces error messages and call stacks.
1433    
1434    =back
1435    
1436    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1437    The trace level is specified using the C<-trace> command-line option. For example,
1438    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1439    all tracing at level 3.
1440    
1441        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1442    
1443    Standard tracing is output to the standard output and echoed to the file
1444    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1445    process ID. You can also specify the C<user> parameter to put a user ID
1446    instead of a process ID in the trace file name. So, for example
1447    
1448    The default trace level is 2. To get all messages, specify a trace level of 4.
1449    For a genome-by-genome update, use 3.
1450    
1451        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1452    
1453    would send the trace output to C<traceBruce.log> in the temporary directory.
1454    
1455    The I<options> parameter is a reference to a hash containing the command-line
1456    options, their default values, and an explanation of what they mean. Command-line
1457    options may be in the form of switches or keywords. In the case of a switch, the
1458    option value is 1 if it is specified and 0 if it is not specified. In the case
1459    of a keyword, the value is separated from the option name by an equal sign. You
1460    can see this last in the command-line example above.
1461    
1462    You can specify a different default trace level by setting C<$options->{trace}>
1463    prior to calling this method.
1464    
1465    An example at this point would help. Consider, for example, the command-line utility
1466    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1467    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1468    the following code.
1469    
1470        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1471                            { safe => [0, "use database transactions"],
1472                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1473                              start => [' ', "start with this genome"],
1474                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1475                            "<command> <transactionDirectory> <IDfile>",
1476                          @ARGV);
1477    
1478    
1479    The call to C<ParseCommand> specifies the default values for the options and
1480    stores the actual options in a hash that is returned as C<$options>. The
1481    positional parameters are returned in C<@parameters>.
1482    
1483    The following is a sample command line for C<TransactFeatures>.
1484    
1485        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1486    
1487    Single and double hyphens are equivalent. So, you could also code the
1488    above command as
1489    
1490        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1491    
1492    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1493    parameters, and would find themselves in I<@parameters> after executing the
1494    above code fragment. The tracing would be set to level 2, and the categories
1495    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1496    and C<DocUtils> was included because it came in within the first parameter
1497    to this method. The I<$options> hash would be
1498    
1499        { trace => 2, sql => 0, safe => 0,
1500          noAlias => 1, start => ' ', tblFiles => 0 }
1501    
1502    Use of C<StandardSetup> in this way provides a simple way of performing
1503    standard tracing setup and command-line parsing. Note that the caller is
1504    not even aware of the command-line switches C<-trace> and C<-sql>, which
1505    are used by this method to control the tracing. If additional tracing features
1506    need to be added in the future, they can be processed by this method without
1507    upsetting the command-line utilities.
1508    
1509    If the C<background> option is specified on the command line, then the
1510    standard and error outputs will be directed to files in the temporary
1511    directory, using the same suffix as the trace file. So, if the command
1512    line specified
1513    
1514        -user=Bruce -background
1515    
1516    then the trace output would go to C<traceBruce.log>, the standard output to
1517    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1518    simplify starting a command in the background.
1519    
1520    The user name is also used as the tracing key for L</Emergency Tracing>.
1521    Specifying a value of C<E> for the trace level causes emergency tracing to
1522    be used instead of custom tracing. If the user name is not specified,
1523    the tracing key is taken from the C<Tracing> environment variable. If there
1524    is no value for that variable, the tracing key will be computed from the active
1525    login ID.
1526    
1527    Since the default situation in StandardSetup is to trace to the standard
1528    output, errors that occur in command-line scripts will not generate
1529    RSS events. To force the events, use the C<warn> option.
1530    
1531        TransactFeatures -background -warn register ../xacts IDs.tbl
1532    
1533    Finally, if the special option C<-help> is specified, the option
1534    names will be traced at level 0 and the program will exit without processing.
1535    This provides a limited help capability. For example, if the user enters
1536    
1537        TransactFeatures -help
1538    
1539    he would see the following output.
1540    
1541        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1542            -trace    tracing level (default E)
1543            -sql      trace SQL commands
1544            -safe     use database transactions
1545            -noAlias  do not expect aliases in CHANGE transactions
1546            -start    start with this genome
1547            -tblFiles output TBL files containing the corrected IDs
1548    
1549    The caller has the option of modifying the tracing scheme by placing a value
1550    for C<trace> in the incoming options hash. The default value can be overridden,
1551    or the tracing to the standard output can be turned off by suffixing a minus
1552    sign to the trace level. So, for example,
1553    
1554        { trace => [0, "tracing level (default 0)"],
1555           ...
1556    
1557    would set the default trace level to 0 instead of E, while
1558    
1559        { trace => ["2-", "tracing level (default 2)"],
1560           ...
1561    
1562    would set the default to 2, but trace only to the log file, not to the
1563    standard output.
1564    
1565    The parameters to this method are as follows.
1566    
1567    =over 4
1568    
1569    =item categories
1570    
1571    Reference to a list of tracing category names. These should be names of
1572    packages whose internal workings will need to be debugged to get the
1573    command working.
1574    
1575    =item options
1576    
1577    Reference to a hash containing the legal options for the current command mapped
1578    to their default values and descriptions. The user can override the defaults
1579    by specifying the options as command-line switches prefixed by a hyphen.
1580    Tracing-related options may be added to this hash. If the C<-h> option is
1581    specified on the command line, the option descriptions will be used to
1582    explain the options. To turn off tracing to the standard output, add a
1583    minus sign to the value for C<trace> (see above).
1584    
1585    =item parmHelp
1586    
1587    A string that vaguely describes the positional parameters. This is used
1588    if the user specifies the C<-h> option.
1589    
1590    =item argv
1591    
1592    List of command line parameters, including the option switches, which must
1593    precede the positional parameters and be prefixed by a hyphen.
1594    
1595  =item RETURN  =item RETURN
1596    
1597  Escaped equivalent of the real string.  Returns a list. The first element of the list is the reference to a hash that
1598    maps the command-line option switches to their values. These will either be the
1599    default values or overrides specified on the command line. The remaining
1600    elements of the list are the position parameters, in order.
1601    
1602  =back  =back
1603    
1604  =cut  =cut
1605    
1606  sub Escape {  sub StandardSetup {
1607      # Get the parameter.      # Get the parameters.
1608      my ($realString) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
1609      # Initialize the return variable.      # Get the default tracing key.
1610      my $retVal = "";      my $tkey = EmergencyKey();
1611      # Loop through the parameter string, looking for sequences to escape.      # Save the command line.
1612      while (length $realString > 0) {      $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1613          # Look for the first sequence to escape.      # Add the tracing options.
1614          if ($realString =~ /^(.*?)([\n\t\r\\])/) {      if (! exists $options->{trace}) {
1615              # Here we found it. The text preceding the sequence is in $1. The sequence          $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
             # 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;  
1616              }              }
1617        $options->{sql} = [0, "turn on SQL tracing"];
1618        $options->{help} = [0, "display command-line options"];
1619        $options->{user} = [$tkey, "tracing key"];
1620        $options->{background} = [0, "spool standard and error output"];
1621        $options->{warn} = [0, "send errors to RSS feed"];
1622        # Create a parsing hash from the options hash. The parsing hash
1623        # contains the default values rather than the default value
1624        # and the description. While we're at it, we'll memorize the
1625        # length of the longest option name.
1626        my $longestName = 0;
1627        my %parseOptions = ();
1628        for my $key (keys %{$options}) {
1629            if (length $key > $longestName) {
1630                $longestName = length $key;
1631            }
1632            $parseOptions{$key} = $options->{$key}->[0];
1633        }
1634        # Parse the command line.
1635        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1636        # Get the logfile suffix.
1637        my $suffix = $retOptions->{user};
1638        # Check for background mode.
1639        if ($retOptions->{background}) {
1640            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1641            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1642            open STDOUT, ">$outFileName";
1643            open STDERR, ">$errFileName";
1644            # Check for phone support. If we have phone support and a phone number,
1645            # we want to turn it on.
1646            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1647                $retOptions->{phone} = $ENV{PHONE};
1648            }
1649        }
1650        # Now we want to set up tracing. First, we need to know if the user
1651        # wants emergency tracing.
1652        if ($retOptions->{trace} eq 'E') {
1653            ETracing($retOptions->{user});
1654          } else {          } else {
1655              # Here there are no more escape sequences. The rest of the string is          # Here the tracing is controlled from the command line.
1656              # transferred unmodified.          my @cats = @{$categories};
1657              $retVal .= $realString;          if ($retOptions->{sql}) {
1658              $realString = "";              push @cats, "SQL";
1659          }          }
1660            if ($retOptions->{warn}) {
1661                push @cats, "Feed";
1662      }      }
1663      # Return the result.          # Add the default categories.
1664      return $retVal;          push @cats, "Tracer";
1665            # Next, we create the category string by joining the categories.
1666            my $cats = join(" ", @cats);
1667            # Check to determine whether or not the caller wants to turn off tracing
1668            # to the standard output.
1669            my $traceLevel = $retOptions->{trace};
1670            my $textOKFlag = 1;
1671            if ($traceLevel =~ /^(.)-/) {
1672                $traceLevel = $1;
1673                $textOKFlag = 0;
1674            }
1675            # Now we set up the trace mode.
1676            my $traceMode;
1677            # Verify that we can open a file in the FIG temporary directory.
1678            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1679            if (open TESTTRACE, ">$traceFileName") {
1680                # Here we can trace to a file.
1681                $traceMode = ">$traceFileName";
1682                if ($textOKFlag) {
1683                    # Echo to standard output if the text-OK flag is set.
1684                    $traceMode = "+$traceMode";
1685                }
1686                # Close the test file.
1687                close TESTTRACE;
1688            } else {
1689                # Here we can't trace to a file. Complain about this.
1690                warn "Could not open trace file $traceFileName: $!\n";
1691                # We trace to the standard output if it's
1692                # okay, and the error log otherwise.
1693                if ($textOKFlag) {
1694                    $traceMode = "TEXT";
1695                } else {
1696                    $traceMode = "WARN";
1697                }
1698            }
1699            # Now set up the tracing.
1700            TSetup("$traceLevel $cats", $traceMode);
1701        }
1702        # Check for the "help" option. If it is specified, dump the command-line
1703        # options and exit the program.
1704        if ($retOptions->{help}) {
1705            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1706            print "$1 [options] $parmHelp\n";
1707            for my $key (sort keys %{$options}) {
1708                my $name = Pad($key, $longestName, 0, ' ');
1709                my $desc = $options->{$key}->[1];
1710                if ($options->{$key}->[0]) {
1711                    $desc .= " (default " . $options->{$key}->[0] . ")";
1712                }
1713                print "  $name $desc\n";
1714            }
1715            exit(0);
1716        }
1717        # Trace the options, if applicable.
1718        if (T(3)) {
1719            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1720            Trace("Selected options: " . join(", ", sort @parms) . ".");
1721        }
1722        # Return the parsed parameters.
1723        return ($retOptions, @retParameters);
1724  }  }
1725    
1726  =head3 UnEscape  =head3 ReadOptions
1727    
1728  C<< my $realString = Tracer::UnEscape($codedString); >>      my %options = Tracer::ReadOptions($fileName);
1729    
1730  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Read a set of options from a file. Each option is encoded in a line of text that has the
1731  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  format
1732  be deleted.  
1733    I<optionName>C<=>I<optionValue>C<; >I<comment>
1734    
1735    The option name must consist entirely of letters, digits, and the punctuation characters
1736    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1737    character is a semi-colon will be ignored. The return hash will map each option name to
1738    the corresponding option value.
1739    
1740  =over 4  =over 4
1741    
1742  =item codedString  =item fileName
1743    
1744  String to un-escape.  Name of the file containing the option data.
1745    
1746  =item RETURN  =item RETURN
1747    
1748  Returns a copy of the original string with the escape sequences converted to their actual  Returns a hash mapping the option names specified in the file to their corresponding option
1749  values.  value.
1750    
1751  =back  =back
1752    
1753  =cut  =cut
1754    
1755  sub UnEscape {  sub ReadOptions {
1756      # Get the parameter.      # Get the parameters.
1757      my ($codedString) = @_;      my ($fileName) = @_;
1758      # Initialize the return variable.      # Open the file.
1759      my $retVal = "";      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1760      # Only proceed if the incoming string is nonempty.      # Count the number of records read.
1761      if (defined $codedString) {      my ($records, $comments) = 0;
1762          # Loop through the parameter string, looking for escape sequences. We can't do      # Create the return hash.
1763          # translating because it causes problems with the escaped slash. ("\\t" becomes      my %retVal = ();
1764          # "\<tab>" no matter what we do.)      # Loop through the file, accumulating key-value pairs.
1765          while (length $codedString > 0) {      while (my $line = <CONFIGFILE>) {
1766              # Look for the first escape sequence.          # Denote we've read a line.
1767              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {          $records++;
1768                  # Here we found it. The text preceding the sequence is in $1. The sequence          # Determine the line type.
1769                  # itself is in $2. First, move the clear text to the return variable.          if ($line =~ /^\s*[\n\r]/) {
1770                  $retVal .= $1;              # A blank line is a comment.
1771                  $codedString = substr $codedString, (2 + length $1);              $comments++;
1772                  # Get the escape value.          } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1773                  my $char = $2;              # Here we have an option assignment.
1774                  # If we have a "\r", we are done.              retVal{$1} = $2;
1775                  if ($char ne 'r') {          } elsif ($line =~ /^\s*;/) {
1776                      # Here it's not an 'r', so we convert it.              # Here we have a text comment.
1777                      $char =~ tr/\\tn/\\\t\n/;              $comments++;
                     $retVal .= $char;  
                 }  
1778              } else {              } else {
1779                  # Here there are no more escape sequences. The rest of the string is              # Here we have an invalid line.
1780                  # transferred unmodified.              Trace("Invalid option statement in record $records.") if T(0);
                 $retVal .= $codedString;  
                 $codedString = "";  
             }  
1781          }          }
1782      }      }
1783      # Return the result.      # Return the hash created.
1784      return $retVal;      return %retVal;
1785  }  }
1786    
1787  =head3 ParseRecord  =head3 GetOptions
1788    
1789        Tracer::GetOptions(\%defaults, \%options);
1790    
1791    Merge a specified set of options into a table of defaults. This method takes two hash references
1792    as input and uses the data from the second to update the first. If the second does not exist,
1793    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1794    exist in the first.
1795    
1796    Consider the following example.
1797    
1798        my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1799    
1800  C<< my @fields = Tracer::ParseRecord($line); >>  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1801    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1802    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1803    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1804    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1805    
1806  Parse a tab-delimited data line. The data line is split into field values. Embedded tab      {databaseType => 'Oracle'}
1807  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
1808  These will automatically be converted.  an error will occur because the B<databaseType> option does not exist.
1809    
1810  =over 4  =over 4
1811    
1812  =item line  =item defaults
1813    
1814  Line of data containing the tab-delimited fields.  Table of default option values.
1815    
1816    =item options
1817    
1818    Table of overrides, if any.
1819    
1820  =item RETURN  =item RETURN
1821    
1822  Returns a list of the fields found in the data line.  Returns a reference to the default table passed in as the first parameter.
1823    
1824  =back  =back
1825    
1826  =cut  =cut
1827    
1828  sub ParseRecord {  sub GetOptions {
1829      # Get the parameter.      # Get the parameters.
1830      my ($line) = @_;      my ($defaults, $options) = @_;
1831      # Remove the trailing new-line, if any.      # Check for overrides.
1832      chomp $line;      if ($options) {
1833      # Split the line read into pieces using the tab character.          # Loop through the overrides.
1834      my @retVal = split /\t/, $line;          while (my ($option, $setting) = each %{$options}) {
1835      # Trim and fix the escapes in each piece.              # Insure this override exists.
1836      for my $value (@retVal) {              if (!exists $defaults->{$option}) {
1837          # Trim leading whitespace.                  croak "Unrecognized option $option encountered.";
1838          $value =~ s/^\s+//;              } else {
1839          # Trim trailing whitespace.                  # Apply the override.
1840          $value =~ s/\s+$//;                  $defaults->{$option} = $setting;
1841          # 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;  
1842      }      }
1843      # Return the result.      }
1844      return @retVal;      # Return the merged table.
1845        return $defaults;
1846  }  }
1847    
1848  =head3 Merge  =head3 MergeOptions
1849    
1850  C<< my @mergedList = Tracer::Merge(@inputList); >>      Tracer::MergeOptions(\%table, \%defaults);
1851    
1852  Sort a list of strings and remove duplicates.  Merge default values into a hash table. This method looks at the key-value pairs in the
1853    second (default) hash, and if a matching key is not found in the first hash, the default
1854    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1855    checking and no return value.
1856    
1857  =over 4  =over 4
1858    
1859  =item inputList  =item table
1860    
1861  List of scalars to sort and merge.  Hash table to be updated with the default values.
1862    
1863  =item RETURN  =item defaults
1864    
1865  Returns a list containing the same elements sorted in ascending order with duplicates  Default values to be merged into the first hash table if they are not already present.
 removed.  
1866    
1867  =back  =back
1868    
1869  =cut  =cut
1870    
1871  sub Merge {  sub MergeOptions {
1872      # Get the input list in sort order.      # Get the parameters.
1873      my @inputList = sort @_;      my ($table, $defaults) = @_;
1874      # Only proceed if the list has at least two elements.      # Loop through the defaults.
1875      if (@inputList > 1) {      while (my ($key, $value) = each %{$defaults}) {
1876          # Now we want to move through the list splicing out duplicates.          if (!exists $table->{$key}) {
1877          my $i = 0;              $table->{$key} = $value;
         while ($i < @inputList) {  
             # Get the current entry.  
             my $thisEntry = $inputList[$i];  
             # Find out how many elements duplicate the current entry.  
             my $j = $i + 1;  
             my $dup1 = $i + 1;  
             while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };  
             # If the number is nonzero, splice out the duplicates found.  
             if ($j > $dup1) {  
                 splice @inputList, $dup1, $j - $dup1;  
             }  
             # Now the element at position $dup1 is different from the element before it  
             # at position $i. We push $i forward one position and start again.  
             $i++;  
1878          }          }
1879      }      }
     # Return the merged list.  
     return @inputList;  
1880  }  }
1881    
1882  =head3 Percent  =head3 ParseCommand
1883    
1884  C<< my $percent = Tracer::Percent($number, $base); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1885    
1886  Returns the percent of the base represented by the given number. If the base  Parse a command line consisting of a list of parameters. The initial parameters may be option
1887  is zero, returns zero.  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1888    off and merged into a table of default options. The remainder of the command line is
1889    returned as a list of positional arguments. For example, consider the following invocation.
1890    
1891        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1892    
1893    In this case, the list @words will be treated as a command line and there are two options available,
1894    B<errors> and B<logFile>. If @words has the following format
1895    
1896        -logFile=error.log apple orange rutabaga
1897    
1898    then at the end of the invocation, C<$options> will be
1899    
1900        { errors => 0, logFile => 'error.log' }
1901    
1902    and C<@arguments> will contain
1903    
1904        apple orange rutabaga
1905    
1906    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1907    support for quote characters. Options can be specified with single or double hyphens.
1908    
1909  =over 4  =over 4
1910    
1911  =item number  =item optionTable
1912    
1913  Percent numerator.  Table of default options.
1914    
1915  =item base  =item inputList
1916    
1917  Percent base.  List of words on the command line.
1918    
1919  =item RETURN  =item RETURN
1920    
1921  Returns the percentage of the base represented by the numerator.  Returns a reference to the option table and a list of the positional arguments.
1922    
1923  =back  =back
1924    
1925  =cut  =cut
1926    
1927  sub Percent {  sub ParseCommand {
1928      # Get the parameters.      # Get the parameters.
1929      my ($number, $base) = @_;      my ($optionTable, @inputList) = @_;
1930      # Declare the return variable.      # Process any options in the input list.
1931      my $retVal = 0;      my %overrides = ();
1932      # Compute the percent.      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1933      if ($base != 0) {          # Get the current option.
1934          $retVal = $number * 100 / $base;          my $arg = shift @inputList;
1935            # Pull out the option name.
1936            $arg =~ /^--?([^=]*)/g;
1937            my $name = $1;
1938            # Check for an option value.
1939            if ($arg =~ /\G=(.*)$/g) {
1940                # Here we have a value for the option.
1941                $overrides{$name} = UnEscape($1);
1942            } else {
1943                # Here there is no value, so we use 1.
1944                $overrides{$name} = 1;
1945      }      }
     # Return the result.  
     return $retVal;  
1946  }  }
1947        # Merge the options into the defaults.
1948        GetOptions($optionTable, \%overrides);
1949        # Translate the remaining parameters.
1950        my @retVal = ();
1951        for my $inputParm (@inputList) {
1952            push @retVal, UnEscape($inputParm);
1953        }
1954        # Return the results.
1955        return ($optionTable, @retVal);
1956    }
1957    
1958    
1959    =head2 File Utility Methods
1960    
1961  =head3 GetFile  =head3 GetFile
1962    
1963  C<< my @fileContents = Tracer::GetFile($fileName); >>      my @fileContents = Tracer::GetFile($fileName);
1964    
1965      or      or
1966    
1967  C<< my $fileContents = Tracer::GetFile($fileName); >>      my $fileContents = Tracer::GetFile($fileName);
1968    
1969  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
1970  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 1598  Line 2003 
2003      # Close it.      # Close it.
2004      close $handle;      close $handle;
2005      my $actualLines = @retVal;      my $actualLines = @retVal;
2006        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2007      # Return the file's contents in the desired format.      # Return the file's contents in the desired format.
2008      if (wantarray) {      if (wantarray) {
2009          return @retVal;          return @retVal;
# Line 1608  Line 2014 
2014    
2015  =head3 PutFile  =head3 PutFile
2016    
2017  C<< Tracer::PutFile($fileName, \@lines); >>      Tracer::PutFile($fileName, \@lines);
2018    
2019  Write out a file from a list of lines of text.  Write out a file from a list of lines of text.
2020    
# Line 1633  Line 2039 
2039      my ($fileName, $lines) = @_;      my ($fileName, $lines) = @_;
2040      # Open the output file.      # Open the output file.
2041      my $handle = Open(undef, ">$fileName");      my $handle = Open(undef, ">$fileName");
2042        # Count the lines written.
2043      if (ref $lines ne 'ARRAY') {      if (ref $lines ne 'ARRAY') {
2044          # Here we have a scalar, so we write it raw.          # Here we have a scalar, so we write it raw.
2045          print $handle $lines;          print $handle $lines;
2046            Trace("Scalar put to file $fileName.") if T(File => 3);
2047      } else {      } else {
2048          # Write the lines one at a time.          # Write the lines one at a time.
2049            my $count = 0;
2050          for my $line (@{$lines}) {          for my $line (@{$lines}) {
2051              print $handle "$line\n";              print $handle "$line\n";
2052                $count++;
2053            }
2054            Trace("$count lines put to file $fileName.") if T(File => 3);
2055        }
2056        # Close the output file.
2057        close $handle;
2058    }
2059    
2060    =head3 ParseRecord
2061    
2062        my @fields = Tracer::ParseRecord($line);
2063    
2064    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2065    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2066    These will automatically be converted.
2067    
2068    =over 4
2069    
2070    =item line
2071    
2072    Line of data containing the tab-delimited fields.
2073    
2074    =item RETURN
2075    
2076    Returns a list of the fields found in the data line.
2077    
2078    =back
2079    
2080    =cut
2081    
2082    sub ParseRecord {
2083        # Get the parameter.
2084        my ($line) = @_;
2085        # Remove the trailing new-line, if any.
2086        chomp $line;
2087        # Split the line read into pieces using the tab character.
2088        my @retVal = split /\t/, $line;
2089        # Trim and fix the escapes in each piece.
2090        for my $value (@retVal) {
2091            # Trim leading whitespace.
2092            $value =~ s/^\s+//;
2093            # Trim trailing whitespace.
2094            $value =~ s/\s+$//;
2095            # Delete the carriage returns.
2096            $value =~ s/\r//g;
2097            # Convert the escapes into their real values.
2098            $value =~ s/\\t/"\t"/ge;
2099            $value =~ s/\\n/"\n"/ge;
2100        }
2101        # Return the result.
2102        return @retVal;
2103    }
2104    
2105    =head3 Merge
2106    
2107        my @mergedList = Tracer::Merge(@inputList);
2108    
2109    Sort a list of strings and remove duplicates.
2110    
2111    =over 4
2112    
2113    =item inputList
2114    
2115    List of scalars to sort and merge.
2116    
2117    =item RETURN
2118    
2119    Returns a list containing the same elements sorted in ascending order with duplicates
2120    removed.
2121    
2122    =back
2123    
2124    =cut
2125    
2126    sub Merge {
2127        # Get the input list in sort order.
2128        my @inputList = sort @_;
2129        # Only proceed if the list has at least two elements.
2130        if (@inputList > 1) {
2131            # Now we want to move through the list splicing out duplicates.
2132            my $i = 0;
2133            while ($i < @inputList) {
2134                # Get the current entry.
2135                my $thisEntry = $inputList[$i];
2136                # Find out how many elements duplicate the current entry.
2137                my $j = $i + 1;
2138                my $dup1 = $i + 1;
2139                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2140                # If the number is nonzero, splice out the duplicates found.
2141                if ($j > $dup1) {
2142                    splice @inputList, $dup1, $j - $dup1;
2143                }
2144                # Now the element at position $dup1 is different from the element before it
2145                # at position $i. We push $i forward one position and start again.
2146                $i++;
2147          }          }
2148      }      }
2149      # Close the output file.      # Return the merged list.
2150      close $handle;      return @inputList;
2151  }  }
2152    
2153  =head3 QTrace  =head3 Open
2154    
2155  C<< my $data = QTrace($format); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2156    
2157  Return the queued trace data in the specified format.  Open a file.
2158    
2159  =over 4  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2160    function. The mode is specified using Unix-like shell information. So, for
2161    example,
2162    
2163  =item format      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2164    
2165  C<html> to format the data as an HTML list, C<text> to format it as straight text.  would open for output appended to the specified file, and
2166    
2167  =back      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2168    
2169  =cut  would open a pipe that sorts the records written and removes duplicates. Note
2170    the use of file handle syntax in the Open call. To use anonymous file handles,
2171    code as follows.
2172    
2173  sub QTrace {      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
     # Get the parameter.  
     my ($format) = @_;  
     # Create the return variable.  
     my $retVal = "";  
     # Only proceed if there is an actual queue.  
     if (@Queue) {  
         # Process according to the format.  
         if ($format =~ m/^HTML$/i) {  
             # Convert the queue into an HTML list.  
             $retVal = "<ul>\n";  
             for my $line (@Queue) {  
                 my $escapedLine = CGI::escapeHTML($line);  
                 $retVal .= "<li>$escapedLine</li>\n";  
             }  
             $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
             # Convert the queue into a list of text lines.  
             $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
     }  
     # Return the formatted list.  
     return $retVal;  
 }  
2174    
2175  =head3 Confess  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2176    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2177    failed open will throw an exception and the third parameter will be used to construct
2178    an error message. If the parameter is omitted, a standard message is constructed
2179    using the file spec.
2180    
2181  C<< Confess($message); >>      Could not open "/usr/spool/news/twitlog"
2182    
2183  Trace the call stack and abort the program with the specified message. When used with  Note that the mode characters are automatically cleaned from the file name.
2184  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  The actual error message from the file system will be captured and appended to the
2185  So, for example  message in any case.
2186    
2187  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      Could not open "/usr/spool/news/twitlog": file not found.
2188    
2189  Will abort the program with a stack trace if the value of C<$recNum> is negative.  In some versions of PERL the only error message we get is a number, which
2190    corresponds to the C++ C<errno> value.
2191    
2192  =over 4      Could not open "/usr/spool/news/twitlog": 6.
2193    
2194  =item message  =over 4
2195    
2196  Message to include in the trace.  =item fileHandle
2197    
2198  =back  File handle. If this parameter is C<undef>, a file handle will be generated
2199    and returned as the value of this method.
2200    
2201  =cut  =item fileSpec
2202    
2203  sub Confess {  File name and mode, as per the PERL C<open> function.
     # Get the parameters.  
     my ($message) = @_;  
     # Trace the call stack.  
     Cluck($message);  
     # Abort the program.  
     croak(">>> $message");  
 }  
2204    
2205  =head3 Assert  =item message (optional)
2206    
2207  C<< Assert($condition1, $condition2, ... $conditionN); >>  Error message to use if the open fails. If omitted, a standard error message
2208    will be generated. In either case, the error information from the file system
2209    is appended to the message. To specify a conditional open that does not throw
2210    an error if it fails, use C<0>.
2211    
2212  Return TRUE if all the conditions are true. This method can be used in conjunction with  =item RETURN
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
2213    
2214  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  Returns the name of the file handle assigned to the file, or C<undef> if the
2215    open failed.
2216    
2217  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =back
2218    
2219  =cut  =cut
2220  sub Assert {  
2221      my $retVal = 1;  sub Open {
2222      LOOP: for my $condition (@_) {      # Get the parameters.
2223          if (! $condition) {      my ($fileHandle, $fileSpec, $message) = @_;
2224              $retVal = 0;      # Attempt to open the file.
2225              last LOOP;      my $rv = open $fileHandle, $fileSpec;
2226        # If the open failed, generate an error message.
2227        if (! $rv) {
2228            # Save the system error message.
2229            my $sysMessage = $!;
2230            # See if we need a default message.
2231            if (!$message) {
2232                # Clean any obvious mode characters and leading spaces from the
2233                # filename.
2234                my ($fileName) = FindNamePart($fileSpec);
2235                $message = "Could not open \"$fileName\"";
2236          }          }
2237            # Terminate with an error using the supplied message and the
2238            # error message from the file system.
2239            Confess("$message: $!");
2240      }      }
2241      return $retVal;      # Return the file handle.
2242        return $fileHandle;
2243  }  }
2244    
2245  =head3 Cluck  =head3 FindNamePart
2246    
2247  C<< Cluck($message); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2248    
2249  Trace the call stack. Note that for best results, you should qualify the call with a  Extract the portion of a file specification that contains the file name.
2250  trace condition. For example,  
2251    A file specification is the string passed to an C<open> call. It specifies the file
2252    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2253    method assumes that the file name is whatever follows the first angle bracket
2254    sequence.  So, for example, in the following strings the file name is
2255    C</usr/fig/myfile.txt>.
2256    
2257  C<< Cluck("Starting record parse.") if T(3); >>      >>/usr/fig/myfile.txt
2258        </usr/fig/myfile.txt
2259        | sort -u > /usr/fig/myfile.txt
2260    
2261  will only trace the stack if the trace level for the package is 3 or more.  If the method cannot find a file name using its normal methods, it will return the
2262    whole incoming string.
2263    
2264  =over 4  =over 4
2265    
2266  =item message  =item fileSpec
2267    
2268  Message to include in the trace.  File specification string from which the file name is to be extracted.
2269    
2270    =item RETURN
2271    
2272    Returns a three-element list. The first element contains the file name portion of
2273    the specified string, or the whole string if a file name cannot be found via normal
2274    methods. The second element contains the start position of the file name portion and
2275    the third element contains the length.
2276    
2277  =back  =back
2278    
2279  =cut  =cut
2280    #: Return Type $;
2281  sub Cluck {  sub FindNamePart {
2282      # Get the parameters.      # Get the parameters.
2283      my ($message) = @_;      my ($fileSpec) = @_;
2284      # Trace what's happening.      # Default to the whole input string.
2285      Trace("Stack trace for event: $message");      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2286      my $confession = longmess($message);      # Parse out the file name if we can.
2287      # Convert the confession to a series of trace messages. Note we skip any      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2288      # messages relating to calls into Tracer.          $retVal = $2;
2289      for my $line (split /\s*\n/, $confession) {          $len = length $retVal;
2290          Trace($line) if ($line !~ /Tracer\.pm/);          $pos = (length $fileSpec) - (length $3) - $len;
2291      }      }
2292        # Return the result.
2293        return ($retVal, $pos, $len);
2294  }  }
2295    
2296  =head3 Min  =head3 OpenDir
   
 C<< my $min = Min($value1, $value2, ... $valueN); >>  
   
 Return the minimum argument. The arguments are treated as numbers.  
   
 =over 4  
2297    
2298  =item $value1, $value2, ... $valueN      my @files = OpenDir($dirName, $filtered, $flag);
2299    
2300  List of numbers to compare.  Open a directory and return all the file names. This function essentially performs
2301    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2302    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2303    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2304    filtered out of the return list. If the directory does not open and I<$flag> is not
2305    set, an exception is thrown. So, for example,
2306    
2307  =item RETURN      my @files = OpenDir("/Volumes/fig/contigs", 1);
2308    
2309  Returns the lowest number in the list.  is effectively the same as
2310    
2311  =back      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2312        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2313    
2314  =cut  Similarly, the following code
2315    
2316  sub Min {      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
     # Get the parameters. Note that we prime the return value with the first parameter.  
     my ($retVal, @values) = @_;  
     # Loop through the remaining parameters, looking for the lowest.  
     for my $value (@values) {  
         if ($value < $retVal) {  
             $retVal = $value;  
         }  
     }  
     # Return the minimum found.  
     return $retVal;  
 }  
2317    
2318  =head3 Max  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2319    automatically returns an empty list if the directory fails to open.
2320    
2321  C<< my $max = Max($value1, $value2, ... $valueN); >>  =over 4
2322    
2323  Return the maximum argument. The arguments are treated as numbers.  =item dirName
2324    
2325  =over 4  Name of the directory to open.
2326    
2327  =item $value1, $value2, ... $valueN  =item filtered
2328    
2329  List of numbers to compare.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2330    from the list, else FALSE.
2331    
2332  =item RETURN  =item flag
2333    
2334  Returns the highest number in the list.  TRUE if a failure to open is okay, else FALSE
2335    
2336  =back  =back
2337    
2338  =cut  =cut
2339    #: Return Type @;
2340  sub Max {  sub OpenDir {
2341      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2342      my ($retVal, @values) = @_;      my ($dirName, $filtered, $flag) = @_;
2343      # Loop through the remaining parameters, looking for the highest.      # Declare the return variable.
2344      for my $value (@values) {      my @retVal = ();
2345          if ($value > $retVal) {      # Open the directory.
2346              $retVal = $value;      if (opendir(my $dirHandle, $dirName)) {
2347            # The directory opened successfully. Get the appropriate list according to the
2348            # strictures of the filter parameter.
2349            if ($filtered) {
2350                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2351            } else {
2352                @retVal = readdir $dirHandle;
2353          }          }
2354        } elsif (! $flag) {
2355            # Here the directory would not open and it's considered an error.
2356            Confess("Could not open directory $dirName.");
2357      }      }
2358      # Return the maximum found.      # Return the result.
2359      return $retVal;      return @retVal;
2360  }  }
2361    
 =head3 AddToListMap  
   
 C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>  
2362    
2363  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  =head3 Insure
 is created for the key. Otherwise, the new value is pushed onto the list.  
2364    
2365  =over 4      Insure($dirName, $chmod);
2366    
2367  =item hash  Insure a directory is present.
2368    
2369  Reference to the target hash.  =over 4
2370    
2371  =item key  =item dirName
2372    
2373  Key for which the value is to be added.  Name of the directory to check. If it does not exist, it will be created.
2374    
2375  =item value1, value2, ... valueN  =item chmod (optional)
2376    
2377  List of values to add to the key's value list.  Security privileges to be given to the directory if it is created.
2378    
2379  =back  =back
2380    
2381  =cut  =cut
2382    
2383  sub AddToListMap {  sub Insure {
2384      # Get the parameters.      my ($dirName, $chmod) = @_;
2385      my ($hash, $key, @values) = @_;      if (! -d $dirName) {
2386      # Process according to whether or not the key already has a value.          Trace("Creating $dirName directory.") if T(2);
2387      if (! exists $hash->{$key}) {          eval {
2388          $hash->{$key} = [@values];              mkpath $dirName;
2389      } else {              # If we have permissions specified, set them here.
2390          push @{$hash->{$key}}, @values;              if (defined($chmod)) {
2391                    chmod $chmod, $dirName;
2392                }
2393            };
2394            if ($@) {
2395                Confess("Error creating $dirName: $@");
2396      }      }
2397  }  }
2398    }
2399    
2400    =head3 ChDir
2401    
2402        ChDir($dirName);
2403    
2404    Change to the specified directory.
2405    
2406  =head3 DebugMode  =over 4
2407    
2408  C<< if (Tracer::DebugMode) { ...code... } >>  =item dirName
2409    
2410  Return TRUE if debug mode has been turned on, else abort.  Name of the directory to which we want to change.
2411    
2412  Certain CGI scripts are too dangerous to exist in the production  =back
 environment. This method provides a simple way to prevent them  
 from working unless they are explicitly turned on by creating a password  
 cookie via the B<SetPassword> script.  If debugging mode  
 is not turned on, an error will occur.  
2413    
2414  =cut  =cut
2415    
2416  sub DebugMode {  sub ChDir {
2417      # Declare the return variable.      my ($dirName) = @_;
2418      my $retVal = 0;      if (! -d $dirName) {
2419      # Check the debug configuration.          Confess("Cannot change to directory $dirName: no such directory.");
     my $password = CGI::cookie("DebugMode");  
     my $encrypted = Digest::MD5::md5_hex($password);  
     if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {  
         $retVal = 1;  
2420      } else {      } else {
2421          # Here debug mode is off, so we generate an error.          Trace("Changing to directory $dirName.") if T(File => 4);
2422          Confess("Cannot use this facility without logging in.");          my $okFlag = chdir $dirName;
2423            if (! $okFlag) {
2424                Confess("Error switching to directory $dirName.");
2425            }
2426      }      }
     # Return the determination indicator.  
     return $retVal;  
2427  }  }
2428    
2429  =head3 Strip  =head3 SetPermissions
2430    
2431  C<< my $string = Tracer::Strip($line); >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2432    
2433  Strip all line terminators off a string. This is necessary when dealing with files  Set the permissions for a directory and all the files and folders inside it.
2434  that may have been transferred back and forth several times among different  In addition, the group ownership will be changed to the specified value.
2435  operating environments.  
2436    This method is more vulnerable than most to permission and compatability
2437    problems, so it does internal error recovery.
2438    
2439  =over 4  =over 4
2440    
2441  =item line  =item dirName
2442    
2443  Line of text to be stripped.  Name of the directory to process.
2444    
2445  =item RETURN  =item group
2446    
2447  The same line of text with all the line-ending characters chopped from the end.  Name of the group to be assigned.
2448    
2449  =back  =item mask
2450    
2451  =cut  Permission mask. Bits that are C<1> in this mask will be ORed into the
2452    permission bits of any file or directory that does not already have them
2453    set to 1.
2454    
2455  sub Strip {  =item otherMasks
     # Get a copy of the parameter string.  
     my ($string) = @_;  
     my $retVal = (defined $string ? $string : "");  
     # Strip the line terminator characters.  
     $retVal =~ s/(\r|\n)+$//g;  
     # Return the result.  
     return $retVal;  
 }  
2456    
2457  =head3 Pad  Map of search patterns to permission masks. If a directory name matches
2458    one of the patterns, that directory and all its members and subdirectories
2459    will be assigned the new pattern. For example, the following would
2460    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2461    
2462  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2463    
2464  Pad a string to a specified length. The pad character will be a  The list is ordered, so the following would use 0777 for C<tmp1> and
2465  space, and the padding will be on the right side unless specified  0666 for C<tmp>, C<tmp2>, or C<tmp3>.
 in the third parameter.  
2466    
2467  =over 4      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2468                                                       '^tmp' => 0666);
2469    
2470  =item string  Note that the pattern matches are all case-insensitive, and only directory
2471    names are matched, not file names.
2472    
2473  String to be padded.  =back
2474    
2475  =item len  =cut
2476    
2477  Desired length of the padded string.  sub SetPermissions {
2478        # Get the parameters.
2479        my ($dirName, $group, $mask, @otherMasks) = @_;
2480        # Set up for error recovery.
2481        eval {
2482            # Switch to the specified directory.
2483            ChDir($dirName);
2484            # Get the group ID.
2485            my $gid = getgrnam($group);
2486            # Get the mask for tracing.
2487            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2488            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2489            my $fixCount = 0;
2490            my $lookCount = 0;
2491            # @dirs will be a stack of directories to be processed.
2492            my @dirs = (getcwd());
2493            while (scalar(@dirs) > 0) {
2494                # Get the current directory.
2495                my $dir = pop @dirs;
2496                # Check for a match to one of the specified directory names. To do
2497                # that, we need to pull the individual part of the name off of the
2498                # whole path.
2499                my $simpleName = $dir;
2500                if ($dir =~ m!/([^/]+)$!) {
2501                    $simpleName = $1;
2502                }
2503                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2504                # Search for a match.
2505                my $match = 0;
2506                my $i;
2507                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2508                    my $pattern = $otherMasks[$i];
2509                    if ($simpleName =~ /$pattern/i) {
2510                        $match = 1;
2511                    }
2512                }
2513                # Check for a match. Note we use $i-1 because the loop added 2
2514                # before terminating due to the match.
2515                if ($match && $otherMasks[$i-1] != $mask) {
2516                    # This directory matches one of the incoming patterns, and it's
2517                    # a different mask, so we process it recursively with that mask.
2518                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2519                } else {
2520                    # Here we can process normally. Get all of the non-hidden members.
2521                    my @submems = OpenDir($dir, 1);
2522                    for my $submem (@submems) {
2523                        # Get the full name.
2524                        my $thisMem = "$dir/$submem";
2525                        Trace("Checking member $thisMem.") if T(4);
2526                        $lookCount++;
2527                        if ($lookCount % 1000 == 0) {
2528                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2529                        }
2530                        # Fix the group.
2531                        chown -1, $gid, $thisMem;
2532                        # Insure this member is not a symlink.
2533                        if (! -l $thisMem) {
2534                            # Get its info.
2535                            my $fileInfo = stat $thisMem;
2536                            # Only proceed if we got the info. Otherwise, it's a hard link
2537                            # and we want to skip it anyway.
2538                            if ($fileInfo) {
2539                                my $fileMode = $fileInfo->mode;
2540                                if (($fileMode & $mask) != $mask) {
2541                                    # Fix this member.
2542                                    $fileMode |= $mask;
2543                                    chmod $fileMode, $thisMem;
2544                                    $fixCount++;
2545                                }
2546                                # If it's a subdirectory, stack it.
2547                                if (-d $thisMem) {
2548                                    push @dirs, $thisMem;
2549                                }
2550                            }
2551                        }
2552                    }
2553                }
2554            }
2555            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2556        };
2557        # Check for an error.
2558        if ($@) {
2559            Confess("SetPermissions error: $@");
2560        }
2561    }
2562    
2563  =item left (optional)  =head3 GetLine
2564    
2565  TRUE if the string is to be left-padded; otherwise it will be padded on the right.      my @data = Tracer::GetLine($handle);
2566    
2567  =item padChar (optional)  Read a line of data from a tab-delimited file.
2568    
2569  Character to use for padding. The default is a space.  =over 4
2570    
2571    =item handle
2572    
2573    Open file handle from which to read.
2574    
2575  =item RETURN  =item RETURN
2576    
2577  Returns a copy of the original string with the pad character added to the  Returns a list of the fields in the record read. The fields are presumed to be
2578  specified end so that it achieves the desired length.  tab-delimited. If we are at the end of the file, then an empty list will be
2579    returned. If an empty line is read, a single list item consisting of a null
2580    string will be returned.
2581    
2582  =back  =back
2583    
2584  =cut  =cut
2585    
2586  sub Pad {  sub GetLine {
2587      # Get the parameters.      # Get the parameters.
2588      my ($string, $len, $left, $padChar) = @_;      my ($handle) = @_;
2589      # Compute the padding character.      # Declare the return variable.
2590      if (! defined $padChar) {      my @retVal = ();
2591          $padChar = " ";      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2592        # Read from the file.
2593        my $line = <$handle>;
2594        # Only proceed if we found something.
2595        if (defined $line) {
2596            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2597            # upload control and have a nonstandard EOL combination.
2598            $line =~ s/(\r|\n)+$//;
2599            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2600            if (T(File => 4)) {
2601                my $escapedLine = $line;
2602                $escapedLine =~ s/\n/\\n/g;
2603                $escapedLine =~ s/\r/\\r/g;
2604                $escapedLine =~ s/\t/\\t/g;
2605                Trace("Line read: -->$escapedLine<--");
2606      }      }
2607      # Compute the number of spaces needed.          # If the line is empty, return a single empty string; otherwise, parse
2608      my $needed = $len - length $string;          # it into fields.
2609      # Copy the string into the return variable.          if ($line eq "") {
2610      my $retVal = $string;              push @retVal, "";
     # Only proceed if padding is needed.  
     if ($needed > 0) {  
         # Create the pad string.  
         my $pad = $padChar x $needed;  
         # Affix it to the return value.  
         if ($left) {  
             $retVal = $pad . $retVal;  
2611          } else {          } else {
2612              $retVal .= $pad;              push @retVal, split /\t/,$line;
2613          }          }
2614        } else {
2615            # Trace the reason the read failed.
2616            Trace("End of file: $!") if T(File => 3);
2617      }      }
2618      # Return the result.      # Return the result.
2619      return $retVal;      return @retVal;
2620  }  }
2621    
2622  =head3 EOF  =head3 PutLine
2623    
2624  This is a constant that is lexically greater than any useful string.      Tracer::PutLine($handle, \@fields, $eol);
2625    
2626  =cut  Write a line of data to a tab-delimited file. The specified field values will be
2627    output in tab-separated form, with a trailing new-line.
2628    
2629  sub EOF {  =over 4
     return "\xFF\xFF\xFF\xFF\xFF";  
 }  
2630    
2631  =head3 TICK  =item handle
2632    
2633  C<< my @results = TICK($commandString); >>  Output file handle.
2634    
2635  Perform a back-tick operation on a command. If this is a Windows environment, any leading  =item fields
2636  dot-slash (C<./> will be removed. So, for example, if you were doing  
2637    List of field values.
2638    
2639    =item eol (optional)
2640    
2641    End-of-line character (default is "\n").
2642    
2643    =back
2644    
2645      `./protein.cgi`  =cut
2646    
2647  from inside a CGI script, it would work fine in Unix, but would issue an error message  sub PutLine {
2648  in Windows complaining that C<'.'> is not a valid command. If instead you code      # Get the parameters.
2649        my ($handle, $fields, $eol) = @_;
2650        # Write the data.
2651        print $handle join("\t", @{$fields}) . ($eol || "\n");
2652    }
2653    
     TICK("./protein.cgi")  
2654    
2655  it will work correctly in both environments.  =head3 PrintLine
2656    
2657  =over 4      Tracer::PrintLine($line);
2658    
2659  =item commandString  Print a line of text with a trailing new-line.
2660    
2661  The command string to pass to the system.  =over 4
2662    
2663  =item RETURN  =item line
2664    
2665  Returns the standard output from the specified command, as a list.  Line of text to print.
2666    
2667  =back  =back
2668    
2669  =cut  =cut
2670  #: Return Type @;  
2671  sub TICK {  sub PrintLine {
2672      # Get the parameters.      # Get the parameters.
2673      my ($commandString) = @_;      my ($line) = @_;
2674      # Chop off the dot-slash if this is Windows.      # Print the line.
2675      if ($FIG_Config::win_mode) {      print "$line\n";
         $commandString =~ s!^\./!!;  
     }  
     # Activate the command and return the result.  
     return `$commandString`;  
2676  }  }
2677    
 =head3 ScriptSetup  
2678    
2679  C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  =head2 Other Useful Methods
2680    
2681  Perform standard tracing and debugging setup for scripts. The value returned is  =head3 ParseParm
 the CGI object followed by a pre-built variable hash.  
2682    
2683  The C<Trace> form parameter is used to determine whether or not tracing is active and      my $listValue = Tracer::ParseParm($string);
 which trace modules (other than C<Tracer> itself) should be turned on. Specifying  
 the C<CGI> trace module will trace parameter and environment information. Parameters are  
 traced at level 3 and environment variables at level 4. To trace to a file instead of to  
 the web page, set C<TF> to 1. At the end of the script, the client should call  
 L</ScriptFinish> to output the web page.  
2684    
2685  In some situations, it is not practical to invoke tracing via form parameters. For this  Convert a parameter into a list reference. If the parameter is undefined,
2686  situation, you can turn on emergency tracing from the debugging control panel.  an undefined value will be returned. Otherwise, it will be parsed as a
2687  Tracing will then be turned on automatically for all programs that use the L</ETracing>  comma-separated list of values.
 method, which includes every program that uses this method or L</StandardSetup>.  
2688    
2689  =over 4  =over 4
2690    
2691  =item noTrace (optional)  =item string
2692    
2693  If specified, tracing will be suppressed. This is useful if the script wants to set up  Incoming string.
 tracing manually.  
2694    
2695  =item RETURN  =item RETURN
2696    
2697  Returns a two-element list consisting of a CGI query object and a variable hash for  Returns a reference to a list of values, or C<undef> if the incoming value
2698  the output page.  was undefined.
2699    
2700  =back  =back
2701    
2702  =cut  =cut
2703    
2704  sub ScriptSetup {  sub ParseParm {
2705      # Get the parameters.      # Get the parameters.
2706      my ($noTrace) = @_;      my ($string) = @_;
2707      # Get the CGI query object.      # Declare the return variable.
2708      my $cgi = CGI->new();      my $retVal;
2709      # Set up tracing if it's not suppressed.      # Check for data.
2710      ETracing($cgi) unless $noTrace;      if (defined $string) {
2711      # Create the variable hash.          # We have some, so split it into a list.
2712      my $varHash = { results => '' };          $retVal = [ split /\s*,\s*/, $string];
2713      # Return the query object and variable hash.      }
2714      return ($cgi, $varHash);      # Return the result.
2715        return $retVal;
2716  }  }
2717    
2718  =head3 ETracing  =head3 Now
   
 C<< ETracing($parameter); >>  
   
 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  
2719    
2720  A parameter from which the tracing key is computed. If it is a scalar,      my $string = Tracer::Now();
 that scalar is used as the tracing key. If it is a CGI object, the  
 tracing key is taken from the C<IP> cookie. If it is omitted, the  
 tracing key is taken from the C<TRACING> environment variable. If it  
 is a CGI object and emergency tracing is not on, the C<Trace> and  
 C<TF> parameters will be used to determine the type of tracing.  
2721    
2722  =back  Return a displayable time stamp containing the local time. Whatever format this
2723    method produces must be parseable by L</ParseDate>.
2724    
2725  =cut  =cut
2726    
2727  sub ETracing {  sub Now {
2728      # Get the parameter.      return DisplayTime(time);
     my ($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;  
         } else {  
             # Emergency tracing is on. Pull off the destination and  
             # the trace level;  
             $dest = shift @tracing;  
             my $level = shift @tracing;  
             # Convert the destination to a real tracing destination.  
             # temp directory.  
             $dest = EmergencyTracingDest($tkey, $dest);  
             # Insure Tracer is specified.  
             my %moduleHash = map { $_ => 1 } @tracing;  
             $moduleHash{Tracer} = 1;  
             # Set the trace parameter.  
             $tracing = join(" ", $level, sort keys %moduleHash);  
         }  
     } elsif (defined $cgi) {  
         # There's no emergency tracing, but we have a CGI object, so check  
         # for tracing from the form parameters.  
         if ($cgi->param('Trace')) {  
             # Here the user has requested tracing via a form.  
             $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");  
             $tracing = $cgi->param('Trace') . " Tracer";  
         }  
     }  
     # Setup the tracing we've determined from all the stuff above.  
     TSetup($tracing, $dest);  
     # If we're a web script, trace the parameter and environment data.  
     if (defined $cgi) {  
         TraceParms($cgi);  
     }  
2729  }  }
2730    
2731  =head3 EmergencyFileName  =head3 DisplayTime
2732    
2733  C<< my $fileName = Tracer::EmergencyFileName($tkey); >>      my $string = Tracer::DisplayTime($time);
2734    
2735  Return the emergency tracing file name. This is the file that specifies  Convert a time value to a displayable time stamp. Whatever format this
2736  the tracing information.  method produces must be parseable by L</ParseDate>.
2737    
2738  =over 4  =over 4
2739    
2740  =item tkey  =item time
2741    
2742  Tracing key for the current program.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2743    
2744  =item RETURN  =item RETURN
2745    
2746  Returns the name of the file to contain the emergency tracing information.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2747    
2748  =back  =back
2749    
2750  =cut  =cut
2751    
2752  sub EmergencyFileName {  sub DisplayTime {
2753      # Get the parameters.      my ($time) = @_;
2754      my ($tkey) = @_;      my $retVal = "(n/a)";
2755      # Compute the emergency tracing file name.      if (defined $time) {
2756      return "$FIG_Config::temp/Emergency$tkey.txt";          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2757            $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2758                      _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2759        }
2760        return $retVal;
2761  }  }
2762    
2763  =head3 EmergencyFileTarget  # Pad a number to 2 digits.
2764    sub _p2 {
2765        my ($value) = @_;
2766        $value = "0$value" if ($value < 10);
2767        return $value;
2768    }
2769    
2770  C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>  =head3 Escape
2771    
2772  Return the emergency tracing target file name. This is the file that receives      my $codedString = Tracer::Escape($realString);
2773  the tracing output for file-based tracing.  
2774    Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2775    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2776    result is to reverse the effect of L</UnEscape>.
2777    
2778  =over 4  =over 4
2779    
2780  =item tkey  =item realString
2781    
2782  Tracing key for the current program.  String to escape.
2783    
2784  =item RETURN  =item RETURN
2785    
2786  Returns the name of the file to contain the trace output.  Escaped equivalent of the real string.
2787    
2788  =back  =back
2789    
2790  =cut  =cut
2791    
2792  sub EmergencyFileTarget {  sub Escape {
2793      # Get the parameters.      # Get the parameter.
2794      my ($tkey) = @_;      my ($realString) = @_;
2795      # Compute the emergency tracing file name.      # Initialize the return variable.
2796      return "$FIG_Config::temp/trace$tkey.log";      my $retVal = "";
2797        # Loop through the parameter string, looking for sequences to escape.
2798        while (length $realString > 0) {
2799            # Look for the first sequence to escape.
2800            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2801                # Here we found it. The text preceding the sequence is in $1. The sequence
2802                # itself is in $2. First, move the clear text to the return variable.
2803                $retVal .= $1;
2804                # Strip the processed section off the real string.
2805                $realString = substr $realString, (length $2) + (length $1);
2806                # Get the matched character.
2807                my $char = $2;
2808                # If we have a CR, we are done.
2809                if ($char ne "\r") {
2810                    # It's not a CR, so encode the escape sequence.
2811                    $char =~ tr/\t\n/tn/;
2812                    $retVal .= "\\" . $char;
2813                }
2814            } else {
2815                # Here there are no more escape sequences. The rest of the string is
2816                # transferred unmodified.
2817                $retVal .= $realString;
2818                $realString = "";
2819            }
2820        }
2821        # Return the result.
2822        return $retVal;
2823  }  }
2824    
2825  =head3 EmergencyTracingDest  =head3 UnEscape
2826    
2827  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>      my $realString = Tracer::UnEscape($codedString);
2828    
2829  This method converts an emergency tracing destination to a real  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2830  tracing destination. The main difference is that if the  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2831  destination is C<FILE> or C<APPEND>, we convert it to file  be deleted.
 output.  
2832    
2833  =over 4  =over 4
2834    
2835  =item tkey  =item codedString
   
 Tracing key for this environment.  
   
 =item myDest  
2836    
2837  Destination from the emergency tracing file.  String to un-escape.
2838    
2839  =item RETURN  =item RETURN
2840    
2841  Returns a destination that can be passed into L</TSetup>.  Returns a copy of the original string with the escape sequences converted to their actual
2842    values.
2843    
2844  =back  =back
2845    
2846  =cut  =cut
2847    
2848  sub EmergencyTracingDest {  sub UnEscape {
2849      # Get the parameters.      # Get the parameter.
2850      my ($tkey, $myDest) = @_;      my ($codedString) = @_;
2851      # Declare the return variable.      # Initialize the return variable.
2852      my $retVal;      my $retVal = "";
2853      # Process according to the destination value.      # Only proceed if the incoming string is nonempty.
2854      if ($myDest eq 'FILE') {      if (defined $codedString) {
2855          $retVal = ">" . EmergencyFileTarget($tkey);          # Loop through the parameter string, looking for escape sequences. We can't do
2856      } elsif ($myDest eq 'APPEND') {          # translating because it causes problems with the escaped slash. ("\\t" becomes
2857          $retVal = ">>" . EmergencyFileTarget($tkey);          # "\<tab>" no matter what we do.)
2858            while (length $codedString > 0) {
2859                # Look for the first escape sequence.
2860                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2861                    # Here we found it. The text preceding the sequence is in $1. The sequence
2862                    # itself is in $2. First, move the clear text to the return variable.
2863                    $retVal .= $1;
2864                    $codedString = substr $codedString, (2 + length $1);
2865                    # Get the escape value.
2866                    my $char = $2;
2867                    # If we have a "\r", we are done.
2868                    if ($char ne 'r') {
2869                        # Here it's not an 'r', so we convert it.
2870                        $char =~ tr/\\tn/\\\t\n/;
2871                        $retVal .= $char;
2872                    }
2873      } else {      } else {
2874          $retVal = $myDest;                  # Here there are no more escape sequences. The rest of the string is
2875                    # transferred unmodified.
2876                    $retVal .= $codedString;
2877                    $codedString = "";
2878                }
2879            }
2880      }      }
2881      # Return the result.      # Return the result.
2882      return $retVal;      return $retVal;
2883  }  }
2884    
2885  =head3 Emergency  =head3 Percent
   
 C<< Emergency($key, $hours, $dest, $level, @modules); >>  
   
 Turn on emergency tracing. This method can only be invoked over the web and is  
 should not be called if debug mode is off. 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  
   
 =item tkey  
2886    
2887  The tracing key. This is used to identify the control file and the trace file.      my $percent = Tracer::Percent($number, $base);
2888    
2889  =item hours  Returns the percent of the base represented by the given number. If the base
2890    is zero, returns zero.
2891    
2892  Number of hours to keep emergency tracing alive.  =over 4
2893    
2894  =item dest  =item number
2895    
2896  Tracing destination. If no path information is specified for a file  Percent numerator.
 destination, it is put in the FIG temporary directory.  
2897    
2898  =item level  =item base
2899    
2900  Tracing level. A higher level means more trace messages.  Percent base.
2901    
2902  =item modules  =item RETURN
2903    
2904  A list of the tracing modules to activate.  Returns the percentage of the base represented by the numerator.
2905    
2906  =back  =back
2907    
2908  =cut  =cut
2909    
2910  sub Emergency {  sub Percent {
2911      # Get the parameters.      # Get the parameters.
2912      my ($tkey, $hours, $dest, $level, @modules) = @_;      my ($number, $base) = @_;
2913      # Create the emergency file.      # Declare the return variable.
2914      my $specFile = EmergencyFileName($tkey);      my $retVal = 0;
2915      my $outHandle = Open(undef, ">$specFile");      # Compute the percent.
2916      print $outHandle join("\n", $hours, $dest, $level, @modules, "");      if ($base != 0) {
2917            $retVal = $number * 100 / $base;
2918        }
2919        # Return the result.
2920        return $retVal;
2921  }  }
2922    
2923  =head3 EmergencyKey  =head3 Constrain
2924    
2925  C<< my $tkey = EmergencyKey($parameter); >>      my $constrained = Constrain($value, $min, $max);
2926    
2927  Return the Key to be used for emergency tracing. This could be an IP address,  Modify a numeric value to bring it to a point in between a maximum and a minimum.
  a session ID, or a user name, depending on the environment.  
2928    
2929  =over 4  =over 4
2930    
2931  =item parameter  =item value
2932    
2933  Parameter defining the method for finding the tracing key. If it is a scalar,  Value to constrain.
2934  then it is presumed to be the tracing key itself. If it is a CGI object, then  
2935  the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is  =item min (optional)
2936  taken from the C<TRACING> environment variable.  
2937    Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
2938    
2939    =item max (optional)
2940    
2941    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
2942    
2943  =item RETURN  =item RETURN
2944    
2945  Returns the key to be used for labels in emergency tracing.  Returns the incoming value, constrained according to the other parameters.
2946    
2947  =back  =back
2948    
2949  =cut  =cut
2950    
2951  sub EmergencyKey {  sub Constrain {
2952      # Get the parameters.      # Get the parameters.
2953      my ($parameter) = @_;      my ($value, $min, $max) = @_;
2954      # Declare the return variable.      # Declare the return variable.
2955      my $retVal;      my $retVal = $value;
2956      # Determine the parameter type.      # Apply the minimum constraint.
2957      if (! defined $parameter) {      if (defined $min && $retVal < $min) {
2958          # Here we're supposed to check the environment.          $retVal = $min;
2959          $retVal = $ENV{TRACING};      }
2960      } else {      # Apply the maximum constraint.
2961          my $ptype = ref $parameter;      if (defined $max && $retVal > $max) {
2962          if ($ptype eq 'CGI') {          $retVal = $max;
             # Here we were invoked from a web page. Look for a cookie.  
             $retVal = $parameter->cookie('IP');  
         } elsif (! $ptype) {  
             # Here the key was passed in.  
             $retVal = $parameter;  
         }  
     }  
     # If no luck finding a key, use the PID.  
     if (! defined $retVal) {  
         $retVal = $$;  
2963      }      }
2964      # Return the result.      # Return the result.
2965      return $retVal;      return $retVal;
2966  }  }
2967    
2968    =head3 Min
2969    
2970  =head3 TraceParms      my $min = Min($value1, $value2, ... $valueN);
   
 C<< Tracer::TraceParms($cgi); >>  
2971    
2972  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Return the minimum argument. The arguments are treated as numbers.
 at level CGI => 4.  
2973    
2974  =over 4  =over 4
2975    
2976  =item cgi  =item $value1, $value2, ... $valueN
2977    
2978  CGI query object containing the parameters to trace.  List of numbers to compare.
2979    
2980    =item RETURN
2981    
2982    Returns the lowest number in the list.
2983    
2984  =back  =back
2985    
2986  =cut  =cut
2987    
2988  sub TraceParms {  sub Min {
2989      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
2990      my ($cgi) = @_;      my ($retVal, @values) = @_;
2991      if (T(CGI => 3)) {      # Loop through the remaining parameters, looking for the lowest.
2992          # Here we want to trace the parameter data.      for my $value (@values) {
2993          my @names = $cgi->param;          if ($value < $retVal) {
2994          for my $parmName (sort @names) {              $retVal = $value;
             # Note we skip the Trace parameters, which are for our use only.  
             if ($parmName ne 'Trace' && $parmName ne 'TF') {  
                 my @values = $cgi->param($parmName);  
                 Trace("CGI: $parmName = " . join(", ", @values));  
             }  
         }  
         # Display the request method.  
         my $method = $cgi->request_method();  
         Trace("Method: $method");  
     }  
     if (T(CGI => 4)) {  
         # Here we want the environment data too.  
         for my $envName (sort keys %ENV) {  
             Trace("ENV: $envName = $ENV{$envName}");  
2995          }          }
2996      }      }
2997        # Return the minimum found.
2998        return $retVal;
2999  }  }
3000    
3001  =head3 ScriptFinish  =head3 Max
   
 C<< ScriptFinish($webData, $varHash); >>  
   
 Output a web page at the end of a script. Either the string to be output or the  
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
   
 A typical standard script would loook like the following.  
   
     BEGIN {  
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
3002    
3003      my ($cgi, $varHash) = ScriptSetup();      my $max = Max($value1, $value2, ... $valueN);
     eval {  
         # ... get data from $cgi, put it in $varHash ...  
     };  
     if ($@) {  
         Trace("Script Error: $@") if T(0);  
     }  
     ScriptFinish("Html/MyTemplate.html", $varHash);  
3004    
3005  The idea here is that even if the script fails, you'll see trace messages and  Return the maximum argument. The arguments are treated as numbers.
 useful output.  
3006    
3007  =over 4  =over 4
3008    
3009  =item webData  =item $value1, $value2, ... $valueN
3010    
3011  A string containing either the full web page to be written to the output or the  List of numbers to compare.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3012    
3013  =item varHash (optional)  =item RETURN
3014    
3015  If specified, then a reference to a hash mapping variable names for a template  Returns the highest number in the list.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3016    
3017  =back  =back
3018    
3019  =cut  =cut
3020    
3021  sub ScriptFinish {  sub Max {
3022      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3023      my ($webData, $varHash) = @_;      my ($retVal, @values) = @_;
3024      # Check for a template file situation.      # Loop through the remaining parameters, looking for the highest.
3025      my $outputString;      for my $value (@values) {
3026      if (defined $varHash) {          if ($value > $retVal) {
3027          # Here we have a template file. We need to determine the template type.              $retVal = $value;
         my $template;  
         if ($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";  
3028          }          }
         substr $outputString, $pos, 0, $traceHtml;  
3029      }      }
3030      # Write the output string.      # Return the maximum found.
3031      print $outputString;      return $retVal;
3032  }  }
3033    
3034  =head3 Insure  =head3 Strip
3035    
3036  C<< Insure($dirName); >>      my $string = Tracer::Strip($line);
3037    
3038  Insure a directory is present.  Strip all line terminators off a string. This is necessary when dealing with files
3039    that may have been transferred back and forth several times among different
3040    operating environments.
3041    
3042  =over 4  =over 4
3043    
3044  =item dirName  =item line
   
 Name of the directory to check. If it does not exist, it will be created.  
   
 =back  
   
 =cut  
   
 sub Insure {  
     my ($dirName) = @_;  
     if (! -d $dirName) {  
         Trace("Creating $dirName directory.") if T(2);  
         eval { mkpath $dirName; };  
         if ($@) {  
             Confess("Error creating $dirName: $@");  
         }  
     }  
 }  
   
 =head3 ChDir  
   
 C<< ChDir($dirName); >>  
   
 Change to the specified directory.  
3045    
3046  =over 4  Line of text to be stripped.
3047    
3048  =item dirName  =item RETURN
3049    
3050  Name of the directory to which we want to change.  The same line of text with all the line-ending characters chopped from the end.
3051    
3052  =back  =back
3053    
3054  =cut  =cut
3055    
3056  sub ChDir {  sub Strip {
3057      my ($dirName) = @_;      # Get a copy of the parameter string.
3058      if (! -d $dirName) {      my ($string) = @_;
3059          Confess("Cannot change to directory $dirName: no such directory.");      my $retVal = (defined $string ? $string : "");
3060      } else {      # Strip the line terminator characters.
3061          Trace("Changing to directory $dirName.") if T(4);      $retVal =~ s/(\r|\n)+$//g;
3062          my $okFlag = chdir $dirName;      # Return the result.
3063          if (! $okFlag) {      return $retVal;
             Confess("Error switching to directory $dirName.");  
         }  
     }  
3064  }  }
3065    
3066  =head3 SendSMS  =head3 Pad
3067    
3068  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3069    
3070  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  Pad a string to a specified length. The pad character will be a
3071  user name, password, and API ID for the relevant account in the hash reference variable  space, and the padding will be on the right side unless specified
3072  I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For  in the third parameter.
 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  
3073    
3074      $phone =  { user => 'BruceTheHumanPet',  =over 4
                 password => 'silly',  
                 api_id => '2561022' };  
3075    
3076  The original purpose of this method was to insure Bruce would be notified immediately when the  =item string
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3077    
3078  The message ID will be returned if successful, and C<undef> if an error occurs.  String to be padded.
3079    
3080  =over 4  =item len
3081    
3082  =item phoneNumber  Desired length of the padded string.
3083    
3084  Phone number to receive the message, in international format. A United States phone number  =item left (optional)
 would be prefixed by "1". A British phone number would be prefixed by "44".  
3085    
3086  =item msg  TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3087    
3088  Message to send to the specified phone.  =item padChar (optional)
3089    
3090    Character to use for padding. The default is a space.
3091    
3092  =item RETURN  =item RETURN
3093    
3094  Returns the message ID if successful, and C<undef> if the message could not be sent.  Returns a copy of the original string with the pad character added to the
3095    specified end so that it achieves the desired length.
3096    
3097  =back  =back
3098    
3099  =cut  =cut
3100    
3101  sub SendSMS {  sub Pad {
3102      # Get the parameters.      # Get the parameters.
3103      my ($phoneNumber, $msg) = @_;      my ($string, $len, $left, $padChar) = @_;
3104      # Declare the return variable. If we do not change it, C<undef> will be returned.      # Compute the padding character.
3105      my $retVal;      if (! defined $padChar) {
3106      # Only proceed if we have phone support.          $padChar = " ";
     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);  
3107              }              }
3108        # Compute the number of spaces needed.
3109        my $needed = $len - length $string;
3110        # Copy the string into the return variable.
3111        my $retVal = $string;
3112        # Only proceed if padding is needed.
3113        if ($needed > 0) {
3114            # Create the pad string.
3115            my $pad = $padChar x $needed;
3116            # Affix it to the return value.
3117            if ($left) {
3118                $retVal = $pad . $retVal;
3119            } else {
3120                $retVal .= $pad;
3121          }          }
3122      }      }
3123      # Return the result.      # Return the result.
3124      return $retVal;      return $retVal;
3125  }  }
3126    
3127  =head3 CommaFormat  =head3 EOF
3128    
3129  C<< my $formatted = Tracer::CommaFormat($number); >>  This is a constant that is lexically greater than any useful string.
3130    
3131  Insert commas into a number.  =cut
3132    
3133  =over 4  sub EOF {
3134        return "\xFF\xFF\xFF\xFF\xFF";
3135    }
3136    
3137  =item number  =head3 TICK
3138    
3139  A sequence of digits.      my @results = TICK($commandString);
3140    
3141  =item RETURN  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3142    dot-slash (C<./> will be removed. So, for example, if you were doing
3143    
3144  Returns the same digits with commas strategically inserted.      `./protein.cgi`
3145    
3146  =back  from inside a CGI script, it would work fine in Unix, but would issue an error message
3147    in Windows complaining that C<'.'> is not a valid command. If instead you code
3148    
3149  =cut      TICK("./protein.cgi")
3150    
3151  sub CommaFormat {  it will work correctly in both environments.
     # Get the parameters.  
     my ($number) = @_;  
     # Pad the length up to a multiple of three.  
     my $padded = "$number";  
     $padded = " " . $padded while length($padded) % 3 != 0;  
     # This is a fancy PERL trick. The parentheses in the SPLIT pattern  
     # cause the delimiters to be included in the output stream. The  
     # GREP removes the empty strings in between the delimiters.  
     my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));  
     # Clean out the spaces.  
     $retVal =~ s/ //g;  
     # Return the result.  
     return $retVal;  
 }  
 =head3 SetPermissions  
3152    
3153  C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  =over 4
3154    
3155  Set the permissions for a directory and all the files and folders inside it.  =item commandString
 In addition, the group ownership will be changed to the specified value.  
3156    
3157  This method is more vulnerable than most to permission and compatability  The command string to pass to the system.
 problems, so it does internal error recovery.  
3158    
3159  =over 4  =item RETURN
3160    
3161  =item dirName  Returns the standard output from the specified command, as a list.
3162    
3163  Name of the directory to process.  =back
3164    
3165  =item group  =cut
3166    #: Return Type @;
3167    sub TICK {
3168        # Get the parameters.
3169        my ($commandString) = @_;
3170        # Chop off the dot-slash if this is Windows.
3171        if ($FIG_Config::win_mode) {
3172            $commandString =~ s!^\./!!;
3173        }
3174        # Activate the command and return the result.
3175        return `$commandString`;
3176    }
3177    
 Name of the group to be assigned.  
3178    
3179  =item mask  =head3 CommaFormat
3180    
3181  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.  
3182    
3183  =item otherMasks  Insert commas into a number.
3184    
3185  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>.  
3186    
3187      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  =item number
3188    
3189  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>.  
3190    
3191      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  =item RETURN
                                                    '^tmp' => 0666);  
3192    
3193  Note that the pattern matches are all case-insensitive, and only directory  Returns the same digits with commas strategically inserted.
 names are matched, not file names.  
3194    
3195  =back  =back
3196    
3197  =cut  =cut
3198    
3199  sub SetPermissions {  sub CommaFormat {
3200      # Get the parameters.      # Get the parameters.
3201      my ($dirName, $group, $mask, @otherMasks) = @_;      my ($number) = @_;
3202      # Set up for error recovery.      # Pad the length up to a multiple of three.
3203      eval {      my $padded = "$number";
3204          # Switch to the specified directory.      $padded = " " . $padded while length($padded) % 3 != 0;
3205          ChDir($dirName);      # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3206          # Get the group ID.      # cause the delimiters to be included in the output stream. The
3207          my $gid = getgrnam($group);      # GREP removes the empty strings in between the delimiters.
3208          # Get the mask for tracing.      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3209          my $traceMask = sprintf("%04o", $mask) . "($mask)";      # Clean out the spaces.
3210          Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(2);      $retVal =~ s/ //g;
3211          my $fixCount = 0;      # Return the result.
3212          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(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(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(2);  
     };  
     # Check for an error.