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revision 1.84, Thu May 3 12:28:00 2007 UTC revision 1.103, Fri May 9 04:21:45 2008 UTC
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1  #  # -*- perl -*-
2    ########################################################################
3  # Copyright (c) 2003-2006 University of Chicago and Fellowship  # Copyright (c) 2003-2006 University of Chicago and Fellowship
4  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
5  #  #
# Line 13  Line 14 
14  # at info@ci.uchicago.edu or the Fellowship for Interpretation of  # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15  # Genomes at veronika@thefig.info or download a copy from  # Genomes at veronika@thefig.info or download a copy from
16  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
17  #  ########################################################################
18    
19  package Tracer;  package Tracer;
20    
21      require Exporter;      require Exporter;
22      @ISA = ('Exporter');      @ISA = ('Exporter');
23      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn);
24      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
25      use strict;      use strict;
26      use Carp qw(longmess croak);      use Carp qw(longmess croak carp);
27      use CGI;      use CGI;
28      use Cwd;      use Cwd;
29      use FIG_Config;      use FIG_Config;
# Line 35  Line 36 
36      use Time::HiRes 'gettimeofday';      use Time::HiRes 'gettimeofday';
37      use URI::Escape;      use URI::Escape;
38      use Time::Local;      use Time::Local;
39        use POSIX qw(strftime);
40        use Time::Zone;
41    
42    
43  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
44    
# Line 159  Line 163 
163    
164  Sometimes, you need a way for tracing to happen automatically without putting parameters  Sometimes, you need a way for tracing to happen automatically without putting parameters
165  in a form or on the command line. Emergency tracing does this. You invoke emergency tracing  in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
166  from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.  from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
167  Emergency tracing requires you specify a tracing key. For command-line tools, the key is  that you specify a tracing key. For command-line tools, the key is
168  taken from the C<TRACING> environment variable. For web services, the key is taken from  taken from the C<TRACING> environment variable. For web services, the key is taken from
169  a cookie. Either way, the key tells the tracing facility who you are, so that you control  a cookie. Either way, the key tells the tracing facility who you are, so that you control
170  the tracing in your environment without stepping on other users.  the tracing in your environment without stepping on other users.
# Line 183  Line 187 
187    
188  The web script will look for the tracing key in the cookies, and the command-line  The web script will look for the tracing key in the cookies, and the command-line
189  script will look for it in the C<TRACING> environment variable. If you are  script will look for it in the C<TRACING> environment variable. If you are
190  using the L</StandardScript> or L</StandardSetup> methods, emergency tracing  using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
191  will be configured automatically.  will be configured automatically.
192    
 NOTE: to configure emergency tracing from the command line instead of the Debugging  
 Control Panel (see below), use the C<trace.pl> script.  
   
 =head3 Debugging Control Panel  
   
 The debugging control panel provides several tools to assist in development of  
 SEED and Sprout software. You access the debugging control panel from the URL  
 C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,  
 for example, the panel access point for the development NMPDR system is  
 C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to  
 find out what the password is. From this page, you can also specify a tracing  
 key. If you don't specify a key, one will be generated for you.  
   
 =head4 Emergency Tracing Form  
   
 At the bottom of the debugging control panel is a form that allows you to  
 specify a trace level and tracing categories. Special and common categories  
 are listed with check boxes. You can hold your mouse over a check box to see  
 what its category does. In general, however, a category name is the same as  
 the name of the package in which the trace message occurs.  
   
 Additional categories can be entered in an input box, delimited by spaces or commas.  
   
 The B<Activate> button turns on Emergency tracing at the level you specify with the  
 specified categories active. The B<Terminate> button turns tracing off. The  
 B<Show File> button displays the current contents of the trace file. The tracing  
 form at the bottom of the control panel is designed for emergency tracing, so it  
 will only affect programs that call L</ETracing>, L</StandardScript>,  
 or L</StandardSetup>.  
   
 =head4 Script Form  
   
 The top form of the debugging control panel allows you to enter a tiny script and  
 have the output generated in a formatted table. Certain object variables are  
 predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),  
 and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.  
   
 The last line of the script must be a scalar, but it can be a reference to a hash,  
 a list, a list of lists, and various other combinations. If you select the appropriate  
 data type in the dropdown box, the output will be formatted accordingly. The form  
 also has controls for specifying tracing. These controls override any emergency  
 tracing in effect.  
   
 =head4 Database Query Forms  
   
 The forms between the script form and the emergency tracing form allow you to  
 make queries against the database. The FIG query form allows simple queries against  
 a single FIG table. The Sprout query form uses the B<GetAll> method to do a  
 multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>  
 package, and it takes five parameters.  
   
     GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);  
   
 Each of the five parameters corresponds to a text box on the query form:  
   
 =over 4  
   
 =item Objects  
   
 Comma-separated list containing the names of the entity and relationship objects to be retrieved.  
   
 =item Filter  
   
 WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  
 be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form  
 B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a  
 field, I<objectName> is the name of the entity or relationship object containing the field, and  
 I<number> is the 1-based position of the object in the object list. Any parameters  
 specified in the filter clause should be specified in the B<Params> field.  
 The fields in a filter clause can come from primary entity relations,  
 relationship relations, or secondary entity relations; however, all of the  
 entities and relationships involved must be included in the list of object names.  
   
 =item Params  
   
 List of the parameters to be substituted in for the parameters marks in the filter clause. This  
 is a comma-separated list without any quoting or escaping.  
   
 =item fields  
   
 Comma-separated list of the fields to be returned in each element of the list returned. Fields  
 are specified in the same manner as in the filter clause.  
   
 =item count  
   
 Maximum number of records to return. If omitted or 0, all available records will be returned.  
   
 =back  
   
 B<GetAll> automatically joins together the entities and relationships listed in the object  
 names. This simplifies the coding of the filter clause, but it means that some queries are  
 not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation  
 that has yet to be addressed.  
   
193  =cut  =cut
194    
195  # Declare the configuration variables.  # Declare the configuration variables.
196    
197  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
198  my $TeeFlag = 0;            # TRUE if output is going to a file and to the  my $TeeFlag = 0;            # TRUE if output is going to a file and to the
199                              # standard output                              # standard output
200  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
201                              # hash of active category names                              # hash of active category names
202    my @LevelNames = qw(error warn notice info detail);
203  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
204                              # messages                              # messages
205  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
206  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
207    my $LastLevel = 0;          # level of the last test call
208  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
209  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
210    my $SavedCGI;               # CGI object passed to ETracing
211    umask 2;                    # Fix the damn umask so everything is group-writable.
212    
213    =head2 Tracing Methods
214    
215    =head3 Setups
216    
217        my $count = Tracer::Setups();
218    
219    Return the number of times L</TSetup> has been called.
220    
221    This method allows for the creation of conditional tracing setups where, for example, we
222    may want to set up tracing if nobody else has done it before us.
223    
224    =cut
225    
226  =head2 Public Methods  sub Setups {
227        return $SetupCount;
228    }
229    
230  =head3 TSetup  =head3 TSetup
231    
232  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
233    
234  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
235  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 350  Line 279 
279          }          }
280      }      }
281      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
282      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
283      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
284        # the standard output (tee mode).
285      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
286          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
287              $TeeFlag = 1;              $TeeFlag = 1;
288              $target = substr($target, 1);              $target = substr($target, 1);
289          }          }
290          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
291                # We need to initialize the file (which clears it).
292              open TRACEFILE, $target;              open TRACEFILE, $target;
293              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
294              close TRACEFILE;              close TRACEFILE;
295                # Set to append mode now that the file has been cleared.
296              $Destination = ">$target";              $Destination = ">$target";
297          } else {          } else {
298              $Destination = $target;              $Destination = $target;
# Line 372  Line 304 
304      $SetupCount++;      $SetupCount++;
305  }  }
306    
307  =head3 StandardSetup  =head3 SetLevel
   
 C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>  
308    
309  This method performs standard command-line parsing and tracing setup. The return      Tracer::SetLevel($newLevel);
 values are a hash of the command-line options and a list of the positional  
 parameters. Tracing is automatically set up and the command-line options are  
 validated.  
310    
311  This is a complex method that does a lot of grunt work. The parameters can  Modify the trace level. A higher trace level will cause more messages to appear.
 be more easily understood, however, once they are examined individually.  
312    
313  The I<categories> parameter is the most obtuse. It is a reference to a list of  =over 4
 special-purpose tracing categories. Most tracing categories are PERL package  
 names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,  
 B<ERDB>, and B<SproutLoad> packages, you would specify the categories  
314    
315      ["Sprout", "SproutLoad", "ERDB"]  =item newLevel
316    
317  This would cause trace messages in the specified three packages to appear in  Proposed new trace level.
 the output. There are two special tracing categories that are automatically  
 handled by this method. In other words, if you used L</TSetup> you would need  
 to include these categories manually, but if you use this method they are turned  
 on automatically.  
318    
319  =over 4  =back
320    
321  =item SQL  =cut
322    
323  Traces SQL commands and activity.  sub SetLevel {
324        $TraceLevel = $_[0];
325    }
326    
327  =item Tracer  =head3 ParseDate
328    
329  Traces error messages and call stacks.      my $time = Tracer::ParseDate($dateString);
330    
331  =back  Convert a date into a PERL time number. This method expects a date-like string
332    and parses it into a number. The string must be vaguely date-like or it will
333    return an undefined value. Our requirement is that a month and day be
334    present and that three pieces of the date string (time of day, month and day,
335    year) be separated by likely delimiters, such as spaces, commas, and such-like.
336    
337  C<SQL> is only turned on if the C<-sql> option is specified in the command line.  If a time of day is present, it must be in military time with two digits for
338  The trace level is specified using the C<-trace> command-line option. For example,  everything but the hour.
 the following command line for C<TransactFeatures> turns on SQL tracing and runs  
 all tracing at level 3.  
339    
340      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  The year must be exactly four digits.
341    
342  Standard tracing is output to the standard output and echoed to the file  Additional stuff can be in the string. We presume it's time zones or weekdays or something
343  C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the  equally innocuous. This means, however, that a sufficiently long sentence with date-like
344  process ID. You can also specify the C<user> parameter to put a user ID  parts in it may be interpreted as a date. Hopefully this will not be a problem.
 instead of a process ID in the trace file name. So, for example  
345    
346  The default trace level is 2. To get all messages, specify a trace level of 4.  It should be guaranteed that this method will parse the output of the L</Now> function.
 For a genome-by-genome update, use 3.  
347    
348      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  The parameters are as follows.
349    
350  would send the trace output to C<traceBruce.log> in the temporary directory.  =over 4
351    
352  The I<options> parameter is a reference to a hash containing the command-line  =item dateString
 options, their default values, and an explanation of what they mean. Command-line  
 options may be in the form of switches or keywords. In the case of a switch, the  
 option value is 1 if it is specified and 0 if it is not specified. In the case  
 of a keyword, the value is separated from the option name by an equal sign. You  
 can see this last in the command-line example above.  
353    
354  You can specify a different default trace level by setting C<$options->{trace}>  The date string to convert.
 prior to calling this method.  
355    
356  An example at this point would help. Consider, for example, the command-line utility  =item RETURN
 C<TransactFeatures>. It accepts a list of positional parameters plus the options  
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
357    
358      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
359                          { safe => [0, "use database transactions"],  the date string is invalid. A valid date string must contain a month and day.
                           noAlias => [0, "do not expect aliases in CHANGE transactions"],  
                           start => [' ', "start with this genome"],  
                           tblFiles => [0, "output TBL files containing the corrected IDs"] },  
                         "<command> <transactionDirectory> <IDfile>",  
                       @ARGV);  
360    
361    =back
362    
363  The call to C<ParseCommand> specifies the default values for the options and  =cut
 stores the actual options in a hash that is returned as C<$options>. The  
 positional parameters are returned in C<@parameters>.  
364    
365  The following is a sample command line for C<TransactFeatures>.  # Universal month conversion table.
366    use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
367                                Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
368                                Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
369                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
370                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
371                                Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
372                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
373                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
374                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
375                                Oct =>  9, October  =>   9, '10' =>  9,
376                                Nov => 10, November =>  10, '11' => 10,
377                                Dec => 11, December =>  11, '12' => 11
378                            };
379    
380      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  sub ParseDate {
381        # Get the parameters.
382        my ($dateString) = @_;
383        # Declare the return variable.
384        my $retVal;
385        # Find the month and day of month. There are two ways that can happen. We check for the
386        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
387        # won't be fooled into thinking the month is Sunday.
388        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
389            my ($mon, $mday) = (MONTHS->{$1}, $2);
390            # Insist that the month and day are valid.
391            if (defined($mon) && $2 >= 1 && $2 <= 31) {
392                # Find the time.
393                my ($hour, $min, $sec) = (0, 0, 0);
394                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
395                    ($hour, $min, $sec) = ($1, $2, $3);
396                }
397                # Find the year.
398                my $year;
399                if ($dateString =~ /\b(\d{4})\b/) {
400                    $year = $1;
401                } else {
402                    # Get the default year, which is this one. Note we must convert it to
403                    # the four-digit value expected by "timelocal".
404                    (undef, undef, undef, undef, undef, $year) = localtime();
405                    $year += 1900;
406                }
407                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
408            }
409        }
410        # Return the result.
411        return $retVal;
412    }
413    
414  Single and double hyphens are equivalent. So, you could also code the  =head3 LogErrors
 above command as  
415    
416      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl      Tracer::LogErrors($fileName);
417    
418  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  Route the standard error output to a log file.
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
419    
420      { trace => 2, sql => 0, safe => 0,  =over 4
       noAlias => 1, start => ' ', tblFiles => 0 }  
421    
422  Use of C<StandardSetup> in this way provides a simple way of performing  =item fileName
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
423    
424  If the C<background> option is specified on the command line, then the  Name of the file to receive the error output.
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
425    
426      -user=Bruce -background  =back
427    
428  then the trace output would go to C<traceBruce.log>, the standard output to  =cut
 C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to  
 simplify starting a command in the background.  
429    
430  The user name is also used as the tracing key for L</Emergency Tracing>.  sub LogErrors {
431  Specifying a value of C<E> for the trace level causes emergency tracing to      # Get the file name.
432  be used instead of custom tracing. If the user name is not specified,      my ($fileName) = @_;
433  the tracing key is taken from the C<Tracing> environment variable. If there      # Open the file as the standard error output.
434  is no value for that variable, the tracing key will be computed from the PID.      open STDERR, '>', $fileName;
435    }
436    
437  Finally, if the special option C<-help> is specified, the option  =head3 Trace
 names will be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
438    
439      TransactFeatures -help      Trace($message);
440    
441  he would see the following output.  Write a trace message to the target location specified in L</TSetup>. If there has not been
442    any prior call to B<TSetup>.
443    
444      TransactFeatures [options] <command> <transactionDirectory> <IDfile>  =over 4
         -trace    tracing level (default E)  
         -sql      trace SQL commands  
         -safe     use database transactions  
         -noAlias  do not expect aliases in CHANGE transactions  
         -start    start with this genome  
         -tblFiles output TBL files containing the corrected IDs  
445    
446  The caller has the option of modifying the tracing scheme by placing a value  =item message
 for C<trace> in the incoming options hash. The default value can be overridden,  
 or the tracing to the standard output can be turned off by suffixing a minus  
 sign to the trace level. So, for example,  
447    
448      { trace => [0, "tracing level (default 0)"],  Message to write.
        ...  
449    
450  would set the default trace level to 0 instead of E, while  =back
451    
452      { trace => ["2-", "tracing level (default 2)"],  =cut
        ...  
453    
454  would set the default to 2, but trace only to the log file, not to the  sub Trace {
455  standard output.      # Get the parameters.
456        my ($message) = @_;
457        # Strip off any line terminators at the end of the message. We will add
458        # new-line stuff ourselves.
459        my $stripped = Strip($message);
460        # Compute the caller information.
461        my ($callPackage, $callFile, $callLine) = caller();
462        my $callFileTitle = basename($callFile);
463        # Check the caller.
464        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
465        # Get the timestamp.
466        my $timeStamp = Now();
467        # Build the prefix.
468        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
469        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
470        # Format the message.
471        my $formatted = "$prefix $stripped";
472        # Process according to the destination.
473        if ($Destination eq "TEXT") {
474            # Write the message to the standard output.
475            print "$formatted\n";
476        } elsif ($Destination eq "ERROR") {
477            # Write the message to the error output. Here, we want our prefix fields.
478            print STDERR "$formatted\n";
479        } elsif ($Destination eq "WARN") {
480            # Emit the message to the standard error output. It is presumed that the
481            # error logger will add its own prefix fields, the notable exception being
482            # the caller info.
483            print STDERR "$callerInfo$stripped\n";
484        } elsif ($Destination eq "QUEUE") {
485            # Push the message into the queue.
486            push @Queue, "$formatted";
487        } elsif ($Destination eq "HTML") {
488            # Convert the message to HTML and write it to the standard output.
489            my $escapedMessage = CGI::escapeHTML($stripped);
490            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
491        } elsif ($Destination =~ m/^>>/) {
492            # Write the trace message to an output file.
493            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
494            print TRACING "$formatted\n";
495            close TRACING;
496            # If the Tee flag is on, echo it to the standard output.
497            if ($TeeFlag) {
498                print "$formatted\n";
499            }
500        }
501    }
502    
503  The parameters to this method are as follows.  =head3 T
504    
505  =over 4      my $switch = T($category, $traceLevel);
506    
507  =item categories      or
508    
509  Reference to a list of tracing category names. These should be names of      my $switch = T($traceLevel);
 packages whose internal workings will need to be debugged to get the  
 command working.  
510    
511  =item options  Return TRUE if the trace level is at or above a specified value and the specified category
512    is active, else FALSE. If no category is specified, the caller's package name is used.
513    
514  Reference to a hash containing the legal options for the current command mapped  =over 4
 to their default values and descriptions. The user can override the defaults  
 by specifying the options as command-line switches prefixed by a hyphen.  
 Tracing-related options may be added to this hash. If the C<-h> option is  
 specified on the command line, the option descriptions will be used to  
 explain the options. To turn off tracing to the standard output, add a  
 minus sign to the value for C<trace> (see above).  
515    
516  =item parmHelp  =item category
517    
518  A string that vaguely describes the positional parameters. This is used  Category to which the message belongs. If not specified, the caller's package name is
519  if the user specifies the C<-h> option.  used.
520    
521  =item argv  =item traceLevel
522    
523  List of command line parameters, including the option switches, which must  Relevant tracing level.
 precede the positional parameters and be prefixed by a hyphen.  
524    
525  =item RETURN  =item RETURN
526    
527  Returns a list. The first element of the list is the reference to a hash that  TRUE if a message at the specified trace level would appear in the trace, else FALSE.
 maps the command-line option switches to their values. These will either be the  
 default values or overrides specified on the command line. The remaining  
 elements of the list are the position parameters, in order.  
528    
529  =back  =back
530    
531  =cut  =cut
532    
533  sub StandardSetup {  sub T {
534        # Declare the return variable.
535        my $retVal = 0;
536        # Only proceed if tracing is turned on.
537        if ($Destination ne "NONE") {
538      # Get the parameters.      # Get the parameters.
539      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
540      # Get the default tracing key.          if (!defined $traceLevel) {
541      my $tkey = EmergencyKey();              # Here we have no category, so we need to get the calling package.
542      # Add the tracing options.              # The calling package is normally the first parameter. If it is
543      if (! exists $options->{trace}) {              # omitted, the first parameter will be the tracelevel. So, the
544          $options->{trace} = ['E', "tracing level (E for emergency tracing)"];              # first thing we do is shift the so-called category into the
545      }              # $traceLevel variable where it belongs.
546      $options->{sql} = [0, "turn on SQL tracing"];              $traceLevel = $category;
547      $options->{help} = [0, "display command-line options"];              my ($package, $fileName, $line) = caller;
548      $options->{user} = [$tkey, "tracing key"];              # If there is no calling package, we default to "main".
549      $options->{background} = [0, "spool standard and error output"];              if (!$package) {
550      # Create a parsing hash from the options hash. The parsing hash                  $category = "main";
     # contains the default values rather than the default value  
     # and the description. While we're at it, we'll memorize the  
     # length of the longest option name.  
     my $longestName = 0;  
     my %parseOptions = ();  
     for my $key (keys %{$options}) {  
         if (length $key > $longestName) {  
             $longestName = length $key;  
         }  
         $parseOptions{$key} = $options->{$key}->[0];  
     }  
     # Parse the command line.  
     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);  
     # Get the logfile suffix.  
     my $suffix = $retOptions->{user};  
     # Check for background mode.  
     if ($retOptions->{background}) {  
         my $outFileName = "$FIG_Config::temp/out$suffix.log";  
         my $errFileName = "$FIG_Config::temp/err$suffix.log";  
         open STDOUT, ">$outFileName";  
         open STDERR, ">$errFileName";  
     }  
     # Now we want to set up tracing. First, we need to know if the user  
     # wants emergency tracing.  
     if ($retOptions->{trace} eq 'E') {  
         ETracing($retOptions->{user});  
     } else {  
         # Here the tracing is controlled from the command line.  
         my @cats = @{$categories};  
         if ($retOptions->{sql}) {  
             push @cats, "SQL";  
         }  
         # Add the default categories.  
         push @cats, "Tracer";  
         # Next, we create the category string by joining the categories.  
         my $cats = join(" ", @cats);  
         # Check to determine whether or not the caller wants to turn off tracing  
         # to the standard output.  
         my $traceLevel = $retOptions->{trace};  
         my $textOKFlag = 1;  
         if ($traceLevel =~ /^(.)-/) {  
             $traceLevel = $1;  
             $textOKFlag = 0;  
         }  
         # Now we set up the trace mode.  
         my $traceMode;  
         # Verify that we can open a file in the FIG temporary directory.  
         my $traceFileName = "$FIG_Config::temp/trace$suffix.log";  
         if (open TESTTRACE, ">$traceFileName") {  
             # Here we can trace to a file.  
             $traceMode = ">$traceFileName";  
             if ($textOKFlag) {  
                 # Echo to standard output if the text-OK flag is set.  
                 $traceMode = "+$traceMode";  
             }  
             # Close the test file.  
             close TESTTRACE;  
         } else {  
             # Here we can't trace to a file. We trace to the standard output if it's  
             # okay, and the error log otherwise.  
             if ($textOKFlag) {  
                 $traceMode = "TEXT";  
551              } else {              } else {
552                  $traceMode = "WARN";                  my @cats = split /::/, $package;
553              }                  $category = $cats[$#cats];
         }  
         # Now set up the tracing.  
         TSetup("$traceLevel $cats", $traceMode);  
     }  
     # Check for the "h" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($retOptions->{help}) {  
         $0 =~ m#[/\\](\w+)(\.pl)?$#i;  
         print "$1 [options] $parmHelp\n";  
         for my $key (sort keys %{$options}) {  
             my $name = Pad($key, $longestName, 0, ' ');  
             my $desc = $options->{$key}->[1];  
             if ($options->{$key}->[0]) {  
                 $desc .= " (default " . $options->{$key}->[0] . ")";  
554              }              }
             print "  $name $desc\n";  
555          }          }
556          exit(0);          # Save the category name and level.
557            $LastCategory = $category;
558            $LastLevel = $traceLevel;
559            # Convert it to lower case before we hash it.
560            $category = lc $category;
561            # Validate the trace level.
562            if (ref $traceLevel) {
563                Confess("Bad trace level.");
564            } elsif (ref $TraceLevel) {
565                Confess("Bad trace config.");
566      }      }
567      # Trace the options, if applicable.          # Make the check. Note that level 0 shows even if the category is turned off.
568      if (T(3)) {          $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
         my @parms = grep { $retOptions->{$_} } keys %{$retOptions};  
         Trace("Selected options: " . join(", ", sort @parms) . ".");  
569      }      }
570      # Return the parsed parameters.      # Return the computed result.
571      return ($retOptions, @retParameters);      return $retVal;
572  }  }
573    
574  =head3 Setups  =head3 QTrace
575    
576  C<< my $count = Tracer::Setups(); >>      my $data = QTrace($format);
577    
578  Return the number of times L</TSetup> has been called.  Return the queued trace data in the specified format.
579    
580  This method allows for the creation of conditional tracing setups where, for example, we  =over 4
581  may want to set up tracing if nobody else has done it before us.  
582    =item format
583    
584    C<html> to format the data as an HTML list, C<text> to format it as straight text.
585    
586    =back
587    
588  =cut  =cut
589    
590  sub Setups {  sub QTrace {
591      return $SetupCount;      # Get the parameter.
592        my ($format) = @_;
593        # Create the return variable.
594        my $retVal = "";
595        # Only proceed if there is an actual queue.
596        if (@Queue) {
597            # Process according to the format.
598            if ($format =~ m/^HTML$/i) {
599                # Convert the queue into an HTML list.
600                $retVal = "<ul>\n";
601                for my $line (@Queue) {
602                    my $escapedLine = CGI::escapeHTML($line);
603                    $retVal .= "<li>$escapedLine</li>\n";
604                }
605                $retVal .= "</ul>\n";
606            } elsif ($format =~ m/^TEXT$/i) {
607                # Convert the queue into a list of text lines.
608                $retVal = join("\n", @Queue) . "\n";
609            }
610            # Clear the queue.
611            @Queue = ();
612        }
613        # Return the formatted list.
614        return $retVal;
615  }  }
616    
617  =head3 Open  =head3 Confess
   
 C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  
618    
619  Open a file.      Confess($message);
620    
621  The I<$fileSpec> is essentially the second argument of the PERL C<open>  Trace the call stack and abort the program with the specified message. When used with
622  function. The mode is specified using Unix-like shell information. So, for  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
623  example,  So, for example
624    
625      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
626    
627  would open for output appended to the specified file, and  Will abort the program with a stack trace if the value of C<$recNum> is negative.
628    
629      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  =over 4
630    
631  would open a pipe that sorts the records written and removes duplicates. Note  =item message
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
632    
633      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  Message to include in the trace.
634    
635  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  =back
 the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a  
 failed open will throw an exception and the third parameter will be used to construct  
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
636    
637      Could not open "/usr/spool/news/twitlog"  =cut
638    
639  Note that the mode characters are automatically cleaned from the file name.  sub Confess {
640  The actual error message from the file system will be captured and appended to the      # Get the parameters.
641  message in any case.      my ($message) = @_;
642        # Set up the category and level.
643        $LastCategory = "(confess)";
644        $LastLevel = 0;
645        if (! defined($FIG_Config::no_tool_hdr)) {
646            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
647            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
648            # Only proceed if the tool header file is actually present.
649            if (-f $toolHeaderFile) {
650                my $fh;
651                if (open $fh, "<$toolHeaderFile") {
652                    my @lines = <$fh>;
653                    Trace("Tool header has " . scalar(@lines) . " lines.");
654                }
655            }
656        }
657        # Trace the call stack.
658        Cluck($message);
659        # Abort the program.
660        croak(">>> $message");
661    }
662    
663      Could not open "/usr/spool/news/twitlog": file not found.  =head3 Warn
664    
665  In some versions of PERL the only error message we get is a number, which      Warn($message);
 corresponds to the C++ C<errno> value.  
666    
667      Could not open "/usr/spool/news/twitlog": 6.  This method traces an important message. If an RSS feed is configured
668    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
669    then the message will be echoed to the feed. In general, a tracing
670    destination of C<WARN> indicates that the caller is running as a web
671    service in a production environment; however, this is not a requirement.
672    
673    To force warnings into the RSS feed even when the tracing destination
674    is not C<WARN>, simply specify the C<Feed> tracing module. This can be
675    configured automatically when L</StandardSetup> is used.
676    
677    The L</Cluck> method calls this one for its final message. Since
678    L</Confess> calls L</Cluck>, this means that any error which is caught
679    and confessed will put something in the feed. This insures that someone
680    will be alerted relatively quickly when a failure occurs.
681    
682  =over 4  =over 4
683    
684  =item fileHandle  =item message
685    
686  File handle. If this parameter is C<undef>, a file handle will be generated  Message to be traced.
 and returned as the value of this method.  
687    
688  =item fileSpec  =back
689    
690  File name and mode, as per the PERL C<open> function.  =cut
691    
692  =item message (optional)  sub Warn {
693        # Get the parameters.
694        my ($message) = @_;
695        # Trace the message.
696        Trace($message);
697        # Check for feed forcing.
698        my $forceFeed = exists $Categories{feed};
699        # An error here would be disastrous. Note, however, that we aren't too worried
700        # about losing events. The error log is always available for the occasions where
701        # we mess up. Note that if debug mode is specified, we do this stuff even in a
702        # test environment.
703        eval {
704            # Do we need to put this in the RSS feed?
705            if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
706                # Yes. We now need to compute the date, the link, and the title.
707                # First, the date, in a very specific format.
708                my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
709                    (tz_local_offset() / 30);
710                # Environment data goes in here. We start with the date.
711                my $environment = "$date.  ";
712                # If we need to recap the message (because it's too long to be a title), we'll
713                # put it in here.
714                my $recap;
715                # Copy the message and remove excess space.
716                my $title = $message;
717                $title =~ s/\s+/ /gs;
718                # If it's too long, we have to split it up.
719                if (length $title > 60) {
720                    # Put the full message in the environment string.
721                    $recap = $title;
722                    # Excerpt it as the title.
723                    $title = substr($title, 0, 50) . "...";
724                }
725                # If we have a CGI object, then this is a web error. Otherwise, it's
726                # command-line.
727                if (defined $SavedCGI) {
728                    # We're in a web service. The environment is the user's IP, and the link
729                    # is the URL that got us here.
730                    my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
731                    $environment .= "Event Reported at IP address $key.";
732                    my $url = $SavedCGI->url(-full => 1, -query => 1);
733                    # We need the user agent string and (if available) the referrer.
734                    # The referrer will be the link.
735                    $environment .= "User Agent $ENV{HTTP_USER_AGENT}";
736                    if ($ENV{HTTP_REFERER}) {
737                        my $link = $ENV{HTTP_REFERER};
738                        $environment .= " referred from <a href=\"$link\">$link</a>.";
739                    } else {
740                        $environment .= " referrer unknown.";
741                    }
742                    # Close off the sentence with the original link.
743                    $environment .= " URL of error is <a href=\"$url\">$url</a>.";
744                } else {
745                    # No CGI object, so we're a command-line tool. Use the tracing
746                    # key and the PID as the user identifier, and add the command.
747                    my $key = EmergencyKey();
748                    $environment .= "Event Reported by $key Process $$. Command $ENV{_}.";
749                }
750                # Build a GUID. We use the current time, the title, and the process ID,
751                # then digest the result.
752                my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
753                # Finally, the description. This is a stack trace plus various environmental stuff.
754                my $stackTrace = "";
755                my @trace = LongMess();
756                # Only proceed if we got something back.
757                if (scalar(@trace) > 0) {
758                    $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
759                    $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
760                }
761                # We got the stack trace. Now it's time to put it all together.
762                # We have a goofy thing here in that we need to HTML-escape some sections of the description
763                # twice. They will be escaped once here, and then once when written by XML::Simple. They are
764                # unescaped once when processed by the RSS reader, and stuff in the description is treated as
765                # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
766                # our <br>s and <pre>s are used to format the description.
767                $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
768                my $description = "$recap$environment  $stackTrace";
769                # Okay, we have all the pieces. Create a hash of the new event.
770                my $newItem = { title => $title,
771                                description => $description,
772                                category => $LastCategory,
773                                pubDate => $date,
774                                guid => $guid,
775                               };
776                # We need XML capability for this.
777                require XML::Simple;
778                # The RSS document goes in here.
779                my $rss;
780                # Get the name of the RSS file. It's in the FIG temporary directory.
781                my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
782                # Does it exist?
783                if (-s $fileName) {
784                    # Slurp it in.
785                    $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
786                } else {
787                    my $size = -s $fileName;
788                    # Create an empty channel.
789                    $rss = {
790                        channel => {
791                            title => 'NMPDR Warning Feed',
792                            link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
793                            description => "Important messages regarding the status of the NMPDR.",
794                            generator => "NMPDR Trace Facility",
795                            docs => "http://blogs.law.harvard.edu/tech/rss",
796                            item => []
797                        },
798                    };
799                }
800                # Get the channel object.
801                my $channel = $rss->{channel};
802                # Update the last-build date.
803                $channel->{lastBuildDate} = $date;
804                # Get the item array.
805                my $items = $channel->{item};
806                # Insure it has only 100 entries.
807                while (scalar @{$items} > 100) {
808                    pop @{$items};
809                }
810                # Add our new item at the front.
811                unshift @{$items}, $newItem;
812                # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
813                # the requirements for those.
814                my $xml = XML::Simple::XMLout($rss, NoAttr => 1, RootName => undef, XmlDecl => '');
815                # Here we put in the root and declaration. The problem is that the root has to have the version attribute
816                # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
817                $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
818                # We don't use Open here because we can't afford an error.
819                if (open XMLOUT, ">$fileName") {
820                    print XMLOUT $xml;
821                    close XMLOUT;
822                }
823            }
824        };
825        if ($@) {
826            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
827            # (which is a good thing).
828            my $error = $@;
829            Trace("Feed Error: $error") if T(Feed => 0);
830        }
831    }
832    
833  Error message to use if the open fails. If omitted, a standard error message  =head3 Assert
 will be generated. In either case, the error information from the file system  
 is appended to the message. To specify a conditional open that does not throw  
 an error if it fails, use C<0>.  
834    
835  =item RETURN      Assert($condition1, $condition2, ... $conditionN);
836    
837  Returns the name of the file handle assigned to the file, or C<undef> if the  Return TRUE if all the conditions are true. This method can be used in conjunction with
838  open failed.  the OR operator and the L</Confess> method as a debugging assert.
839    So, for example
840    
841  =back      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
842    
843    Will abort the program with a stack trace if the value of C<$recNum> is negative.
844    
845    =cut
846    sub Assert {
847        my $retVal = 1;
848        LOOP: for my $condition (@_) {
849            if (! $condition) {
850                $retVal = 0;
851                last LOOP;
852            }
853        }
854        return $retVal;
855    }
856    
857    =head3 Cluck
858    
859        Cluck($message);
860    
861    Trace the call stack. Note that for best results, you should qualify the call with a
862    trace condition. For example,
863    
864        Cluck("Starting record parse.") if T(3);
865    
866    will only trace the stack if the trace level for the package is 3 or more.
867    
868    =over 4
869    
870    =item message
871    
872    Message to include in the trace.
873    
874    =back
875    
876    =cut
877    
878    sub Cluck {
879        # Get the parameters.
880        my ($message) = @_;
881        # Trace what's happening.
882        Trace("Stack trace for event: $message");
883        # Get the stack trace.
884        my @trace = LongMess();
885        # Convert the trace to a series of messages.
886        for my $line (@trace) {
887            # Replace the tab at the beginning with spaces.
888            $line =~ s/^\t/    /;
889            # Trace the line.
890            Trace($line);
891        }
892        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
893        Warn($message);
894    }
895    
896    =head3 LongMess
897    
898        my @lines = Tracer::LongMess();
899    
900    Return a stack trace with all tracing methods removed. The return will be in the form of a list
901    of message strings.
902    
903    =cut
904    
905    sub LongMess {
906        # Declare the return variable.
907        my @retVal = ();
908        my $confession = longmess("");
909        for my $line (split /\s*\n/, $confession) {
910            unless ($line =~ /Tracer\.pm/) {
911                # Here we have a line worth keeping. Push it onto the result list.
912                push @retVal, $line;
913            }
914        }
915        # Return the result.
916        return @retVal;
917    }
918    
919    =head3 ScriptSetup (deprecated)
920    
921        my ($cgi, $varHash) = ScriptSetup($noTrace);
922    
923    Perform standard tracing and debugging setup for scripts. The value returned is
924    the CGI object followed by a pre-built variable hash. At the end of the script,
925    the client should call L</ScriptFinish> to output the web page.
926    
927    This method calls L</ETracing> to configure tracing, which allows the tracing
928    to be configured via the emergency tracing form on the debugging control panel.
929    Tracing will then be turned on automatically for all programs that use the L</ETracing>
930    method, which includes every program that uses this method or L</StandardSetup>.
931    
932    =over 4
933    
934    =item noTrace (optional)
935    
936    If specified, tracing will be suppressed. This is useful if the script wants to set up
937    tracing manually.
938    
939    =item RETURN
940    
941    Returns a two-element list consisting of a CGI query object and a variable hash for
942    the output page.
943    
944    =back
945    
946    =cut
947    
948    sub ScriptSetup {
949        # Get the parameters.
950        my ($noTrace) = @_;
951        # Get the CGI query object.
952        my $cgi = CGI->new();
953        # Set up tracing if it's not suppressed.
954        ETracing($cgi) unless $noTrace;
955        # Create the variable hash.
956        my $varHash = { results => '' };
957        # Return the query object and variable hash.
958        return ($cgi, $varHash);
959    }
960    
961    =head3 ETracing
962    
963        ETracing($parameter);
964    
965    Set up emergency tracing. Emergency tracing is tracing that is turned
966    on automatically for any program that calls this method. The emergency
967    tracing parameters are stored in a a file identified by a tracing key.
968    If this method is called with a CGI object, then the tracing key is
969    taken from a cookie. If it is called with no parameters, then the tracing
970    key is taken from an environment variable. If it is called with a string,
971    the tracing key is that string.
972    
973    =over 4
974    
975    =item parameter
976    
977    A parameter from which the tracing key is computed. If it is a scalar,
978    that scalar is used as the tracing key. If it is a CGI object, the
979    tracing key is taken from the C<IP> cookie. If it is omitted, the
980    tracing key is taken from the C<TRACING> environment variable. If it
981    is a CGI object and emergency tracing is not on, the C<Trace> and
982    C<TF> parameters will be used to determine the type of tracing.
983    
984    =back
985    
986    =cut
987    
988    sub ETracing {
989        # Get the parameter.
990        my ($parameter) = @_;
991        # Check for CGI mode.
992        if (defined $parameter && ref $parameter eq 'CGI') {
993            $SavedCGI = $parameter;
994        } else {
995            $SavedCGI = undef;
996        }
997        # Default to no tracing except errors.
998        my ($tracing, $dest) = ("0", "WARN");
999        # Check for emergency tracing.
1000        my $tkey = EmergencyKey($parameter);
1001        my $emergencyFile = EmergencyFileName($tkey);
1002        if (-e $emergencyFile) {
1003            # We have the file. Read in the data.
1004            my @tracing = GetFile($emergencyFile);
1005            # Pull off the time limit.
1006            my $expire = shift @tracing;
1007            # Convert it to seconds.
1008            $expire *= 3600;
1009            # Check the file data.
1010            my $stat = stat($emergencyFile);
1011            my ($now) = gettimeofday;
1012            if ($now - $stat->mtime > $expire) {
1013                # Delete the expired file.
1014                unlink $emergencyFile;
1015            } else {
1016                # Emergency tracing is on. Pull off the destination and
1017                # the trace level;
1018                $dest = shift @tracing;
1019                my $level = shift @tracing;
1020                # Convert the destination to a real tracing destination.
1021                # temp directory.
1022                $dest = EmergencyTracingDest($tkey, $dest);
1023                # Insure Tracer is specified.
1024                my %moduleHash = map { $_ => 1 } @tracing;
1025                $moduleHash{Tracer} = 1;
1026                # Set the trace parameter.
1027                $tracing = join(" ", $level, sort keys %moduleHash);
1028            }
1029        } elsif (defined $SavedCGI) {
1030            # There's no emergency tracing, but we have a CGI object, so check
1031            # for tracing from the form parameters.
1032            if ($SavedCGI->param('Trace')) {
1033                # Here the user has requested tracing via a form.
1034                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1035                $tracing = $SavedCGI->param('Trace') . " Tracer";
1036            }
1037        }
1038        # Setup the tracing we've determined from all the stuff above.
1039        TSetup($tracing, $dest);
1040        # Check to see if we're a web script.
1041        if (defined $SavedCGI) {
1042            # Yes we are. Trace the form and environment data.
1043            TraceParms($SavedCGI);
1044            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1045            # emitted by the script in its raw form.
1046            if (T(Raw => 3)) {
1047                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1048            }
1049        }
1050    }
1051    
1052    =head3 EmergencyFileName
1053    
1054        my $fileName = Tracer::EmergencyFileName($tkey);
1055    
1056    Return the emergency tracing file name. This is the file that specifies
1057    the tracing information.
1058    
1059    =over 4
1060    
1061    =item tkey
1062    
1063    Tracing key for the current program.
1064    
1065    =item RETURN
1066    
1067    Returns the name of the file to contain the emergency tracing information.
1068    
1069    =back
1070    
1071    =cut
1072    
1073    sub EmergencyFileName {
1074        # Get the parameters.
1075        my ($tkey) = @_;
1076        # Compute the emergency tracing file name.
1077        return "$FIG_Config::temp/Emergency$tkey.txt";
1078    }
1079    
1080    =head3 EmergencyFileTarget
1081    
1082        my $fileName = Tracer::EmergencyFileTarget($tkey);
1083    
1084    Return the emergency tracing target file name. This is the file that receives
1085    the tracing output for file-based tracing.
1086    
1087    =over 4
1088    
1089    =item tkey
1090    
1091    Tracing key for the current program.
1092    
1093    =item RETURN
1094    
1095    Returns the name of the file to contain the trace output.
1096    
1097    =back
1098    
1099    =cut
1100    
1101    sub EmergencyFileTarget {
1102        # Get the parameters.
1103        my ($tkey) = @_;
1104        # Compute the emergency tracing file name.
1105        return "$FIG_Config::temp/trace$tkey.log";
1106    }
1107    
1108    =head3 EmergencyTracingDest
1109    
1110        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1111    
1112    This method converts an emergency tracing destination to a real
1113    tracing destination. The main difference is that if the
1114    destination is C<FILE> or C<APPEND>, we convert it to file
1115    output. If the destination is C<DUAL>, we convert it to file
1116    and standard output.
1117    
1118    =over 4
1119    
1120    =item tkey
1121    
1122    Tracing key for this environment.
1123    
1124    =item myDest
1125    
1126    Destination from the emergency tracing file.
1127    
1128    =item RETURN
1129    
1130    Returns a destination that can be passed into L</TSetup>.
1131    
1132    =back
1133    
1134    =cut
1135    
1136    sub EmergencyTracingDest {
1137        # Get the parameters.
1138        my ($tkey, $myDest) = @_;
1139        # Declare the return variable.
1140        my $retVal = $myDest;
1141        # Process according to the destination value.
1142        if ($myDest eq 'FILE') {
1143            $retVal = ">" . EmergencyFileTarget($tkey);
1144        } elsif ($myDest eq 'APPEND') {
1145            $retVal = ">>" . EmergencyFileTarget($tkey);
1146        } elsif ($myDest eq 'DUAL') {
1147            $retVal = "+>" . EmergencyFileTarget($tkey);
1148        } elsif ($myDest eq 'WARN') {
1149            $retVal = "WARN";
1150        }
1151        # Return the result.
1152        return $retVal;
1153    }
1154    
1155    =head3 Emergency
1156    
1157        Emergency($key, $hours, $dest, $level, @modules);
1158    
1159    Turn on emergency tracing. This method is normally invoked over the web from
1160    a debugging console, but it can also be called by the C<trace.pl> script.
1161    The caller specifies the duration of the emergency in hours, the desired tracing
1162    destination, the trace level, and a list of the trace modules to activate.
1163    For the length of the duration, when a program in an environment with the
1164    specified tracing key active invokes a Sprout CGI script, tracing will be
1165    turned on automatically. See L</TSetup> for more about tracing setup and
1166    L</ETracing> for more about emergency tracing.
1167    
1168    =over 4
1169    
1170    =item tkey
1171    
1172    The tracing key. This is used to identify the control file and the trace file.
1173    
1174    =item hours
1175    
1176    Number of hours to keep emergency tracing alive.
1177    
1178    =item dest
1179    
1180    Tracing destination. If no path information is specified for a file
1181    destination, it is put in the FIG temporary directory.
1182    
1183    =item level
1184    
1185    Tracing level. A higher level means more trace messages.
1186    
1187    =item modules
1188    
1189    A list of the tracing modules to activate.
1190    
1191    =back
1192    
1193    =cut
1194    
1195    sub Emergency {
1196        # Get the parameters.
1197        my ($tkey, $hours, $dest, $level, @modules) = @_;
1198        # Create the emergency file.
1199        my $specFile = EmergencyFileName($tkey);
1200        my $outHandle = Open(undef, ">$specFile");
1201        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1202    }
1203    
1204    =head3 EmergencyKey
1205    
1206        my $tkey = EmergencyKey($parameter);
1207    
1208    Return the Key to be used for emergency tracing. This could be an IP address,
1209     a session ID, or a user name, depending on the environment.
1210    
1211    =over 4
1212    
1213    =item parameter
1214    
1215    Parameter defining the method for finding the tracing key. If it is a scalar,
1216    then it is presumed to be the tracing key itself. If it is a CGI object, then
1217    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1218    taken from the C<TRACING> environment variable.
1219    
1220    =item RETURN
1221    
1222    Returns the key to be used for labels in emergency tracing.
1223    
1224    =back
1225    
1226  =cut  =cut
1227    
1228  sub Open {  sub EmergencyKey {
1229      # Get the parameters.      # Get the parameters.
1230      my ($fileHandle, $fileSpec, $message) = @_;      my ($parameter) = @_;
1231      # Attempt to open the file.      # Declare the return variable.
1232      my $rv = open $fileHandle, $fileSpec;      my $retVal;
1233      # If the open failed, generate an error message.      # Determine the parameter type.
1234      if (! $rv) {      if (! defined $parameter) {
1235          # Save the system error message.          # Here we're supposed to check the environment. If that fails, we
1236          my $sysMessage = $!;          # get the effective login ID.
1237          # See if we need a default message.          $retVal = $ENV{TRACING} || scalar getpwuid($<);
1238          if (!$message) {      } else {
1239              # Clean any obvious mode characters and leading spaces from the          my $ptype = ref $parameter;
1240              # filename.          if ($ptype eq 'CGI') {
1241              my ($fileName) = FindNamePart($fileSpec);              # Here we were invoked from a web page. Look for a cookie.
1242              $message = "Could not open \"$fileName\"";              $retVal = $parameter->cookie('IP');
1243            } elsif (! $ptype) {
1244                # Here the key was passed in.
1245                $retVal = $parameter;
1246            }
1247        }
1248        # If no luck finding a key, use the PID.
1249        if (! defined $retVal) {
1250            $retVal = $$;
1251        }
1252        # Return the result.
1253        return $retVal;
1254    }
1255    
1256    
1257    =head3 TraceParms
1258    
1259        Tracer::TraceParms($cgi);
1260    
1261    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1262    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1263    
1264    =over 4
1265    
1266    =item cgi
1267    
1268    CGI query object containing the parameters to trace.
1269    
1270    =back
1271    
1272    =cut
1273    
1274    sub TraceParms {
1275        # Get the parameters.
1276        my ($cgi) = @_;
1277        if (T(CGI => 2)) {
1278            # Here we trace the GET-style URL for the script.
1279            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1280        }
1281        if (T(CGI => 3)) {
1282            # Here we want to trace the parameter data.
1283            my @names = $cgi->param;
1284            for my $parmName (sort @names) {
1285                # Note we skip the Trace parameters, which are for our use only.
1286                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1287                    my @values = $cgi->param($parmName);
1288                    Trace("[CGI] $parmName = " . join(", ", @values));
1289                }
1290            }
1291            # Display the request method.
1292            my $method = $cgi->request_method();
1293            Trace("Method: $method");
1294        }
1295        if (T(CGI => 4)) {
1296            # Here we want the environment data too.
1297            for my $envName (sort keys %ENV) {
1298                Trace("[ENV] $envName = $ENV{$envName}");
1299            }
1300        }
1301    }
1302    
1303    =head3 TraceImages
1304    
1305        Tracer::TraceImages($htmlString);
1306    
1307    Trace information about all of an html document's images. The tracing
1308    will be for type "IMG" at level 3. The image's source string
1309    will be displayed. This is generally either the URL of the image or
1310    raw data for the image itself. If the source is too long, only the first 300
1311    characters will be shown at trace level 3. The entire source will be shown,
1312    however, at trace level 4. This method is not very smart, and might catch
1313    Javascript code, but it is still useful when debugging the arcane
1314    behavior of images in multiple browser environments.
1315    
1316    =over 4
1317    
1318    =item htmlString
1319    
1320    HTML text for an outgoing web page.
1321    
1322    =back
1323    
1324    =cut
1325    
1326    sub TraceImages {
1327        # Only proceed if we're at the proper trace level.
1328        if (T(IMG => 3)) {
1329            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1330            # into a variable called "$htmlString". This is because we expect html strings to be
1331            # long, and don't want to copy them any more than we have to.
1332            Trace(length($_[0]) . " characters in web page.");
1333            # Loop through the HTML, culling image tags.
1334            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1335                # Extract the source string and determine whether or not it's too long.
1336                my $srcString = $1;
1337                my $pos = pos($_[0]) - length($srcString);
1338                my $excess = length($srcString) - 300;
1339                # We'll put the display string in here.
1340                my $srcDisplay = $srcString;
1341                # If it's a data string, split it at the comma.
1342                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1343                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1344                # a long string, however, we only show the first 300 characters.
1345                if ($excess > 0 && ! T(IMG => 4)) {
1346                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1347                }
1348                # Output the trace message.
1349                Trace("Image tag at position $pos:\n$srcDisplay");
1350            }
1351        }
1352    }
1353    
1354    
1355    =head3 ScriptFinish (deprecated)
1356    
1357        ScriptFinish($webData, $varHash);
1358    
1359    Output a web page at the end of a script. Either the string to be output or the
1360    name of a template file can be specified. If the second parameter is omitted,
1361    it is assumed we have a string to be output; otherwise, it is assumed we have the
1362    name of a template file. The template should have the variable C<DebugData>
1363    specified in any form that invokes a standard script. If debugging mode is turned
1364    on, a form field will be put in that allows the user to enter tracing data.
1365    Trace messages will be placed immediately before the terminal C<BODY> tag in
1366    the output, formatted as a list.
1367    
1368    A typical standard script would loook like the following.
1369    
1370        BEGIN {
1371            # Print the HTML header.
1372            print "CONTENT-TYPE: text/html\n\n";
1373        }
1374        use Tracer;
1375        use CGI;
1376        use FIG;
1377        # ... more uses ...
1378    
1379        my ($cgi, $varHash) = ScriptSetup();
1380        eval {
1381            # ... get data from $cgi, put it in $varHash ...
1382        };
1383        if ($@) {
1384            Trace("Script Error: $@") if T(0);
1385        }
1386        ScriptFinish("Html/MyTemplate.html", $varHash);
1387    
1388    The idea here is that even if the script fails, you'll see trace messages and
1389    useful output.
1390    
1391    =over 4
1392    
1393    =item webData
1394    
1395    A string containing either the full web page to be written to the output or the
1396    name of a template file from which the page is to be constructed. If the name
1397    of a template file is specified, then the second parameter must be present;
1398    otherwise, it must be absent.
1399    
1400    =item varHash (optional)
1401    
1402    If specified, then a reference to a hash mapping variable names for a template
1403    to their values. The template file will be read into memory, and variable markers
1404    will be replaced by data in this hash reference.
1405    
1406    =back
1407    
1408    =cut
1409    
1410    sub ScriptFinish {
1411        # Get the parameters.
1412        my ($webData, $varHash) = @_;
1413        # Check for a template file situation.
1414        my $outputString;
1415        if (defined $varHash) {
1416            # Here we have a template file. We need to determine the template type.
1417            my $template;
1418            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1419                $template = "$FIG_Config::template_url/$webData";
1420            } else {
1421                $template = "<<$webData";
1422            }
1423            $outputString = PageBuilder::Build($template, $varHash, "Html");
1424        } else {
1425            # Here the user gave us a raw string.
1426            $outputString = $webData;
1427        }
1428        # Check for trace messages.
1429        if ($Destination ne "NONE" && $TraceLevel > 0) {
1430            # We have trace messages, so we want to put them at the end of the body. This
1431            # is either at the end of the whole string or at the beginning of the BODY
1432            # end-tag.
1433            my $pos = length $outputString;
1434            if ($outputString =~ m#</body>#gi) {
1435                $pos = (pos $outputString) - 7;
1436            }
1437            # If the trace messages were queued, we unroll them. Otherwise, we display the
1438            # destination.
1439            my $traceHtml;
1440            if ($Destination eq "QUEUE") {
1441                $traceHtml = QTrace('Html');
1442            } elsif ($Destination =~ /^>>(.+)$/) {
1443                # Here the tracing output it to a file. We code it as a hyperlink so the user
1444                # can copy the file name into the clipboard easily.
1445                my $actualDest = $1;
1446                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1447            } else {
1448                # Here we have one of the special destinations.
1449                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1450            }
1451            substr $outputString, $pos, 0, $traceHtml;
1452        }
1453        # Write the output string.
1454        print $outputString;
1455    }
1456    
1457    =head2 Command-Line Utility Methods
1458    
1459    =head3 SendSMS
1460    
1461        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1462    
1463    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1464    user name, password, and API ID for the relevant account in the hash reference variable
1465    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1466    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1467    is C<2561022>, then the FIG_Config file must contain
1468    
1469        $phone =  { user => 'BruceTheHumanPet',
1470                    password => 'silly',
1471                    api_id => '2561022' };
1472    
1473    The original purpose of this method was to insure Bruce would be notified immediately when the
1474    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1475    when you call this method.
1476    
1477    The message ID will be returned if successful, and C<undef> if an error occurs.
1478    
1479    =over 4
1480    
1481    =item phoneNumber
1482    
1483    Phone number to receive the message, in international format. A United States phone number
1484    would be prefixed by "1". A British phone number would be prefixed by "44".
1485    
1486    =item msg
1487    
1488    Message to send to the specified phone.
1489    
1490    =item RETURN
1491    
1492    Returns the message ID if successful, and C<undef> if the message could not be sent.
1493    
1494    =back
1495    
1496    =cut
1497    
1498    sub SendSMS {
1499        # Get the parameters.
1500        my ($phoneNumber, $msg) = @_;
1501        # Declare the return variable. If we do not change it, C<undef> will be returned.
1502        my $retVal;
1503        # Only proceed if we have phone support.
1504        if (! defined $FIG_Config::phone) {
1505            Trace("Phone support not present in FIG_Config.") if T(1);
1506        } else {
1507            # Get the phone data.
1508            my $parms = $FIG_Config::phone;
1509            # Get the Clickatell URL.
1510            my $url = "http://api.clickatell.com/http/";
1511            # Create the user agent.
1512            my $ua = LWP::UserAgent->new;
1513            # Request a Clickatell session.
1514            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1515                                         password => $parms->{password},
1516                                         api_id => $parms->{api_id},
1517                                         to => $phoneNumber,
1518                                         text => $msg});
1519            # Check for an error.
1520            if (! $resp->is_success) {
1521                Trace("Alert failed.") if T(1);
1522            } else {
1523                # Get the message ID.
1524                my $rstring = $resp->content;
1525                if ($rstring =~ /^ID:\s+(.*)$/) {
1526                    $retVal = $1;
1527                } else {
1528                    Trace("Phone attempt failed with $rstring") if T(1);
1529          }          }
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
1530      }      }
1531      # Return the file handle.      }
1532      return $fileHandle;      # Return the result.
1533        return $retVal;
1534  }  }
1535    
1536  =head3 FindNamePart  =head3 StandardSetup
1537    
1538  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>      my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1539    
1540  Extract the portion of a file specification that contains the file name.  This method performs standard command-line parsing and tracing setup. The return
1541    values are a hash of the command-line options and a list of the positional
1542    parameters. Tracing is automatically set up and the command-line options are
1543    validated.
1544    
1545  A file specification is the string passed to an C<open> call. It specifies the file  This is a complex method that does a lot of grunt work. The parameters can
1546  mode and name. In a truly complex situation, it can specify a pipe sequence. This  be more easily understood, however, once they are examined individually.
 method assumes that the file name is whatever follows the first angle bracket  
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
1547    
1548      >>/usr/fig/myfile.txt  The I<categories> parameter is the most obtuse. It is a reference to a list of
1549      </usr/fig/myfile.txt  special-purpose tracing categories. Most tracing categories are PERL package
1550      | sort -u > /usr/fig/myfile.txt  names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1551    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1552    
1553  If the method cannot find a file name using its normal methods, it will return the      ["Sprout", "SproutLoad", "ERDB"]
1554  whole incoming string.  
1555    This would cause trace messages in the specified three packages to appear in
1556    the output. There are two special tracing categories that are automatically
1557    handled by this method. In other words, if you used L</TSetup> you would need
1558    to include these categories manually, but if you use this method they are turned
1559    on automatically.
1560    
1561  =over 4  =over 4
1562    
1563  =item fileSpec  =item SQL
1564    
1565  File specification string from which the file name is to be extracted.  Traces SQL commands and activity.
1566    
1567  =item RETURN  =item Tracer
1568    
1569  Returns a three-element list. The first element contains the file name portion of  Traces error messages and call stacks.
 the specified string, or the whole string if a file name cannot be found via normal  
 methods. The second element contains the start position of the file name portion and  
 the third element contains the length.  
1570    
1571  =back  =back
1572    
1573  =cut  C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1574  #: Return Type $;  The trace level is specified using the C<-trace> command-line option. For example,
1575  sub FindNamePart {  the following command line for C<TransactFeatures> turns on SQL tracing and runs
1576      # Get the parameters.  all tracing at level 3.
     my ($fileSpec) = @_;  
     # Default to the whole input string.  
     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);  
     # Parse out the file name if we can.  
     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {  
         $retVal = $2;  
         $len = length $retVal;  
         $pos = (length $fileSpec) - (length $3) - $len;  
     }  
     # Return the result.  
     return ($retVal, $pos, $len);  
 }  
1577    
1578  =head3 OpenDir      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1579    
1580  C<< my @files = OpenDir($dirName, $filtered, $flag); >>  Standard tracing is output to the standard output and echoed to the file
1581    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1582    process ID. You can also specify the C<user> parameter to put a user ID
1583    instead of a process ID in the trace file name. So, for example
1584    
1585  Open a directory and return all the file names. This function essentially performs  The default trace level is 2. To get all messages, specify a trace level of 4.
1586  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  For a genome-by-genome update, use 3.
 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  
 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be  
 filtered out of the return list. If the directory does not open and I<$flag> is not  
 set, an exception is thrown. So, for example,  
1587    
1588      my @files = OpenDir("/Volumes/fig/contigs", 1);      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1589    
1590  is effectively the same as  would send the trace output to C<traceBruce.log> in the temporary directory.
1591    
1592      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  The I<options> parameter is a reference to a hash containing the command-line
1593      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  options, their default values, and an explanation of what they mean. Command-line
1594    options may be in the form of switches or keywords. In the case of a switch, the
1595    option value is 1 if it is specified and 0 if it is not specified. In the case
1596    of a keyword, the value is separated from the option name by an equal sign. You
1597    can see this last in the command-line example above.
1598    
1599  Similarly, the following code  You can specify a different default trace level by setting C<$options->{trace}>
1600    prior to calling this method.
1601    
1602      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  An example at this point would help. Consider, for example, the command-line utility
1603    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1604    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1605    the following code.
1606    
1607  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1608  automatically returns an empty list if the directory fails to open.                          { safe => [0, "use database transactions"],
1609                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1610                              start => [' ', "start with this genome"],
1611                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1612                            "<command> <transactionDirectory> <IDfile>",
1613                          @ARGV);
1614    
 =over 4  
1615    
1616  =item dirName  The call to C<ParseCommand> specifies the default values for the options and
1617    stores the actual options in a hash that is returned as C<$options>. The
1618    positional parameters are returned in C<@parameters>.
1619    
1620  Name of the directory to open.  The following is a sample command line for C<TransactFeatures>.
1621    
1622  =item filtered      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1623    
1624  TRUE if files whose names begin with a period (C<.>) should be automatically removed  Single and double hyphens are equivalent. So, you could also code the
1625  from the list, else FALSE.  above command as
1626    
1627  =item flag      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1628    
1629  TRUE if a failure to open is okay, else FALSE  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1630    parameters, and would find themselves in I<@parameters> after executing the
1631    above code fragment. The tracing would be set to level 2, and the categories
1632    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1633    and C<DocUtils> was included because it came in within the first parameter
1634    to this method. The I<$options> hash would be
1635    
1636  =back      { trace => 2, sql => 0, safe => 0,
1637          noAlias => 1, start => ' ', tblFiles => 0 }
1638    
1639  =cut  Use of C<StandardSetup> in this way provides a simple way of performing
1640  #: Return Type @;  standard tracing setup and command-line parsing. Note that the caller is
1641  sub OpenDir {  not even aware of the command-line switches C<-trace> and C<-sql>, which
1642      # Get the parameters.  are used by this method to control the tracing. If additional tracing features
1643      my ($dirName, $filtered, $flag) = @_;  need to be added in the future, they can be processed by this method without
1644      # Declare the return variable.  upsetting the command-line utilities.
     my @retVal = ();  
     # Open the directory.  
     if (opendir(my $dirHandle, $dirName)) {  
         # The directory opened successfully. Get the appropriate list according to the  
         # strictures of the filter parameter.  
         if ($filtered) {  
             @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;  
         } else {  
             @retVal = readdir $dirHandle;  
         }  
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
     }  
     # Return the result.  
     return @retVal;  
 }  
1645    
1646  =head3 SetLevel  If the C<background> option is specified on the command line, then the
1647    standard and error outputs will be directed to files in the temporary
1648    directory, using the same suffix as the trace file. So, if the command
1649    line specified
1650    
1651  C<< Tracer::SetLevel($newLevel); >>      -user=Bruce -background
1652    
1653  Modify the trace level. A higher trace level will cause more messages to appear.  then the trace output would go to C<traceBruce.log>, the standard output to
1654    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1655    simplify starting a command in the background.
1656    
1657  =over 4  The user name is also used as the tracing key for L</Emergency Tracing>.
1658    Specifying a value of C<E> for the trace level causes emergency tracing to
1659    be used instead of custom tracing. If the user name is not specified,
1660    the tracing key is taken from the C<Tracing> environment variable. If there
1661    is no value for that variable, the tracing key will be computed from the active
1662    login ID.
1663    
1664  =item newLevel  Since the default situation in StandardSetup is to trace to the standard
1665    output, errors that occur in command-line scripts will not generate
1666    RSS events. To force the events, use the C<warn> option.
1667    
1668  Proposed new trace level.      TransactFeatures -background -warn register ../xacts IDs.tbl
1669    
1670  =back  Finally, if the special option C<-help> is specified, the option
1671    names will be traced at level 0 and the program will exit without processing.
1672    This provides a limited help capability. For example, if the user enters
1673    
1674  =cut      TransactFeatures -help
1675    
1676  sub SetLevel {  he would see the following output.
     $TraceLevel = $_[0];  
 }  
1677    
1678  =head3 Now      TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1679            -trace    tracing level (default E)
1680            -sql      trace SQL commands
1681            -safe     use database transactions
1682            -noAlias  do not expect aliases in CHANGE transactions
1683            -start    start with this genome
1684            -tblFiles output TBL files containing the corrected IDs
1685    
1686  C<< my $string = Tracer::Now(); >>  The caller has the option of modifying the tracing scheme by placing a value
1687    for C<trace> in the incoming options hash. The default value can be overridden,
1688    or the tracing to the standard output can be turned off by suffixing a minus
1689    sign to the trace level. So, for example,
1690    
1691  Return a displayable time stamp containing the local time.      { trace => [0, "tracing level (default 0)"],
1692           ...
1693    
1694  =cut  would set the default trace level to 0 instead of E, while
1695    
1696  sub Now {      { trace => ["2-", "tracing level (default 2)"],
1697      my ($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 $retVal;  
 }  
1698    
1699  # Pad a number to 2 digits.  would set the default to 2, but trace only to the log file, not to the
1700  sub _p2 {  standard output.
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
 }  
1701    
1702  =head3 ParseTraceDate  The parameters to this method are as follows.
1703    
1704  C<< my $time = Tracer::ParseTraceDate($dateString); >>  =over 4
1705    
1706  Convert a date from the trace file into a PERL timestamp.  =item categories
1707    
1708  =over 4  Reference to a list of tracing category names. These should be names of
1709    packages whose internal workings will need to be debugged to get the
1710    command working.
1711    
1712    =item options
1713    
1714    Reference to a hash containing the legal options for the current command mapped
1715    to their default values and descriptions. The user can override the defaults
1716    by specifying the options as command-line switches prefixed by a hyphen.
1717    Tracing-related options may be added to this hash. If the C<-h> option is
1718    specified on the command line, the option descriptions will be used to
1719    explain the options. To turn off tracing to the standard output, add a
1720    minus sign to the value for C<trace> (see above).
1721    
1722    =item parmHelp
1723    
1724    A string that vaguely describes the positional parameters. This is used
1725    if the user specifies the C<-h> option.
1726    
1727  =item dateString  =item argv
1728    
1729  The date string from the trace file. The format of the string is determined by the  List of command line parameters, including the option switches, which must
1730  L</Now> method.  precede the positional parameters and be prefixed by a hyphen.
1731    
1732  =item RETURN  =item RETURN
1733    
1734  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if  Returns a list. The first element of the list is the reference to a hash that
1735  the time string is invalid.  maps the command-line option switches to their values. These will either be the
1736    default values or overrides specified on the command line. The remaining
1737    elements of the list are the position parameters, in order.
1738    
1739  =back  =back
1740    
1741  =cut  =cut
1742    
1743  sub ParseTraceDate {  sub StandardSetup {
1744      # Get the parameters.      # Get the parameters.
1745      my ($dateString) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
1746      # Declare the return variable.      # Get the default tracing key.
1747      my $retVal;      my $tkey = EmergencyKey();
1748      # Parse the date.      # Add the tracing options.
1749      if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {      if (! exists $options->{trace}) {
1750          # Create a time object. Note we need to convert the day, month,          $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
         # and year to a different base. Years count from 1900, and  
         # the internal month value is relocated to January = 0.  
         $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);  
1751      }      }
1752      # Return the result.      $options->{sql} = [0, "turn on SQL tracing"];
1753      return $retVal;      $options->{help} = [0, "display command-line options"];
1754        $options->{user} = [$tkey, "tracing key"];
1755        $options->{background} = [0, "spool standard and error output"];
1756        $options->{warn} = [0, "send errors to RSS feed"];
1757        # Create a parsing hash from the options hash. The parsing hash
1758        # contains the default values rather than the default value
1759        # and the description. While we're at it, we'll memorize the
1760        # length of the longest option name.
1761        my $longestName = 0;
1762        my %parseOptions = ();
1763        for my $key (keys %{$options}) {
1764            if (length $key > $longestName) {
1765                $longestName = length $key;
1766  }  }
1767            $parseOptions{$key} = $options->{$key}->[0];
1768  =head3 LogErrors      }
1769        # Parse the command line.
1770  C<< Tracer::LogErrors($fileName); >>      my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1771        # Get the logfile suffix.
1772  Route the standard error output to a log file.      my $suffix = $retOptions->{user};
1773        # Check for background mode.
1774  =over 4      if ($retOptions->{background}) {
1775            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1776  =item fileName          my $errFileName = "$FIG_Config::temp/err$suffix.log";
1777            open STDOUT, ">$outFileName";
1778  Name of the file to receive the error output.          open STDERR, ">$errFileName";
1779            # Check for phone support. If we have phone support and a phone number,
1780  =back          # we want to turn it on.
1781            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1782  =cut              $retOptions->{phone} = $ENV{PHONE};
1783            }
1784  sub LogErrors {      }
1785      # Get the file name.      # Now we want to set up tracing. First, we need to know if the user
1786      my ($fileName) = @_;      # wants emergency tracing.
1787      # Open the file as the standard error output.      if ($retOptions->{trace} eq 'E') {
1788      open STDERR, '>', $fileName;          ETracing($retOptions->{user});
1789        } else {
1790            # Here the tracing is controlled from the command line.
1791            my @cats = @{$categories};
1792            if ($retOptions->{sql}) {
1793                push @cats, "SQL";
1794            }
1795            if ($retOptions->{warn}) {
1796                push @cats, "Feed";
1797            }
1798            # Add the default categories.
1799            push @cats, "Tracer";
1800            # Next, we create the category string by joining the categories.
1801            my $cats = join(" ", @cats);
1802            # Check to determine whether or not the caller wants to turn off tracing
1803            # to the standard output.
1804            my $traceLevel = $retOptions->{trace};
1805            my $textOKFlag = 1;
1806            if ($traceLevel =~ /^(.)-/) {
1807                $traceLevel = $1;
1808                $textOKFlag = 0;
1809            }
1810            # Now we set up the trace mode.
1811            my $traceMode;
1812            # Verify that we can open a file in the FIG temporary directory.
1813            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1814            if (open TESTTRACE, ">$traceFileName") {
1815                # Here we can trace to a file.
1816                $traceMode = ">$traceFileName";
1817                if ($textOKFlag) {
1818                    # Echo to standard output if the text-OK flag is set.
1819                    $traceMode = "+$traceMode";
1820                }
1821                # Close the test file.
1822                close TESTTRACE;
1823            } else {
1824                # Here we can't trace to a file. Complain about this.
1825                warn "Could not open trace file $traceFileName: $!\n";
1826                # We trace to the standard output if it's
1827                # okay, and the error log otherwise.
1828                if ($textOKFlag) {
1829                    $traceMode = "TEXT";
1830                } else {
1831                    $traceMode = "WARN";
1832                }
1833            }
1834            # Now set up the tracing.
1835            TSetup("$traceLevel $cats", $traceMode);
1836        }
1837        # Check for the "help" option. If it is specified, dump the command-line
1838        # options and exit the program.
1839        if ($retOptions->{help}) {
1840            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1841            print "$1 [options] $parmHelp\n";
1842            for my $key (sort keys %{$options}) {
1843                my $name = Pad($key, $longestName, 0, ' ');
1844                my $desc = $options->{$key}->[1];
1845                if ($options->{$key}->[0]) {
1846                    $desc .= " (default " . $options->{$key}->[0] . ")";
1847                }
1848                print "  $name $desc\n";
1849            }
1850            exit(0);
1851        }
1852        # Trace the options, if applicable.
1853        if (T(3)) {
1854            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1855            Trace("Selected options: " . join(", ", sort @parms) . ".");
1856        }
1857        # Return the parsed parameters.
1858        return ($retOptions, @retParameters);
1859  }  }
1860    
1861  =head3 ReadOptions  =head3 ReadOptions
1862    
1863  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1864    
1865  Read a set of options from a file. Each option is encoded in a line of text that has the  Read a set of options from a file. Each option is encoded in a line of text that has the
1866  format  format
# Line 1069  Line 1921 
1921    
1922  =head3 GetOptions  =head3 GetOptions
1923    
1924  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1925    
1926  Merge a specified set of options into a table of defaults. This method takes two hash references  Merge a specified set of options into a table of defaults. This method takes two hash references
1927  as input and uses the data from the second to update the first. If the second does not exist,  as input and uses the data from the second to update the first. If the second does not exist,
# Line 1078  Line 1930 
1930    
1931  Consider the following example.  Consider the following example.
1932    
1933  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1934    
1935  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1936  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 1086  Line 1938 
1938  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1939  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1940    
1941  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1942    
1943  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1944    
# Line 1130  Line 1982 
1982    
1983  =head3 MergeOptions  =head3 MergeOptions
1984    
1985  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
1986    
1987  Merge default values into a hash table. This method looks at the key-value pairs in the  Merge default values into a hash table. This method looks at the key-value pairs in the
1988  second (default) hash, and if a matching key is not found in the first hash, the default  second (default) hash, and if a matching key is not found in the first hash, the default
# Line 1143  Line 1995 
1995    
1996  Hash table to be updated with the default values.  Hash table to be updated with the default values.
1997    
1998  =item defaults  =item defaults
1999    
2000  Default values to be merged into the first hash table if they are not already present.  Default values to be merged into the first hash table if they are not already present.
2001    
2002  =back  =back
2003    
2004  =cut  =cut
2005    
2006  sub MergeOptions {  sub MergeOptions {
2007      # Get the parameters.      # Get the parameters.
2008      my ($table, $defaults) = @_;      my ($table, $defaults) = @_;
2009      # Loop through the defaults.      # Loop through the defaults.
2010      while (my ($key, $value) = each %{$defaults}) {      while (my ($key, $value) = each %{$defaults}) {
2011          if (!exists $table->{$key}) {          if (!exists $table->{$key}) {
2012              $table->{$key} = $value;              $table->{$key} = $value;
         }  
     }  
 }  
   
 =head3 Trace  
   
 C<< Trace($message); >>  
   
 Write a trace message to the target location specified in L</TSetup>. If there has not been  
 any prior call to B<TSetup>.  
   
 =over 4  
   
 =item message  
   
 Message to write.  
   
 =back  
   
 =cut  
   
 sub Trace {  
     # Get the parameters.  
     my ($message) = @_;  
     # Get the timestamp.  
     my $timeStamp = Now();  
     # Format the message. Note we strip off any line terminators at the end.  
     my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);  
     # Process according to the destination.  
     if ($Destination eq "TEXT") {  
         # Write the message to the standard output.  
         print "$formatted\n";  
     } elsif ($Destination eq "ERROR") {  
         # Write the message to the error output.  
         print STDERR "$formatted\n";  
     } elsif ($Destination eq "QUEUE") {  
         # Push the message into the queue.  
         push @Queue, "$formatted";  
     } elsif ($Destination eq "HTML") {  
         # Convert the message to HTML and write it to the standard output.  
         my $escapedMessage = CGI::escapeHTML($message);  
         print "<p>$formatted</p>\n";  
     } elsif ($Destination eq "WARN") {  
        # Emit the message as a warning.  
        warn $message;  
     } elsif ($Destination =~ m/^>>/) {  
         # Write the trace message to an output file.  
         (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";  
         print TRACING "$formatted\n";  
         close TRACING;  
         # If the Tee flag is on, echo it to the standard output.  
         if ($TeeFlag) {  
             print "$formatted\n";  
         }  
     }  
 }  
   
 =head3 T  
   
 C<< my $switch = T($category, $traceLevel); >>  
   
     or  
   
 C<< my $switch = T($traceLevel); >>  
   
 Return TRUE if the trace level is at or above a specified value and the specified category  
 is active, else FALSE. If no category is specified, the caller's package name is used.  
   
 =over 4  
   
 =item category  
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
   
 Relevant tracing level.  
   
 =item RETURN  
   
 TRUE if a message at the specified trace level would appear in the trace, else FALSE.  
   
 =back  
   
 =cut  
   
 sub T {  
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
         # Get the parameters.  
         my ($category, $traceLevel) = @_;  
         if (!defined $traceLevel) {  
             # Here we have no category, so we need to get the calling package.  
             # The calling package is normally the first parameter. If it is  
             # omitted, the first parameter will be the tracelevel. So, the  
             # first thing we do is shift the so-called category into the  
             # $traceLevel variable where it belongs.  
             $traceLevel = $category;  
             my ($package, $fileName, $line) = caller;  
             # If there is no calling package, we default to "main".  
             if (!$package) {  
                 $category = "main";  
             } else {  
                 $category = $package;  
             }  
         }  
         # Save the category name.  
         $LastCategory = $category;  
         # Convert it to lower case before we hash it.  
         $category = lc $category;  
         # Use the category and tracelevel to compute the result.  
         if (ref $traceLevel) {  
             Confess("Bad trace level.");  
         } elsif (ref $TraceLevel) {  
             Confess("Bad trace config.");  
2013          }          }
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
2014      }      }
     # Return the computed result.  
     return $retVal;  
2015  }  }
2016    
2017  =head3 ParseCommand  =head3 ParseCommand
2018    
2019  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2020    
2021  Parse a command line consisting of a list of parameters. The initial parameters may be option  Parse a command line consisting of a list of parameters. The initial parameters may be option
2022  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2023  off and merged into a table of default options. The remainder of the command line is  off and merged into a table of default options. The remainder of the command line is
2024  returned as a list of positional arguments. For example, consider the following invocation.  returned as a list of positional arguments. For example, consider the following invocation.
2025    
2026  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2027    
2028  In this case, the list @words will be treated as a command line and there are two options available,  In this case, the list @words will be treated as a command line and there are two options available,
2029  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
2030    
2031  C<< -logFile=error.log apple orange rutabaga >>      -logFile=error.log apple orange rutabaga
2032    
2033  then at the end of the invocation, C<$options> will be  then at the end of the invocation, C<$options> will be
2034    
2035  C<< { errors => 0, logFile => 'error.log' } >>      { errors => 0, logFile => 'error.log' }
2036    
2037  and C<@arguments> will contain  and C<@arguments> will contain
2038    
2039  C<< apple orange rutabaga >>      apple orange rutabaga
2040    
2041  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2042  support for quote characters. Options can be specified with single or double hyphens.  support for quote characters. Options can be specified with single or double hyphens.
# Line 1359  Line 2090 
2090      return ($optionTable, @retVal);      return ($optionTable, @retVal);
2091  }  }
2092    
2093  =head3 Escape  
2094    =head2 File Utility Methods
 C<< my $codedString = Tracer::Escape($realString); >>  
   
 Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  
 replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
 result is to reverse the effect of L</UnEscape>.  
   
 =over 4  
   
 =item realString  
   
 String to escape.  
   
 =item RETURN  
   
 Escaped equivalent of the real string.  
   
 =back  
   
 =cut  
   
 sub Escape {  
     # Get the parameter.  
     my ($realString) = @_;  
     # Initialize the return variable.  
     my $retVal = "";  
     # Loop through the parameter string, looking for sequences to escape.  
     while (length $realString > 0) {  
         # Look for the first sequence to escape.  
         if ($realString =~ /^(.*?)([\n\t\r\\])/) {  
             # Here we found it. The text preceding the sequence is in $1. The sequence  
             # itself is in $2. First, move the clear text to the return variable.  
             $retVal .= $1;  
             # Strip the processed section off the real string.  
             $realString = substr $realString, (length $2) + (length $1);  
             # Get the matched character.  
             my $char = $2;  
             # If we have a CR, we are done.  
             if ($char ne "\r") {  
                 # It's not a CR, so encode the escape sequence.  
                 $char =~ tr/\t\n/tn/;  
                 $retVal .= "\\" . $char;  
             }  
         } else {  
             # Here there are no more escape sequences. The rest of the string is  
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
         }  
     }  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 UnEscape  
   
 C<< my $realString = Tracer::UnEscape($codedString); >>  
   
 Replace escape sequences with their actual equivalents. C<\t> will be replaced by  
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
   
 =over 4  
   
 =item codedString  
   
 String to un-escape.  
   
 =item RETURN  
   
 Returns a copy of the original string with the escape sequences converted to their actual  
 values.  
   
 =back  
   
 =cut  
   
 sub UnEscape {  
     # Get the parameter.  
     my ($codedString) = @_;  
     # Initialize the return variable.  
     my $retVal = "";  
     # Only proceed if the incoming string is nonempty.  
     if (defined $codedString) {  
         # Loop through the parameter string, looking for escape sequences. We can't do  
         # translating because it causes problems with the escaped slash. ("\\t" becomes  
         # "\<tab>" no matter what we do.)  
         while (length $codedString > 0) {  
             # Look for the first escape sequence.  
             if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {  
                 # Here we found it. The text preceding the sequence is in $1. The sequence  
                 # itself is in $2. First, move the clear text to the return variable.  
                 $retVal .= $1;  
                 $codedString = substr $codedString, (2 + length $1);  
                 # Get the escape value.  
                 my $char = $2;  
                 # If we have a "\r", we are done.  
                 if ($char ne 'r') {  
                     # Here it's not an 'r', so we convert it.  
                     $char =~ tr/\\tn/\\\t\n/;  
                     $retVal .= $char;  
                 }  
             } else {  
                 # Here there are no more escape sequences. The rest of the string is  
                 # transferred unmodified.  
                 $retVal .= $codedString;  
                 $codedString = "";  
             }  
         }  
     }  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 ParseRecord  
   
 C<< my @fields = Tracer::ParseRecord($line); >>  
   
 Parse a tab-delimited data line. The data line is split into field values. Embedded tab  
 and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
 These will automatically be converted.  
   
 =over 4  
   
 =item line  
   
 Line of data containing the tab-delimited fields.  
   
 =item RETURN  
   
 Returns a list of the fields found in the data line.  
   
 =back  
   
 =cut  
   
 sub ParseRecord {  
     # Get the parameter.  
     my ($line) = @_;  
     # Remove the trailing new-line, if any.  
     chomp $line;  
     # Split the line read into pieces using the tab character.  
     my @retVal = split /\t/, $line;  
     # Trim and fix the escapes in each piece.  
     for my $value (@retVal) {  
         # Trim leading whitespace.  
         $value =~ s/^\s+//;  
         # Trim trailing whitespace.  
         $value =~ s/\s+$//;  
         # Delete the carriage returns.  
         $value =~ s/\r//g;  
         # Convert the escapes into their real values.  
         $value =~ s/\\t/"\t"/ge;  
         $value =~ s/\\n/"\n"/ge;  
     }  
     # Return the result.  
     return @retVal;  
 }  
   
 =head3 Merge  
   
 C<< my @mergedList = Tracer::Merge(@inputList); >>  
   
 Sort a list of strings and remove duplicates.  
   
 =over 4  
   
 =item inputList  
   
 List of scalars to sort and merge.  
   
 =item RETURN  
   
 Returns a list containing the same elements sorted in ascending order with duplicates  
 removed.  
   
 =back  
   
 =cut  
   
 sub Merge {  
     # Get the input list in sort order.  
     my @inputList = sort @_;  
     # Only proceed if the list has at least two elements.  
     if (@inputList > 1) {  
         # Now we want to move through the list splicing out duplicates.  
         my $i = 0;  
         while ($i < @inputList) {  
             # Get the current entry.  
             my $thisEntry = $inputList[$i];  
             # Find out how many elements duplicate the current entry.  
             my $j = $i + 1;  
             my $dup1 = $i + 1;  
             while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };  
             # If the number is nonzero, splice out the duplicates found.  
             if ($j > $dup1) {  
                 splice @inputList, $dup1, $j - $dup1;  
             }  
             # Now the element at position $dup1 is different from the element before it  
             # at position $i. We push $i forward one position and start again.  
             $i++;  
         }  
     }  
     # Return the merged list.  
     return @inputList;  
 }  
   
 =head3 Percent  
   
 C<< my $percent = Tracer::Percent($number, $base); >>  
   
 Returns the percent of the base represented by the given number. If the base  
 is zero, returns zero.  
   
 =over 4  
   
 =item number  
   
 Percent numerator.  
   
 =item base  
   
 Percent base.  
   
 =item RETURN  
   
 Returns the percentage of the base represented by the numerator.  
   
 =back  
   
 =cut  
   
 sub Percent {  
     # Get the parameters.  
     my ($number, $base) = @_;  
     # Declare the return variable.  
     my $retVal = 0;  
     # Compute the percent.  
     if ($base != 0) {  
         $retVal = $number * 100 / $base;  
     }  
     # Return the result.  
     return $retVal;  
 }  
2095    
2096  =head3 GetFile  =head3 GetFile
2097    
2098  C<< my @fileContents = Tracer::GetFile($fileName); >>      my @fileContents = Tracer::GetFile($fileName);
2099    
2100      or      or
2101    
2102  C<< my $fileContents = Tracer::GetFile($fileName); >>      my $fileContents = Tracer::GetFile($fileName);
2103    
2104  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
2105  each line is a list element. In scalar context, line-ends are replaced by C<\n>.  each line is a list element. In scalar context, line-ends are replaced by C<\n>.
# Line 1661  Line 2149 
2149    
2150  =head3 PutFile  =head3 PutFile
2151    
2152  C<< Tracer::PutFile($fileName, \@lines); >>      Tracer::PutFile($fileName, \@lines);
2153    
2154  Write out a file from a list of lines of text.  Write out a file from a list of lines of text.
2155    
# Line 1704  Line 2192 
2192      close $handle;      close $handle;
2193  }  }
2194    
2195  =head3 QTrace  =head3 ParseRecord
2196    
2197  C<< my $data = QTrace($format); >>      my @fields = Tracer::ParseRecord($line);
2198    
2199  Return the queued trace data in the specified format.  Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2200    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2201    These will automatically be converted.
2202    
2203  =over 4  =over 4
2204    
2205  =item format  =item line
2206    
2207  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Line of data containing the tab-delimited fields.
2208    
2209    =item RETURN
2210    
2211    Returns a list of the fields found in the data line.
2212    
2213  =back  =back
2214    
2215  =cut  =cut
2216    
2217  sub QTrace {  sub ParseRecord {
2218      # Get the parameter.      # Get the parameter.
2219      my ($format) = @_;      my ($line) = @_;
2220      # Create the return variable.      # Remove the trailing new-line, if any.
2221      my $retVal = "";      chomp $line;
2222      # Only proceed if there is an actual queue.      # Split the line read into pieces using the tab character.
2223      if (@Queue) {      my @retVal = split /\t/, $line;
2224          # Process according to the format.      # Trim and fix the escapes in each piece.
2225          if ($format =~ m/^HTML$/i) {      for my $value (@retVal) {
2226              # Convert the queue into an HTML list.          # Trim leading whitespace.
2227              $retVal = "<ul>\n";          $value =~ s/^\s+//;
2228              for my $line (@Queue) {          # Trim trailing whitespace.
2229                  my $escapedLine = CGI::escapeHTML($line);          $value =~ s/\s+$//;
2230                  $retVal .= "<li>$escapedLine</li>\n";          # Delete the carriage returns.
2231              }          $value =~ s/\r//g;
2232              $retVal .= "</ul>\n";          # Convert the escapes into their real values.
2233          } elsif ($format =~ m/^TEXT$/i) {          $value =~ s/\\t/"\t"/ge;
2234              # Convert the queue into a list of text lines.          $value =~ s/\\n/"\n"/ge;
             $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
2235      }      }
2236      # Return the formatted list.      # Return the result.
2237      return $retVal;      return @retVal;
2238  }  }
2239    
2240  =head3 Confess  =head3 Merge
2241    
2242  C<< Confess($message); >>      my @mergedList = Tracer::Merge(@inputList);
2243    
2244  Trace the call stack and abort the program with the specified message. When used with  Sort a list of strings and remove duplicates.
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
2245    
2246  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
2247    
2248  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item inputList
2249    
2250  =over 4  List of scalars to sort and merge.
2251    
2252  =item message  =item RETURN
2253    
2254  Message to include in the trace.  Returns a list containing the same elements sorted in ascending order with duplicates
2255    removed.
2256    
2257  =back  =back
2258    
2259  =cut  =cut
2260    
2261  sub Confess {  sub Merge {
2262      # Get the parameters.      # Get the input list in sort order.
2263      my ($message) = @_;      my @inputList = sort @_;
2264      # Trace the call stack.      # Only proceed if the list has at least two elements.
2265      Cluck($message);      if (@inputList > 1) {
2266      # Abort the program.          # Now we want to move through the list splicing out duplicates.
2267      croak(">>> $message");          my $i = 0;
2268            while ($i < @inputList) {
2269                # Get the current entry.
2270                my $thisEntry = $inputList[$i];
2271                # Find out how many elements duplicate the current entry.
2272                my $j = $i + 1;
2273                my $dup1 = $i + 1;
2274                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2275                # If the number is nonzero, splice out the duplicates found.
2276                if ($j > $dup1) {
2277                    splice @inputList, $dup1, $j - $dup1;
2278                }
2279                # Now the element at position $dup1 is different from the element before it
2280                # at position $i. We push $i forward one position and start again.
2281                $i++;
2282            }
2283        }
2284        # Return the merged list.
2285        return @inputList;
2286  }  }
2287    
2288  =head3 Assert  =head3 Open
2289    
2290  C<< Assert($condition1, $condition2, ... $conditionN); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2291    
2292  Return TRUE if all the conditions are true. This method can be used in conjunction with  Open a file.
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
2293    
2294  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2295    function. The mode is specified using Unix-like shell information. So, for
2296    example,
2297    
2298  Will abort the program with a stack trace if the value of C<$recNum> is negative.      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2299    
2300  =cut  would open for output appended to the specified file, and
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
2301    
2302  =head3 Cluck      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2303    
2304  C<< Cluck($message); >>  would open a pipe that sorts the records written and removes duplicates. Note
2305    the use of file handle syntax in the Open call. To use anonymous file handles,
2306    code as follows.
2307    
2308  Trace the call stack. Note that for best results, you should qualify the call with a      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
 trace condition. For example,  
2309    
2310  C<< Cluck("Starting record parse.") if T(3); >>  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2311    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2312    failed open will throw an exception and the third parameter will be used to construct
2313    an error message. If the parameter is omitted, a standard message is constructed
2314    using the file spec.
2315    
2316  will only trace the stack if the trace level for the package is 3 or more.      Could not open "/usr/spool/news/twitlog"
2317    
2318    Note that the mode characters are automatically cleaned from the file name.
2319    The actual error message from the file system will be captured and appended to the
2320    message in any case.
2321    
2322        Could not open "/usr/spool/news/twitlog": file not found.
2323    
2324    In some versions of PERL the only error message we get is a number, which
2325    corresponds to the C++ C<errno> value.
2326    
2327        Could not open "/usr/spool/news/twitlog": 6.
2328    
2329  =over 4  =over 4
2330    
2331  =item message  =item fileHandle
2332    
2333  Message to include in the trace.  File handle. If this parameter is C<undef>, a file handle will be generated
2334    and returned as the value of this method.
2335    
2336    =item fileSpec
2337    
2338    File name and mode, as per the PERL C<open> function.
2339    
2340    =item message (optional)
2341    
2342    Error message to use if the open fails. If omitted, a standard error message
2343    will be generated. In either case, the error information from the file system
2344    is appended to the message. To specify a conditional open that does not throw
2345    an error if it fails, use C<0>.
2346    
2347    =item RETURN
2348    
2349    Returns the name of the file handle assigned to the file, or C<undef> if the
2350    open failed.
2351    
2352  =back  =back
2353    
2354  =cut  =cut
2355    
2356  sub Cluck {  sub Open {
2357      # Get the parameters.      # Get the parameters.
2358      my ($message) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2359      # Trace what's happening.      # Attempt to open the file.
2360      Trace("Stack trace for event: $message");      my $rv = open $fileHandle, $fileSpec;
2361      my $confession = longmess($message);      # If the open failed, generate an error message.
2362      # Convert the confession to a series of trace messages. Note we skip any      if (! $rv) {
2363      # messages relating to calls into Tracer.          # Save the system error message.
2364      for my $line (split /\s*\n/, $confession) {          my $sysMessage = $!;
2365          Trace($line) if ($line !~ /Tracer\.pm/);          # See if we need a default message.
2366            if (!$message) {
2367                # Clean any obvious mode characters and leading spaces from the
2368                # filename.
2369                my ($fileName) = FindNamePart($fileSpec);
2370                $message = "Could not open \"$fileName\"";
2371            }
2372            # Terminate with an error using the supplied message and the
2373            # error message from the file system.
2374            Confess("$message: $!");
2375      }      }
2376        # Return the file handle.
2377        return $fileHandle;
2378  }  }
2379    
2380  =head3 Min  =head3 FindNamePart
2381    
2382  C<< my $min = Min($value1, $value2, ... $valueN); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2383    
2384  Return the minimum argument. The arguments are treated as numbers.  Extract the portion of a file specification that contains the file name.
2385    
2386    A file specification is the string passed to an C<open> call. It specifies the file
2387    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2388    method assumes that the file name is whatever follows the first angle bracket
2389    sequence.  So, for example, in the following strings the file name is
2390    C</usr/fig/myfile.txt>.
2391    
2392        >>/usr/fig/myfile.txt
2393        </usr/fig/myfile.txt
2394        | sort -u > /usr/fig/myfile.txt
2395    
2396    If the method cannot find a file name using its normal methods, it will return the
2397    whole incoming string.
2398    
2399  =over 4  =over 4
2400    
2401  =item $value1, $value2, ... $valueN  =item fileSpec
2402    
2403  List of numbers to compare.  File specification string from which the file name is to be extracted.
2404    
2405    =item RETURN
2406    
2407    Returns a three-element list. The first element contains the file name portion of
2408    the specified string, or the whole string if a file name cannot be found via normal
2409    methods. The second element contains the start position of the file name portion and
2410    the third element contains the length.
2411    
2412    =back
2413    
2414    =cut
2415    #: Return Type $;
2416    sub FindNamePart {
2417        # Get the parameters.
2418        my ($fileSpec) = @_;
2419        # Default to the whole input string.
2420        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2421        # Parse out the file name if we can.
2422        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2423            $retVal = $2;
2424            $len = length $retVal;
2425            $pos = (length $fileSpec) - (length $3) - $len;
2426        }
2427        # Return the result.
2428        return ($retVal, $pos, $len);
2429    }
2430    
2431    =head3 OpenDir
2432    
2433        my @files = OpenDir($dirName, $filtered, $flag);
2434    
2435    Open a directory and return all the file names. This function essentially performs
2436    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2437    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2438    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2439    filtered out of the return list. If the directory does not open and I<$flag> is not
2440    set, an exception is thrown. So, for example,
2441    
2442  =item RETURN      my @files = OpenDir("/Volumes/fig/contigs", 1);
2443    
2444  Returns the lowest number in the list.  is effectively the same as
2445    
2446  =back      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2447        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2448    
2449  =cut  Similarly, the following code
2450    
2451  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;  
 }  
2452    
2453  =head3 Max  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2454    automatically returns an empty list if the directory fails to open.
2455    
2456  C<< my $max = Max($value1, $value2, ... $valueN); >>  =over 4
2457    
2458  Return the maximum argument. The arguments are treated as numbers.  =item dirName
2459    
2460  =over 4  Name of the directory to open.
2461    
2462  =item $value1, $value2, ... $valueN  =item filtered
2463    
2464  List of numbers to compare.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2465    from the list, else FALSE.
2466    
2467  =item RETURN  =item flag
2468    
2469  Returns the highest number in the list.  TRUE if a failure to open is okay, else FALSE
2470    
2471  =back  =back
2472    
2473  =cut  =cut
2474    #: Return Type @;
2475  sub Max {  sub OpenDir {
2476      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2477      my ($retVal, @values) = @_;      my ($dirName, $filtered, $flag) = @_;
2478      # Loop through the remaining parameters, looking for the highest.      # Declare the return variable.
2479      for my $value (@values) {      my @retVal = ();
2480          if ($value > $retVal) {      # Open the directory.
2481              $retVal = $value;      if (opendir(my $dirHandle, $dirName)) {
2482            # The directory opened successfully. Get the appropriate list according to the
2483            # strictures of the filter parameter.
2484            if ($filtered) {
2485                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2486            } else {
2487                @retVal = readdir $dirHandle;
2488          }          }
2489        } elsif (! $flag) {
2490            # Here the directory would not open and it's considered an error.
2491            Confess("Could not open directory $dirName.");
2492      }      }
2493      # Return the maximum found.      # Return the result.
2494      return $retVal;      return @retVal;
2495  }  }
2496    
 =head3 AddToListMap  
   
 C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>  
2497    
2498  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  =head3 Insure
 is created for the key. Otherwise, the new value is pushed onto the list.  
2499    
2500  =over 4      Insure($dirName, $chmod);
2501    
2502  =item hash  Insure a directory is present.
2503    
2504  Reference to the target hash.  =over 4
2505    
2506  =item key  =item dirName
2507    
2508  Key for which the value is to be added.  Name of the directory to check. If it does not exist, it will be created.
2509    
2510  =item value1, value2, ... valueN  =item chmod (optional)
2511    
2512  List of values to add to the key's value list.  Security privileges to be given to the directory if it is created.
2513    
2514  =back  =back
2515    
2516  =cut  =cut
2517    
2518  sub AddToListMap {  sub Insure {
2519      # Get the parameters.      my ($dirName, $chmod) = @_;
2520      my ($hash, $key, @values) = @_;      if (! -d $dirName) {
2521      # Process according to whether or not the key already has a value.          Trace("Creating $dirName directory.") if T(2);
2522      if (! exists $hash->{$key}) {          eval {
2523          $hash->{$key} = [@values];              mkpath $dirName;
2524      } else {              # If we have permissions specified, set them here.
2525          push @{$hash->{$key}}, @values;              if (defined($chmod)) {
2526                    chmod $chmod, $dirName;
2527      }      }
2528            };
2529            if ($@) {
2530                Confess("Error creating $dirName: $@");
2531  }  }
   
 =head3 DebugMode  
   
 C<< if (Tracer::DebugMode) { ...code... } >>  
   
 Return TRUE if debug mode has been turned on, else abort.  
   
 Certain CGI scripts are too dangerous to exist in the production  
 environment. This method provides a simple way to prevent them  
 from working unless they are explicitly turned on by creating a password  
 cookie via the B<SetPassword> script.  If debugging mode  
 is not turned on, an error will occur.  
   
 =cut  
   
 sub DebugMode {  
     # Declare the return variable.  
     my $retVal = 0;  
     # Check the debug configuration.  
     my $password = CGI::cookie("DebugMode");  
     my $encrypted = Digest::MD5::md5_hex($password);  
     if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {  
         $retVal = 1;  
     } else {  
         # Here debug mode is off, so we generate an error.  
         Confess("Cannot use this facility without logging in.");  
2532      }      }
     # Return the determination indicator.  
     return $retVal;  
2533  }  }
2534    
2535  =head3 Strip  =head3 ChDir
2536    
2537  C<< my $string = Tracer::Strip($line); >>      ChDir($dirName);
2538    
2539  Strip all line terminators off a string. This is necessary when dealing with files  Change to the specified directory.
 that may have been transferred back and forth several times among different  
 operating environments.  
2540    
2541  =over 4  =over 4
2542    
2543  =item line  =item dirName
   
 Line of text to be stripped.  
   
 =item RETURN  
2544    
2545  The same line of text with all the line-ending characters chopped from the end.  Name of the directory to which we want to change.
2546    
2547  =back  =back
2548    
2549  =cut  =cut
2550    
2551  sub Strip {  sub ChDir {
2552      # Get a copy of the parameter string.      my ($dirName) = @_;
2553      my ($string) = @_;      if (! -d $dirName) {
2554      my $retVal = (defined $string ? $string : "");          Confess("Cannot change to directory $dirName: no such directory.");
2555      # Strip the line terminator characters.      } else {
2556      $retVal =~ s/(\r|\n)+$//g;          Trace("Changing to directory $dirName.") if T(File => 4);
2557      # Return the result.          my $okFlag = chdir $dirName;
2558      return $retVal;          if (! $okFlag) {
2559                Confess("Error switching to directory $dirName.");
2560            }
2561        }
2562  }  }
2563    
2564  =head3 Pad  =head3 SetPermissions
2565    
2566  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2567    
2568  Pad a string to a specified length. The pad character will be a  Set the permissions for a directory and all the files and folders inside it.
2569  space, and the padding will be on the right side unless specified  In addition, the group ownership will be changed to the specified value.
2570  in the third parameter.  
2571    This method is more vulnerable than most to permission and compatability
2572    problems, so it does internal error recovery.
2573    
2574  =over 4  =over 4
2575    
2576  =item string  =item dirName
2577    
2578  String to be padded.  Name of the directory to process.
2579    
2580  =item len  =item group
2581    
2582  Desired length of the padded string.  Name of the group to be assigned.
2583    
2584  =item left (optional)  =item mask
2585    
2586  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  Permission mask. Bits that are C<1> in this mask will be ORed into the
2587    permission bits of any file or directory that does not already have them
2588    set to 1.
2589    
2590  =item padChar (optional)  =item otherMasks
2591    
2592  Character to use for padding. The default is a space.  Map of search patterns to permission masks. If a directory name matches
2593    one of the patterns, that directory and all its members and subdirectories
2594    will be assigned the new pattern. For example, the following would
2595    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2596    
2597  =item RETURN      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2598    
2599  Returns a copy of the original string with the pad character added to the  The list is ordered, so the following would use 0777 for C<tmp1> and
2600  specified end so that it achieves the desired length.  0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2601    
2602        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2603                                                       '^tmp' => 0666);
2604    
2605    Note that the pattern matches are all case-insensitive, and only directory
2606    names are matched, not file names.
2607    
2608  =back  =back
2609    
2610  =cut  =cut
2611    
2612  sub Pad {  sub SetPermissions {
2613      # Get the parameters.      # Get the parameters.
2614      my ($string, $len, $left, $padChar) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2615      # Compute the padding character.      # Set up for error recovery.
2616      if (! defined $padChar) {      eval {
2617          $padChar = " ";          # Switch to the specified directory.
2618            ChDir($dirName);
2619            # Get the group ID.
2620            my $gid = getgrnam($group);
2621            # Get the mask for tracing.
2622            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2623            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2624            my $fixCount = 0;
2625            my $lookCount = 0;
2626            # @dirs will be a stack of directories to be processed.
2627            my @dirs = (getcwd());
2628            while (scalar(@dirs) > 0) {
2629                # Get the current directory.
2630                my $dir = pop @dirs;
2631                # Check for a match to one of the specified directory names. To do
2632                # that, we need to pull the individual part of the name off of the
2633                # whole path.
2634                my $simpleName = $dir;
2635                if ($dir =~ m!/([^/]+)$!) {
2636                    $simpleName = $1;
2637      }      }
2638      # Compute the number of spaces needed.              Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2639      my $needed = $len - length $string;              # Search for a match.
2640      # Copy the string into the return variable.              my $match = 0;
2641      my $retVal = $string;              my $i;
2642      # Only proceed if padding is needed.              for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2643      if ($needed > 0) {                  my $pattern = $otherMasks[$i];
2644          # Create the pad string.                  if ($simpleName =~ /$pattern/i) {
2645          my $pad = $padChar x $needed;                      $match = 1;
2646          # Affix it to the return value.                  }
2647          if ($left) {              }
2648              $retVal = $pad . $retVal;              # Check for a match. Note we use $i-1 because the loop added 2
2649                # before terminating due to the match.
2650                if ($match && $otherMasks[$i-1] != $mask) {
2651                    # This directory matches one of the incoming patterns, and it's
2652                    # a different mask, so we process it recursively with that mask.
2653                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2654          } else {          } else {
2655              $retVal .= $pad;                  # Here we can process normally. Get all of the non-hidden members.
2656                    my @submems = OpenDir($dir, 1);
2657                    for my $submem (@submems) {
2658                        # Get the full name.
2659                        my $thisMem = "$dir/$submem";
2660                        Trace("Checking member $thisMem.") if T(4);
2661                        $lookCount++;
2662                        if ($lookCount % 1000 == 0) {
2663                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2664                        }
2665                        # Fix the group.
2666                        chown -1, $gid, $thisMem;
2667                        # Insure this member is not a symlink.
2668                        if (! -l $thisMem) {
2669                            # Get its info.
2670                            my $fileInfo = stat $thisMem;
2671                            # Only proceed if we got the info. Otherwise, it's a hard link
2672                            # and we want to skip it anyway.
2673                            if ($fileInfo) {
2674                                my $fileMode = $fileInfo->mode;
2675                                if (($fileMode & $mask) != $mask) {
2676                                    # Fix this member.
2677                                    $fileMode |= $mask;
2678                                    chmod $fileMode, $thisMem;
2679                                    $fixCount++;
2680                                }
2681                                # If it's a subdirectory, stack it.
2682                                if (-d $thisMem) {
2683                                    push @dirs, $thisMem;
2684          }          }
2685      }      }
     # Return the result.  
     return $retVal;  
2686  }  }
   
 =head3 EOF  
   
 This is a constant that is lexically greater than any useful string.  
   
 =cut  
   
 sub EOF {  
     return "\xFF\xFF\xFF\xFF\xFF";  
2687  }  }
   
 =head3 TICK  
   
 C<< my @results = TICK($commandString); >>  
   
 Perform a back-tick operation on a command. If this is a Windows environment, any leading  
 dot-slash (C<./> will be removed. So, for example, if you were doing  
   
     `./protein.cgi`  
   
 from inside a CGI script, it would work fine in Unix, but would issue an error message  
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
   
     TICK("./protein.cgi")  
   
 it will work correctly in both environments.  
   
 =over 4  
   
 =item commandString  
   
 The command string to pass to the system.  
   
 =item RETURN  
   
 Returns the standard output from the specified command, as a list.  
   
 =back  
   
 =cut  
 #: Return Type @;  
 sub TICK {  
     # Get the parameters.  
     my ($commandString) = @_;  
     # Chop off the dot-slash if this is Windows.  
     if ($FIG_Config::win_mode) {  
         $commandString =~ s!^\./!!;  
2688      }      }
2689      # Activate the command and return the result.          }
2690      return `$commandString`;          Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2691        };
2692        # Check for an error.
2693        if ($@) {
2694            Confess("SetPermissions error: $@");
2695        }
2696  }  }
2697    
2698  =head3 ScriptSetup  =head3 GetLine
   
 C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  
2699    
2700  Perform standard tracing and debugging setup for scripts. The value returned is      my @data = Tracer::GetLine($handle);
 the CGI object followed by a pre-built variable hash. At the end of the script,  
 the client should call L</ScriptFinish> to output the web page.  
2701    
2702  This method calls L</ETracing> to configure tracing, which allows the tracing  Read a line of data from a tab-delimited file.
 to be configured via the emergency tracing form on the debugging control panel.  
 Tracing will then be turned on automatically for all programs that use the L</ETracing>  
 method, which includes every program that uses this method or L</StandardSetup>.  
2703    
2704  =over 4  =over 4
2705    
2706  =item noTrace (optional)  =item handle
2707    
2708  If specified, tracing will be suppressed. This is useful if the script wants to set up  Open file handle from which to read.
 tracing manually.  
2709    
2710  =item RETURN  =item RETURN
2711    
2712  Returns a two-element list consisting of a CGI query object and a variable hash for  Returns a list of the fields in the record read. The fields are presumed to be
2713  the output page.  tab-delimited. If we are at the end of the file, then an empty list will be
2714    returned. If an empty line is read, a single list item consisting of a null
2715    string will be returned.
2716    
2717  =back  =back
2718    
2719  =cut  =cut
2720    
2721  sub ScriptSetup {  sub GetLine {
2722      # Get the parameters.      # Get the parameters.
2723      my ($noTrace) = @_;      my ($handle) = @_;
2724      # Get the CGI query object.      # Declare the return variable.
2725      my $cgi = CGI->new();      my @retVal = ();
2726      # Set up tracing if it's not suppressed.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2727      ETracing($cgi) unless $noTrace;      # Read from the file.
2728      # Create the variable hash.      my $line = <$handle>;
2729      my $varHash = { results => '' };      # Only proceed if we found something.
2730      # Return the query object and variable hash.      if (defined $line) {
2731      return ($cgi, $varHash);          # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2732            # upload control and have a nonstandard EOL combination.
2733            $line =~ s/(\r|\n)+$//;
2734            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2735            if (T(File => 4)) {
2736                my $escapedLine = $line;
2737                $escapedLine =~ s/\n/\\n/g;
2738                $escapedLine =~ s/\r/\\r/g;
2739                $escapedLine =~ s/\t/\\t/g;
2740                Trace("Line read: -->$escapedLine<--");
2741  }  }
2742            # If the line is empty, return a single empty string; otherwise, parse
2743  =head3 ETracing          # it into fields.
2744            if ($line eq "") {
2745  C<< ETracing($parameter); >>              push @retVal, "";
   
 Set up emergency tracing. Emergency tracing is tracing that is turned  
 on automatically for any program that calls this method. The emergency  
 tracing parameters are stored in a a file identified by a tracing key.  
 If this method is called with a CGI object, then the tracing key is  
 taken from a cookie. If it is called with no parameters, then the tracing  
 key is taken from an environment variable. If it is called with a string,  
 the tracing key is that string.  
   
 =over 4  
   
 =item parameter  
   
 A parameter from which the tracing key is computed. If it is a scalar,  
 that scalar is used as the tracing key. If it is a CGI object, the  
 tracing key is taken from the C<IP> cookie. If it is omitted, the  
 tracing key is taken from the C<TRACING> environment variable. If it  
 is a CGI object and emergency tracing is not on, the C<Trace> and  
 C<TF> parameters will be used to determine the type of tracing.  
   
 =back  
   
 =cut  
   
 sub ETracing {  
     # Get the parameter.  
     my ($parameter) = @_;  
     # Check for CGI mode.  
     my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);  
     # Default to no tracing except errors.  
     my ($tracing, $dest) = ("0", "WARN");  
     # Check for emergency tracing.  
     my $tkey = EmergencyKey($parameter);  
     my $emergencyFile = EmergencyFileName($tkey);  
     if (-e $emergencyFile) {  
         # We have the file. Read in the data.  
         my @tracing = GetFile($emergencyFile);  
         # Pull off the time limit.  
         my $expire = shift @tracing;  
         # Convert it to seconds.  
         $expire *= 3600;  
         # Check the file data.  
         my $stat = stat($emergencyFile);  
         my ($now) = gettimeofday;  
         if ($now - $stat->mtime > $expire) {  
             # Delete the expired file.  
             unlink $emergencyFile;  
2746          } else {          } else {
2747              # Emergency tracing is on. Pull off the destination and              push @retVal, split /\t/,$line;
             # the trace level;  
             $dest = shift @tracing;  
             my $level = shift @tracing;  
             # Convert the destination to a real tracing destination.  
             # temp directory.  
             $dest = EmergencyTracingDest($tkey, $dest);  
             # Insure Tracer is specified.  
             my %moduleHash = map { $_ => 1 } @tracing;  
             $moduleHash{Tracer} = 1;  
             # Set the trace parameter.  
             $tracing = join(" ", $level, sort keys %moduleHash);  
         }  
     } elsif (defined $cgi) {  
         # There's no emergency tracing, but we have a CGI object, so check  
         # for tracing from the form parameters.  
         if ($cgi->param('Trace')) {  
             # Here the user has requested tracing via a form.  
             $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");  
             $tracing = $cgi->param('Trace') . " Tracer";  
         }  
2748      }      }
2749      # Setup the tracing we've determined from all the stuff above.      } else {
2750      TSetup($tracing, $dest);          # Trace the reason the read failed.
2751      # If we're a web script, trace the parameter and environment data.          Trace("End of file: $!") if T(File => 3);
     if (defined $cgi) {  
         TraceParms($cgi);  
2752      }      }
2753        # Return the result.
2754        return @retVal;
2755  }  }
2756    
2757  =head3 EmergencyFileName  =head3 PutLine
2758    
2759  C<< my $fileName = Tracer::EmergencyFileName($tkey); >>      Tracer::PutLine($handle, \@fields, $eol);
2760    
2761  Return the emergency tracing file name. This is the file that specifies  Write a line of data to a tab-delimited file. The specified field values will be
2762  the tracing information.  output in tab-separated form, with a trailing new-line.
2763    
2764  =over 4  =over 4
2765    
2766  =item tkey  =item handle
2767    
2768  Tracing key for the current program.  Output file handle.
2769    
2770  =item RETURN  =item fields
2771    
2772  Returns the name of the file to contain the emergency tracing information.  List of field values.
2773    
2774    =item eol (optional)
2775    
2776    End-of-line character (default is "\n").
2777    
2778  =back  =back
2779    
2780  =cut  =cut
2781    
2782  sub EmergencyFileName {  sub PutLine {
2783      # Get the parameters.      # Get the parameters.
2784      my ($tkey) = @_;      my ($handle, $fields, $eol) = @_;
2785      # Compute the emergency tracing file name.      # Write the data.
2786      return "$FIG_Config::temp/Emergency$tkey.txt";      print $handle join("\t", @{$fields}) . ($eol || "\n");
2787  }  }
2788    
 =head3 EmergencyFileTarget  
   
 C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>  
2789    
2790  Return the emergency tracing target file name. This is the file that receives  =head3 PrintLine
 the tracing output for file-based tracing.  
2791    
2792  =over 4      Tracer::PrintLine($line);
2793    
2794  =item tkey  Print a line of text with a trailing new-line.
2795    
2796  Tracing key for the current program.  =over 4
2797    
2798  =item RETURN  =item line
2799    
2800  Returns the name of the file to contain the trace output.  Line of text to print.
2801    
2802  =back  =back
2803    
2804  =cut  =cut
2805    
2806  sub EmergencyFileTarget {  sub PrintLine {
2807      # Get the parameters.      # Get the parameters.
2808      my ($tkey) = @_;      my ($line) = @_;
2809      # Compute the emergency tracing file name.      # Print the line.
2810      return "$FIG_Config::temp/trace$tkey.log";      print "$line\n";
2811  }  }
2812    
 =head3 EmergencyTracingDest  
2813    
2814  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>  =head2 Other Useful Methods
2815    
2816  This method converts an emergency tracing destination to a real  =head3 ParseParm
 tracing destination. The main difference is that if the  
 destination is C<FILE> or C<APPEND>, we convert it to file  
 output. If the destination is C<DUAL>, we convert it to file  
 and standard output.  
2817    
2818  =over 4      my $listValue = Tracer::ParseParm($string);
2819    
2820  =item tkey  Convert a parameter into a list reference. If the parameter is undefined,
2821    an undefined value will be returned. Otherwise, it will be parsed as a
2822    comma-separated list of values.
2823    
2824  Tracing key for this environment.  =over 4
2825    
2826  =item myDest  =item string
2827    
2828  Destination from the emergency tracing file.  Incoming string.
2829    
2830  =item RETURN  =item RETURN
2831    
2832  Returns a destination that can be passed into L</TSetup>.  Returns a reference to a list of values, or C<undef> if the incoming value
2833    was undefined.
2834    
2835  =back  =back
2836    
2837  =cut  =cut
2838    
2839  sub EmergencyTracingDest {  sub ParseParm {
2840      # Get the parameters.      # Get the parameters.
2841      my ($tkey, $myDest) = @_;      my ($string) = @_;
2842      # Declare the return variable.      # Declare the return variable.
2843      my $retVal;      my $retVal;
2844      # Process according to the destination value.      # Check for data.
2845      if ($myDest eq 'FILE') {      if (defined $string) {
2846          $retVal = ">" . EmergencyFileTarget($tkey);          # We have some, so split it into a list.
2847      } elsif ($myDest eq 'APPEND') {          $retVal = [ split /\s*,\s*/, $string];
         $retVal = ">>" . EmergencyFileTarget($tkey);  
     } elsif ($myDest eq 'DUAL') {  
         $retVal = "+>" . EmergencyFileTarget($tkey);  
2848      }      }
2849      # Return the result.      # Return the result.
2850      return $retVal;      return $retVal;
2851  }  }
2852    
2853  =head3 Emergency  =head3 Now
   
 C<< Emergency($key, $hours, $dest, $level, @modules); >>  
2854    
2855  Turn on emergency tracing. This method is normally invoked over the web from      my $string = Tracer::Now();
 a debugging console, but it can also be called by the C<trace.pl> script.  
 The caller specifies the duration of the emergency in hours, the desired tracing  
 destination, the trace level, and a list of the trace modules to activate.  
 For the length of the duration, when a program in an environment with the  
 specified tracing key active invokes a Sprout CGI script, tracing will be  
 turned on automatically. See L</TSetup> for more about tracing setup and  
 L</ETracing> for more about emergency tracing.  
2856    
2857  =over 4  Return a displayable time stamp containing the local time. Whatever format this
2858    method produces must be parseable by L</ParseDate>.
2859    
2860  =item tkey  =cut
2861    
2862  The tracing key. This is used to identify the control file and the trace file.  sub Now {
2863        return DisplayTime(time);
2864    }
2865    
2866  =item hours  =head3 DisplayTime
2867    
2868  Number of hours to keep emergency tracing alive.      my $string = Tracer::DisplayTime($time);
2869    
2870  =item dest  Convert a time value to a displayable time stamp. Whatever format this
2871    method produces must be parseable by L</ParseDate>.
2872    
2873  Tracing destination. If no path information is specified for a file  =over 4
 destination, it is put in the FIG temporary directory.  
2874    
2875  =item level  =item time
2876    
2877  Tracing level. A higher level means more trace messages.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2878    
2879  =item modules  =item RETURN
2880    
2881  A list of the tracing modules to activate.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2882    
2883  =back  =back
2884    
2885  =cut  =cut
2886    
2887  sub Emergency {  sub DisplayTime {
2888      # Get the parameters.      my ($time) = @_;
2889      my ($tkey, $hours, $dest, $level, @modules) = @_;      my $retVal = "(n/a)";
2890      # Create the emergency file.      if (defined $time) {
2891      my $specFile = EmergencyFileName($tkey);          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2892      my $outHandle = Open(undef, ">$specFile");          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2893      print $outHandle join("\n", $hours, $dest, $level, @modules, "");                    _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2894        }
2895        return $retVal;
2896  }  }
2897    
2898  =head3 EmergencyKey  # Pad a number to 2 digits.
2899    sub _p2 {
2900        my ($value) = @_;
2901        $value = "0$value" if ($value < 10);
2902        return $value;
2903    }
2904    
2905  C<< my $tkey = EmergencyKey($parameter); >>  =head3 Escape
2906    
2907  Return the Key to be used for emergency tracing. This could be an IP address,      my $codedString = Tracer::Escape($realString);
2908   a session ID, or a user name, depending on the environment.  
2909    Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2910    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2911    result is to reverse the effect of L</UnEscape>.
2912    
2913  =over 4  =over 4
2914    
2915  =item parameter  =item realString
2916    
2917  Parameter defining the method for finding the tracing key. If it is a scalar,  String to escape.
 then it is presumed to be the tracing key itself. If it is a CGI object, then  
 the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is  
 taken from the C<TRACING> environment variable.  
2918    
2919  =item RETURN  =item RETURN
2920    
2921  Returns the key to be used for labels in emergency tracing.  Escaped equivalent of the real string.
2922    
2923  =back  =back
2924    
2925  =cut  =cut
2926    
2927  sub EmergencyKey {  sub Escape {
2928      # Get the parameters.      # Get the parameter.
2929      my ($parameter) = @_;      my ($realString) = @_;
2930      # Declare the return variable.      # Initialize the return variable.
2931      my $retVal;      my $retVal = "";
2932      # Determine the parameter type.      # Loop through the parameter string, looking for sequences to escape.
2933      if (! defined $parameter) {      while (length $realString > 0) {
2934          # Here we're supposed to check the environment.          # Look for the first sequence to escape.
2935          $retVal = $ENV{TRACING};          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2936      } else {              # Here we found it. The text preceding the sequence is in $1. The sequence
2937          my $ptype = ref $parameter;              # itself is in $2. First, move the clear text to the return variable.
2938          if ($ptype eq 'CGI') {              $retVal .= $1;
2939              # Here we were invoked from a web page. Look for a cookie.              # Strip the processed section off the real string.
2940              $retVal = $parameter->cookie('IP');              $realString = substr $realString, (length $2) + (length $1);
2941          } elsif (! $ptype) {              # Get the matched character.
2942              # Here the key was passed in.              my $char = $2;
2943              $retVal = $parameter;              # If we have a CR, we are done.
2944                if ($char ne "\r") {
2945                    # It's not a CR, so encode the escape sequence.
2946                    $char =~ tr/\t\n/tn/;
2947                    $retVal .= "\\" . $char;
2948          }          }
2949            } else {
2950                # Here there are no more escape sequences. The rest of the string is
2951                # transferred unmodified.
2952                $retVal .= $realString;
2953                $realString = "";
2954      }      }
     # If no luck finding a key, use the PID.  
     if (! defined $retVal) {  
         $retVal = $$;  
2955      }      }
2956      # Return the result.      # Return the result.
2957      return $retVal;      return $retVal;
2958  }  }
2959    
2960    =head3 UnEscape
2961    
2962  =head3 TraceParms      my $realString = Tracer::UnEscape($codedString);
   
 C<< Tracer::TraceParms($cgi); >>  
2963    
2964  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2965  at level CGI => 4.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2966    be deleted.
2967    
2968  =over 4  =over 4
2969    
2970  =item cgi  =item codedString
2971    
2972  CGI query object containing the parameters to trace.  String to un-escape.
2973    
2974    =item RETURN
2975    
2976    Returns a copy of the original string with the escape sequences converted to their actual
2977    values.
2978    
2979  =back  =back
2980    
2981  =cut  =cut
2982    
2983  sub TraceParms {  sub UnEscape {
2984      # Get the parameters.      # Get the parameter.
2985      my ($cgi) = @_;      my ($codedString) = @_;
2986      if (T(CGI => 3)) {      # Initialize the return variable.
2987          # Here we want to trace the parameter data.      my $retVal = "";
2988          my @names = $cgi->param;      # Only proceed if the incoming string is nonempty.
2989          for my $parmName (sort @names) {      if (defined $codedString) {
2990              # Note we skip the Trace parameters, which are for our use only.          # Loop through the parameter string, looking for escape sequences. We can't do
2991              if ($parmName ne 'Trace' && $parmName ne 'TF') {          # translating because it causes problems with the escaped slash. ("\\t" becomes
2992                  my @values = $cgi->param($parmName);          # "\<tab>" no matter what we do.)
2993                  Trace("CGI: $parmName = " . join(", ", @values));          while (length $codedString > 0) {
2994              }              # Look for the first escape sequence.
2995                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2996                    # Here we found it. The text preceding the sequence is in $1. The sequence
2997                    # itself is in $2. First, move the clear text to the return variable.
2998                    $retVal .= $1;
2999                    $codedString = substr $codedString, (2 + length $1);
3000                    # Get the escape value.
3001                    my $char = $2;
3002                    # If we have a "\r", we are done.
3003                    if ($char ne 'r') {
3004                        # Here it's not an 'r', so we convert it.
3005                        $char =~ tr/\\tn/\\\t\n/;
3006                        $retVal .= $char;
3007          }          }
3008          # Display the request method.              } else {
3009          my $method = $cgi->request_method();                  # Here there are no more escape sequences. The rest of the string is
3010          Trace("Method: $method");                  # transferred unmodified.
3011                    $retVal .= $codedString;
3012                    $codedString = "";
3013      }      }
     if (T(CGI => 4)) {  
         # Here we want the environment data too.  
         for my $envName (sort keys %ENV) {  
             Trace("ENV: $envName = $ENV{$envName}");  
3014          }          }
3015      }      }
3016        # Return the result.
3017        return $retVal;
3018  }  }
3019    
3020  =head3 ScriptFinish  =head3 Percent
   
 C<< ScriptFinish($webData, $varHash); >>  
   
 Output a web page at the end of a script. Either the string to be output or the  
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
3021    
3022  A typical standard script would loook like the following.      my $percent = Tracer::Percent($number, $base);
3023    
3024      BEGIN {  Returns the percent of the base represented by the given number. If the base
3025          # Print the HTML header.  is zero, returns zero.
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
3026    
3027      my ($cgi, $varHash) = ScriptSetup();  =over 4
     eval {  
         # ... get data from $cgi, put it in $varHash ...  
     };  
     if ($@) {  
         Trace("Script Error: $@") if T(0);  
     }  
     ScriptFinish("Html/MyTemplate.html", $varHash);  
3028    
3029  The idea here is that even if the script fails, you'll see trace messages and  =item number
 useful output.  
3030    
3031  =over 4  Percent numerator.
3032    
3033  =item webData  =item base
3034    
3035  A string containing either the full web page to be written to the output or the  Percent base.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3036    
3037  =item varHash (optional)  =item RETURN
3038    
3039  If specified, then a reference to a hash mapping variable names for a template  Returns the percentage of the base represented by the numerator.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3040    
3041  =back  =back
3042    
3043  =cut  =cut
3044    
3045  sub ScriptFinish {  sub Percent {
3046      # Get the parameters.      # Get the parameters.
3047      my ($webData, $varHash) = @_;      my ($number, $base) = @_;
3048      # Check for a template file situation.      # Declare the return variable.
3049      my $outputString;      my $retVal = 0;
3050      if (defined $varHash) {      # Compute the percent.
3051          # Here we have a template file. We need to determine the template type.      if ($base != 0) {
3052          my $template;          $retVal = $number * 100 / $base;
         if ($FIG_Config::template_url && $webData =~ /\.php$/) {  
             $template = "$FIG_Config::template_url/$webData";  
         } else {  
             $template = "<<$webData";  
         }  
         $outputString = PageBuilder::Build($template, $varHash, "Html");  
     } else {  
         # Here the user gave us a raw string.  
         $outputString = $webData;  
     }  
     # Check for trace messages.  
     if ($Destination ne "NONE" && $TraceLevel > 0) {  
         # We have trace messages, so we want to put them at the end of the body. This  
         # is either at the end of the whole string or at the beginning of the BODY  
         # end-tag.  
         my $pos = length $outputString;  
         if ($outputString =~ m#</body>#gi) {  
             $pos = (pos $outputString) - 7;  
         }  
         # If the trace messages were queued, we unroll them. Otherwise, we display the  
         # destination.  
         my $traceHtml;  
         if ($Destination eq "QUEUE") {  
             $traceHtml = QTrace('Html');  
         } elsif ($Destination =~ /^>>(.+)$/) {  
             # Here the tracing output it to a file. We code it as a hyperlink so the user  
             # can copy the file name into the clipboard easily.  
             my $actualDest = $1;  
             $traceHtml = "<p>Tracing output to $actualDest.</p>\n";  
         } else {  
             # Here we have one of the special destinations.  
             $traceHtml = "<P>Tracing output type is $Destination.</p>\n";  
         }  
         substr $outputString, $pos, 0, $traceHtml;  
3053      }      }
3054      # Write the output string.      # Return the result.
3055      print $outputString;      return $retVal;
3056  }  }
3057    
3058  =head3 Insure  =head3 Constrain
3059    
3060  C<< Insure($dirName); >>      my $constrained = Constrain($value, $min, $max);
3061    
3062  Insure a directory is present.  Modify a numeric value to bring it to a point in between a maximum and a minimum.
3063    
3064  =over 4  =over 4
3065    
3066  =item dirName  =item value
3067    
3068  Name of the directory to check. If it does not exist, it will be created.  Value to constrain.
3069    
3070    =item min (optional)
3071    
3072    Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3073    
3074    =item max (optional)
3075    
3076    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3077    
3078    =item RETURN
3079    
3080    Returns the incoming value, constrained according to the other parameters.
3081    
3082  =back  =back
3083    
3084  =cut  =cut
3085    
3086  sub Insure {  sub Constrain {
3087      my ($dirName) = @_;      # Get the parameters.
3088      if (! -d $dirName) {      my ($value, $min, $max) = @_;
3089          Trace("Creating $dirName directory.") if T(File => 2);      # Declare the return variable.
3090          eval { mkpath $dirName; };      my $retVal = $value;
3091          if ($@) {      # Apply the minimum constraint.
3092              Confess("Error creating $dirName: $@");      if (defined $min && $retVal < $min) {
3093          }          $retVal = $min;
3094        }
3095        # Apply the maximum constraint.
3096        if (defined $max && $retVal > $max) {
3097            $retVal = $max;
3098      }      }
3099        # Return the result.
3100        return $retVal;
3101  }  }
3102    
3103  =head3 ChDir  =head3 Min
3104    
3105  C<< ChDir($dirName); >>      my $min = Min($value1, $value2, ... $valueN);
3106    
3107  Change to the specified directory.  Return the minimum argument. The arguments are treated as numbers.
3108    
3109  =over 4  =over 4
3110    
3111  =item dirName  =item $value1, $value2, ... $valueN
3112    
3113  Name of the directory to which we want to change.  List of numbers to compare.
3114    
3115    =item RETURN
3116    
3117    Returns the lowest number in the list.
3118    
3119  =back  =back
3120    
3121  =cut  =cut
3122    
3123  sub ChDir {  sub Min {
3124      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
3125      if (! -d $dirName) {      my ($retVal, @values) = @_;
3126          Confess("Cannot change to directory $dirName: no such directory.");      # Loop through the remaining parameters, looking for the lowest.
3127      } else {      for my $value (@values) {
3128          Trace("Changing to directory $dirName.") if T(File => 4);          if ($value < $retVal) {
3129          my $okFlag = chdir $dirName;              $retVal = $value;
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
3130          }          }
3131      }      }
3132        # Return the minimum found.
3133        return $retVal;
3134  }  }
3135    
3136  =head3 SendSMS  =head3 Max
3137    
3138  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>      my $max = Max($value1, $value2, ... $valueN);
3139    
3140  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  Return the maximum argument. The arguments are treated as numbers.
 user name, password, and API ID for the relevant account in the hash reference variable  
 I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For  
 example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID  
 is C<2561022>, then the FIG_Config file must contain  
3141    
3142      $phone =  { user => 'BruceTheHumanPet',  =over 4
                 password => 'silly',  
                 api_id => '2561022' };  
3143    
3144  The original purpose of this method was to insure Bruce would be notified immediately when the  =item $value1, $value2, ... $valueN
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3145    
3146  The message ID will be returned if successful, and C<undef> if an error occurs.  List of numbers to compare.
3147    
3148  =over 4  =item RETURN
3149    
3150  =item phoneNumber  Returns the highest number in the list.
3151    
3152  Phone number to receive the message, in international format. A United States phone number  =back
 would be prefixed by "1". A British phone number would be prefixed by "44".  
3153    
3154  =item msg  =cut
3155    
3156  Message to send to the specified phone.  sub Max {
3157        # Get the parameters. Note that we prime the return value with the first parameter.
3158        my ($retVal, @values) = @_;
3159        # Loop through the remaining parameters, looking for the highest.
3160        for my $value (@values) {
3161            if ($value > $retVal) {
3162                $retVal = $value;
3163            }
3164        }
3165        # Return the maximum found.
3166        return $retVal;
3167    }
3168    
3169    
3170    =head3 Strip
3171    
3172        my $string = Tracer::Strip($line);
3173    
3174    Strip all line terminators off a string. This is necessary when dealing with files
3175    that may have been transferred back and forth several times among different
3176    operating environments.
3177    
3178    =over 4
3179    
3180    =item line
3181    
3182    Line of text to be stripped.
3183    
3184  =item RETURN  =item RETURN
3185    
3186  Returns the message ID if successful, and C<undef> if the message could not be sent.  The same line of text with all the line-ending characters chopped from the end.
3187    
3188  =back  =back
3189    
3190  =cut  =cut
3191    
3192  sub SendSMS {  sub Strip {
3193      # Get the parameters.      # Get a copy of the parameter string.
3194      my ($phoneNumber, $msg) = @_;      my ($string) = @_;
3195      # Declare the return variable. If we do not change it, C<undef> will be returned.      my $retVal = (defined $string ? $string : "");
3196      my $retVal;      # Strip the line terminator characters.
3197      # Only proceed if we have phone support.      $retVal =~ s/(\r|\n)+$//g;
     if (! defined $FIG_Config::phone) {  
         Trace("Phone support not present in FIG_Config.") if T(1);  
     } else {  
         # Get the phone data.  
         my $parms = $FIG_Config::phone;  
         # Get the Clickatell URL.  
         my $url = "http://api.clickatell.com/http/";  
         # Create the user agent.  
         my $ua = LWP::UserAgent->new;  
         # Request a Clickatell session.  
         my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},  
                                      password => $parms->{password},  
                                      api_id => $parms->{api_id},  
                                      to => $phoneNumber,  
                                      text => $msg});  
         # Check for an error.  
         if (! $resp->is_success) {  
             Trace("Alert failed.") if T(1);  
         } else {  
             # Get the message ID.  
             my $rstring = $resp->content;  
             if ($rstring =~ /^ID:\s+(.*)$/) {  
                 $retVal = $1;  
             } else {  
                 Trace("Phone attempt failed with $rstring") if T(1);  
             }  
         }  
     }  
3198      # Return the result.      # Return the result.
3199      return $retVal;      return $retVal;
3200  }  }
3201    
3202  =head3 CommaFormat  =head3 Pad
3203    
3204  C<< my $formatted = Tracer::CommaFormat($number); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3205    
3206  Insert commas into a number.  Pad a string to a specified length. The pad character will be a
3207    space, and the padding will be on the right side unless specified
3208    in the third parameter.
3209    
3210  =over 4  =over 4
3211    
3212  =item number  =item string
3213    
3214  A sequence of digits.  String to be padded.
3215    
3216    =item len
3217    
3218    Desired length of the padded string.
3219    
3220    =item left (optional)
3221    
3222    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3223    
3224    =item padChar (optional)
3225    
3226    Character to use for padding. The default is a space.
3227    
3228  =item RETURN  =item RETURN
3229    
3230  Returns the same digits with commas strategically inserted.  Returns a copy of the original string with the pad character added to the
3231    specified end so that it achieves the desired length.
3232    
3233  =back  =back
3234    
3235  =cut  =cut
3236    
3237  sub CommaFormat {  sub Pad {
3238      # Get the parameters.      # Get the parameters.
3239      my ($number) = @_;      my ($string, $len, $left, $padChar) = @_;
3240      # Pad the length up to a multiple of three.      # Compute the padding character.
3241      my $padded = "$number";      if (! defined $padChar) {
3242      $padded = " " . $padded while length($padded) % 3 != 0;          $padChar = " ";
3243      # This is a fancy PERL trick. The parentheses in the SPLIT pattern      }
3244      # cause the delimiters to be included in the output stream. The      # Compute the number of spaces needed.
3245      # GREP removes the empty strings in between the delimiters.      my $needed = $len - length $string;
3246      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));      # Copy the string into the return variable.
3247      # Clean out the spaces.      my $retVal = $string;
3248      $retVal =~ s/ //g;      # Only proceed if padding is needed.
3249        if ($needed > 0) {
3250            # Create the pad string.
3251            my $pad = $padChar x $needed;
3252            # Affix it to the return value.
3253            if ($left) {
3254                $retVal = $pad . $retVal;
3255            } else {
3256                $retVal .= $pad;
3257            }
3258        }
3259      # Return the result.      # Return the result.
3260      return $retVal;      return $retVal;
3261  }  }
 =head3 SetPermissions  
3262    
3263  C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  =head3 EOF
3264    
3265    This is a constant that is lexically greater than any useful string.
3266    
3267  Set the permissions for a directory and all the files and folders inside it.  =cut
 In addition, the group ownership will be changed to the specified value.  
3268    
3269  This method is more vulnerable than most to permission and compatability  sub EOF {
3270  problems, so it does internal error recovery.      return "\xFF\xFF\xFF\xFF\xFF";
3271    }
3272    
3273    =head3 TICK
3274    
3275        my @results = TICK($commandString);
3276    
3277    Perform a back-tick operation on a command. If this is a Windows environment, any leading
3278    dot-slash (C<./> will be removed. So, for example, if you were doing
3279    
3280        `./protein.cgi`
3281    
3282    from inside a CGI script, it would work fine in Unix, but would issue an error message
3283    in Windows complaining that C<'.'> is not a valid command. If instead you code
3284    
3285        TICK("./protein.cgi")
3286    
3287    it will work correctly in both environments.
3288    
3289  =over 4  =over 4
3290    
3291  =item dirName  =item commandString
3292    
3293  Name of the directory to process.  The command string to pass to the system.
3294    
3295  =item group  =item RETURN
3296    
3297    Returns the standard output from the specified command, as a list.
3298    
3299    =back
3300    
3301    =cut
3302    #: Return Type @;
3303    sub TICK {
3304        # Get the parameters.
3305        my ($commandString) = @_;
3306        # Chop off the dot-slash if this is Windows.
3307        if ($FIG_Config::win_mode) {
3308            $commandString =~ s!^\./!!;
3309        }
3310        # Activate the command and return the result.
3311        return `$commandString`;
3312    }
3313    
 Name of the group to be assigned.  
3314    
3315  =item mask  =head3 CommaFormat
3316    
3317  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.  
3318    
3319  =item otherMasks  Insert commas into a number.
3320    
3321  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>.  
3322    
3323      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  =item number
3324    
3325  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>.  
3326    
3327      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  =item RETURN
                                                    '^tmp' => 0666);  
3328    
3329  Note that the pattern matches are all case-insensitive, and only directory  Returns the same digits with commas strategically inserted.
 names are matched, not file names.  
3330    
3331  =back  =back
3332    
3333  =cut  =cut
3334    
3335  sub SetPermissions {  sub CommaFormat {
3336      # Get the parameters.      # Get the parameters.
3337      my ($dirName, $group, $mask, @otherMasks) = @_;      my ($number) = @_;
3338      # Set up for error recovery.      # Pad the length up to a multiple of three.
3339      eval {      my $padded = "$number";
3340          # Switch to the specified directory.      $padded = " " . $padded while length($padded) % 3 != 0;
3341          ChDir($dirName);      # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3342          # Get the group ID.      # cause the delimiters to be included in the output stream. The
3343          my $gid = getgrnam($group);      # GREP removes the empty strings in between the delimiters.
3344          # Get the mask for tracing.      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3345          my $traceMask = sprintf("%04o", $mask) . "($mask)";      # Clean out the spaces.
3346          Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);      $retVal =~ s/ //g;
3347          my $fixCount = 0;      # Return the result.
3348          my $lookCount = 0;      return $retVal;
         # @dirs will be a stack of directories to be processed.  
         my @dirs = (getcwd());  
         while (scalar(@dirs) > 0) {  
             # Get the current directory.  
             my $dir = pop @dirs;  
             # Check for a match to one of the specified directory names. To do  
             # that, we need to pull the individual part of the name off of the  
             # whole path.  
             my $simpleName = $dir;  
             if ($dir =~ m!/([^/]+)$!) {  
                 $simpleName = $1;  
             }  
             Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);  
             # Search for a match.  
             my $match = 0;  
             my $i;  
             for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {  
                 my $pattern = $otherMasks[$i];  
                 if ($simpleName =~ /$pattern/i) {  
                     $match = 1;  
                 }  
             }  
             # Check for a match. Note we use $i-1 because the loop added 2  
             # before terminating due to the match.  
             if ($match && $otherMasks[$i-1] != $mask) {  
                 # This directory matches one of the incoming patterns, and it's  
                 # a different mask, so we process it recursively with that mask.  
                 SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);  
             } else {  
                 # Here we can process normally. Get all of the non-hidden members.  
                 my @submems = OpenDir($dir, 1);  
                 for my $submem (@submems) {  
                     # Get the full name.  
                     my $thisMem = "$dir/$submem";  
                     Trace("Checking member $thisMem.") if T(4);  
                     $lookCount++;  
                     if ($lookCount % 1000 == 0) {  
                         Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);  
                     }  
                     # Fix the group.  
                     chown -1, $gid, $thisMem;  
                     # Insure this member is not a symlink.  
                     if (! -l $thisMem) {  
                         # Get its info.  
                         my $fileInfo = stat $thisMem;  
                         # Only proceed if we got the info. Otherwise, it's a hard link  
                         # and we want to skip it anyway.  
                         if ($fileInfo) {  
                             my $fileMode = $fileInfo->mode;  
                             if (($fileMode & $mask) != $mask) {  
                                 # Fix this member.  
                                 $fileMode |= $mask;  
                                 chmod $fileMode, $thisMem;  
                                 $fixCount++;  
                             }  
                             # If it's a subdirectory, stack it.  
                             if (-d $thisMem) {  
                                 push @dirs, $thisMem;  
                             }  
                         }  
                     }  
                 }  
             }  
         }  
         Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);  
     };  
     # Check for an error.  
     if ($@) {  
         Confess("SetPermissions error: $@");  
     }  
3349  }  }
3350    
3351    
3352  =head3 CompareLists