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revision 1.86, Fri May 18 19:27:17 2007 UTC revision 1.104, Fri May 9 06:22:49 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    my $CommandLine;            # Command line passed to StandardSetup
212    umask 2;                    # Fix the damn umask so everything is group-writable.
213    
214    =head2 Tracing Methods
215    
216    =head3 Setups
217    
218        my $count = Tracer::Setups();
219    
220    Return the number of times L</TSetup> has been called.
221    
222    This method allows for the creation of conditional tracing setups where, for example, we
223    may want to set up tracing if nobody else has done it before us.
224    
225    =cut
226    
227  =head2 Public Methods  sub Setups {
228        return $SetupCount;
229    }
230    
231  =head3 TSetup  =head3 TSetup
232    
233  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
234    
235  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
236  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 350  Line 280 
280          }          }
281      }      }
282      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
283      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
284      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
285        # the standard output (tee mode).
286      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
287          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
288              $TeeFlag = 1;              $TeeFlag = 1;
289              $target = substr($target, 1);              $target = substr($target, 1);
290          }          }
291          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
292                # We need to initialize the file (which clears it).
293              open TRACEFILE, $target;              open TRACEFILE, $target;
294              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
295              close TRACEFILE;              close TRACEFILE;
296                # Set to append mode now that the file has been cleared.
297              $Destination = ">$target";              $Destination = ">$target";
298          } else {          } else {
299              $Destination = $target;              $Destination = $target;
# Line 372  Line 305 
305      $SetupCount++;      $SetupCount++;
306  }  }
307    
308  =head3 StandardSetup  =head3 SetLevel
   
 C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>  
309    
310  This method performs standard command-line parsing and tracing setup. The return      Tracer::SetLevel($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.  
311    
312  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.  
313    
314  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  
315    
316      ["Sprout", "SproutLoad", "ERDB"]  =item newLevel
317    
318  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.  
319    
320  =over 4  =back
321    
322  =item SQL  =cut
323    
324  Traces SQL commands and activity.  sub SetLevel {
325        $TraceLevel = $_[0];
326    }
327    
328  =item Tracer  =head3 ParseDate
329    
330  Traces error messages and call stacks.      my $time = Tracer::ParseDate($dateString);
331    
332  =back  Convert a date into a PERL time number. This method expects a date-like string
333    and parses it into a number. The string must be vaguely date-like or it will
334    return an undefined value. Our requirement is that a month and day be
335    present and that three pieces of the date string (time of day, month and day,
336    year) be separated by likely delimiters, such as spaces, commas, and such-like.
337    
338  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
339  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.  
340    
341      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  The year must be exactly four digits.
342    
343  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
344  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
345  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  
346    
347  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.  
348    
349      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  The parameters are as follows.
350    
351  would send the trace output to C<traceBruce.log> in the temporary directory.  =over 4
352    
353  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.  
354    
355  You can specify a different default trace level by setting C<$options->{trace}>  The date string to convert.
 prior to calling this method.  
356    
357  An example at this point would help. Consider, for example, the command-line utility  =item RETURN
 C<TransactFeatures>. It accepts a list of positional parameters plus the options  
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
358    
359      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
360                          { 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);  
361    
362    =back
363    
364  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<$options>. The  
 positional parameters are returned in C<@parameters>.  
365    
366  The following is a sample command line for C<TransactFeatures>.  # Universal month conversion table.
367    use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
368                                Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
369                                Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
370                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
371                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
372                                Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
373                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
374                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
375                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
376                                Oct =>  9, October  =>   9, '10' =>  9,
377                                Nov => 10, November =>  10, '11' => 10,
378                                Dec => 11, December =>  11, '12' => 11
379                            };
380    
381      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  sub ParseDate {
382        # Get the parameters.
383        my ($dateString) = @_;
384        # Declare the return variable.
385        my $retVal;
386        # Find the month and day of month. There are two ways that can happen. We check for the
387        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
388        # won't be fooled into thinking the month is Sunday.
389        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
390            my ($mon, $mday) = (MONTHS->{$1}, $2);
391            # Insist that the month and day are valid.
392            if (defined($mon) && $2 >= 1 && $2 <= 31) {
393                # Find the time.
394                my ($hour, $min, $sec) = (0, 0, 0);
395                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
396                    ($hour, $min, $sec) = ($1, $2, $3);
397                }
398                # Find the year.
399                my $year;
400                if ($dateString =~ /\b(\d{4})\b/) {
401                    $year = $1;
402                } else {
403                    # Get the default year, which is this one. Note we must convert it to
404                    # the four-digit value expected by "timelocal".
405                    (undef, undef, undef, undef, undef, $year) = localtime();
406                    $year += 1900;
407                }
408                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
409            }
410        }
411        # Return the result.
412        return $retVal;
413    }
414    
415  Single and double hyphens are equivalent. So, you could also code the  =head3 LogErrors
 above command as  
416    
417      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl      Tracer::LogErrors($fileName);
418    
419  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<$options> hash would be  
420    
421      { trace => 2, sql => 0, safe => 0,  =over 4
       noAlias => 1, start => ' ', tblFiles => 0 }  
422    
423  Use of C<StandardSetup> in this way provides a simple way of performing  =item fileName
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
424    
425  If the C<background> option is specified on the command line, then the  Name of the file to receive the error output.
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
426    
427      -user=Bruce -background  =back
428    
429  then the trace output would go to C<traceBruce.log>, the standard output to  =cut
 C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to  
 simplify starting a command in the background.  
430    
431  The user name is also used as the tracing key for L</Emergency Tracing>.  sub LogErrors {
432  Specifying a value of C<E> for the trace level causes emergency tracing to      # Get the file name.
433  be used instead of custom tracing. If the user name is not specified,      my ($fileName) = @_;
434  the tracing key is taken from the C<Tracing> environment variable. If there      # Open the file as the standard error output.
435  is no value for that variable, the tracing key will be computed from the PID.      open STDERR, '>', $fileName;
436    }
437    
438  Finally, if the special option C<-help> is specified, the option  =head3 Trace
 names will be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
439    
440      TransactFeatures -help      Trace($message);
441    
442  he would see the following output.  Write a trace message to the target location specified in L</TSetup>. If there has not been
443    any prior call to B<TSetup>.
444    
445      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  
446    
447  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,  
448    
449      { trace => [0, "tracing level (default 0)"],  Message to write.
        ...  
450    
451  would set the default trace level to 0 instead of E, while  =back
452    
453      { trace => ["2-", "tracing level (default 2)"],  =cut
        ...  
454    
455  would set the default to 2, but trace only to the log file, not to the  sub Trace {
456  standard output.      # Get the parameters.
457        my ($message) = @_;
458        # Strip off any line terminators at the end of the message. We will add
459        # new-line stuff ourselves.
460        my $stripped = Strip($message);
461        # Compute the caller information.
462        my ($callPackage, $callFile, $callLine) = caller();
463        my $callFileTitle = basename($callFile);
464        # Check the caller.
465        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
466        # Get the timestamp.
467        my $timeStamp = Now();
468        # Build the prefix.
469        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
470        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
471        # Format the message.
472        my $formatted = "$prefix $stripped";
473        # Process according to the destination.
474        if ($Destination eq "TEXT") {
475            # Write the message to the standard output.
476            print "$formatted\n";
477        } elsif ($Destination eq "ERROR") {
478            # Write the message to the error output. Here, we want our prefix fields.
479            print STDERR "$formatted\n";
480        } elsif ($Destination eq "WARN") {
481            # Emit the message to the standard error output. It is presumed that the
482            # error logger will add its own prefix fields, the notable exception being
483            # the caller info.
484            print STDERR "$callerInfo$stripped\n";
485        } elsif ($Destination eq "QUEUE") {
486            # Push the message into the queue.
487            push @Queue, "$formatted";
488        } elsif ($Destination eq "HTML") {
489            # Convert the message to HTML and write it to the standard output.
490            my $escapedMessage = CGI::escapeHTML($stripped);
491            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
492        } elsif ($Destination =~ m/^>>/) {
493            # Write the trace message to an output file.
494            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
495            print TRACING "$formatted\n";
496            close TRACING;
497            # If the Tee flag is on, echo it to the standard output.
498            if ($TeeFlag) {
499                print "$formatted\n";
500            }
501        }
502    }
503    
504  The parameters to this method are as follows.  =head3 T
505    
506  =over 4      my $switch = T($category, $traceLevel);
507    
508  =item categories      or
509    
510  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.  
511    
512  =item options  Return TRUE if the trace level is at or above a specified value and the specified category
513    is active, else FALSE. If no category is specified, the caller's package name is used.
514    
515  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).  
516    
517  =item parmHelp  =item category
518    
519  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
520  if the user specifies the C<-h> option.  used.
521    
522  =item argv  =item traceLevel
523    
524  List of command line parameters, including the option switches, which must  Relevant tracing level.
 precede the positional parameters and be prefixed by a hyphen.  
525    
526  =item RETURN  =item RETURN
527    
528  Returns a list. The first element of the list is the reference to a hash that  TRUE if a message at the specified trace level would appear in the trace, else FALSE.
 maps the command-line option switches to their values. These will either be the  
 default values or overrides specified on the command line. The remaining  
 elements of the list are the position parameters, in order.  
529    
530  =back  =back
531    
532  =cut  =cut
533    
534  sub StandardSetup {  sub T {
535        # Declare the return variable.
536        my $retVal = 0;
537        # Only proceed if tracing is turned on.
538        if ($Destination ne "NONE") {
539      # Get the parameters.      # Get the parameters.
540      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
541      # Get the default tracing key.          if (!defined $traceLevel) {
542      my $tkey = EmergencyKey();              # Here we have no category, so we need to get the calling package.
543      # Add the tracing options.              # The calling package is normally the first parameter. If it is
544      if (! exists $options->{trace}) {              # omitted, the first parameter will be the tracelevel. So, the
545          $options->{trace} = ['2', "tracing level (E for emergency tracing)"];              # first thing we do is shift the so-called category into the
546      }              # $traceLevel variable where it belongs.
547      $options->{sql} = [0, "turn on SQL tracing"];              $traceLevel = $category;
548      $options->{help} = [0, "display command-line options"];              my ($package, $fileName, $line) = caller;
549      $options->{user} = [$tkey, "tracing key"];              # If there is no calling package, we default to "main".
550      $options->{background} = [0, "spool standard and error output"];              if (!$package) {
551      # Create a parsing hash from the options hash. The parsing hash                  $category = "main";
     # contains the default values rather than the default value  
     # and the description. While we're at it, we'll memorize the  
     # length of the longest option name.  
     my $longestName = 0;  
     my %parseOptions = ();  
     for my $key (keys %{$options}) {  
         if (length $key > $longestName) {  
             $longestName = length $key;  
         }  
         $parseOptions{$key} = $options->{$key}->[0];  
     }  
     # Parse the command line.  
     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);  
     # Get the logfile suffix.  
     my $suffix = $retOptions->{user};  
     # Check for background mode.  
     if ($retOptions->{background}) {  
         my $outFileName = "$FIG_Config::temp/out$suffix.log";  
         my $errFileName = "$FIG_Config::temp/err$suffix.log";  
         open STDOUT, ">$outFileName";  
         open STDERR, ">$errFileName";  
     }  
     # Now we want to set up tracing. First, we need to know if the user  
     # wants emergency tracing.  
     if ($retOptions->{trace} eq 'E') {  
         ETracing($retOptions->{user});  
     } else {  
         # Here the tracing is controlled from the command line.  
         my @cats = @{$categories};  
         if ($retOptions->{sql}) {  
             push @cats, "SQL";  
         }  
         # Add the default categories.  
         push @cats, "Tracer";  
         # Next, we create the category string by joining the categories.  
         my $cats = join(" ", @cats);  
         # Check to determine whether or not the caller wants to turn off tracing  
         # to the standard output.  
         my $traceLevel = $retOptions->{trace};  
         my $textOKFlag = 1;  
         if ($traceLevel =~ /^(.)-/) {  
             $traceLevel = $1;  
             $textOKFlag = 0;  
         }  
         # Now we set up the trace mode.  
         my $traceMode;  
         # Verify that we can open a file in the FIG temporary directory.  
         my $traceFileName = "$FIG_Config::temp/trace$suffix.log";  
         if (open TESTTRACE, ">$traceFileName") {  
             # Here we can trace to a file.  
             $traceMode = ">$traceFileName";  
             if ($textOKFlag) {  
                 # Echo to standard output if the text-OK flag is set.  
                 $traceMode = "+$traceMode";  
             }  
             # Close the test file.  
             close TESTTRACE;  
         } else {  
             # Here we can't trace to a file. We trace to the standard output if it's  
             # okay, and the error log otherwise.  
             if ($textOKFlag) {  
                 $traceMode = "TEXT";  
552              } else {              } else {
553                  $traceMode = "WARN";                  my @cats = split /::/, $package;
554              }                  $category = $cats[$#cats];
         }  
         # Now set up the tracing.  
         TSetup("$traceLevel $cats", $traceMode);  
     }  
     # Check for the "h" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($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] . ")";  
555              }              }
             print "  $name $desc\n";  
556          }          }
557          exit(0);          # Save the category name and level.
558            $LastCategory = $category;
559            $LastLevel = $traceLevel;
560            # Convert it to lower case before we hash it.
561            $category = lc $category;
562            # Validate the trace level.
563            if (ref $traceLevel) {
564                Confess("Bad trace level.");
565            } elsif (ref $TraceLevel) {
566                Confess("Bad trace config.");
567      }      }
568      # Trace the options, if applicable.          # Make the check. Note that level 0 shows even if the category is turned off.
569      if (T(3)) {          $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
         my @parms = grep { $retOptions->{$_} } keys %{$retOptions};  
         Trace("Selected options: " . join(", ", sort @parms) . ".");  
570      }      }
571      # Return the parsed parameters.      # Return the computed result.
572      return ($retOptions, @retParameters);      return $retVal;
573  }  }
574    
575  =head3 Setups  =head3 QTrace
576    
577  C<< my $count = Tracer::Setups(); >>      my $data = QTrace($format);
578    
579  Return the number of times L</TSetup> has been called.  Return the queued trace data in the specified format.
580    
581  This method allows for the creation of conditional tracing setups where, for example, we  =over 4
582  may want to set up tracing if nobody else has done it before us.  
583    =item format
584    
585    C<html> to format the data as an HTML list, C<text> to format it as straight text.
586    
587    =back
588    
589  =cut  =cut
590    
591  sub Setups {  sub QTrace {
592      return $SetupCount;      # Get the parameter.
593        my ($format) = @_;
594        # Create the return variable.
595        my $retVal = "";
596        # Only proceed if there is an actual queue.
597        if (@Queue) {
598            # Process according to the format.
599            if ($format =~ m/^HTML$/i) {
600                # Convert the queue into an HTML list.
601                $retVal = "<ul>\n";
602                for my $line (@Queue) {
603                    my $escapedLine = CGI::escapeHTML($line);
604                    $retVal .= "<li>$escapedLine</li>\n";
605                }
606                $retVal .= "</ul>\n";
607            } elsif ($format =~ m/^TEXT$/i) {
608                # Convert the queue into a list of text lines.
609                $retVal = join("\n", @Queue) . "\n";
610            }
611            # Clear the queue.
612            @Queue = ();
613        }
614        # Return the formatted list.
615        return $retVal;
616  }  }
617    
618  =head3 Open  =head3 Confess
   
 C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  
619    
620  Open a file.      Confess($message);
621    
622  The I<$fileSpec> is essentially the second argument of the PERL C<open>  Trace the call stack and abort the program with the specified message. When used with
623  function. The mode is specified using Unix-like shell information. So, for  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
624  example,  So, for example
625    
626      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
627    
628  would open for output appended to the specified file, and  Will abort the program with a stack trace if the value of C<$recNum> is negative.
629    
630      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  =over 4
631    
632  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.  
633    
634      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  Message to include in the trace.
635    
636  The I<$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.  
637    
638      Could not open "/usr/spool/news/twitlog"  =cut
639    
640  Note that the mode characters are automatically cleaned from the file name.  sub Confess {
641  The actual error message from the file system will be captured and appended to the      # Get the parameters.
642  message in any case.      my ($message) = @_;
643        # Set up the category and level.
644        $LastCategory = "(confess)";
645        $LastLevel = 0;
646        if (! defined($FIG_Config::no_tool_hdr)) {
647            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
648            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
649            # Only proceed if the tool header file is actually present.
650            if (-f $toolHeaderFile) {
651                my $fh;
652                if (open $fh, "<$toolHeaderFile") {
653                    my @lines = <$fh>;
654                    Trace("Tool header has " . scalar(@lines) . " lines.");
655                }
656            }
657        }
658        # Trace the call stack.
659        Cluck($message);
660        # Abort the program.
661        croak(">>> $message");
662    }
663    
664      Could not open "/usr/spool/news/twitlog": file not found.  =head3 Warn
665    
666  In some versions of PERL the only error message we get is a number, which      Warn($message);
 corresponds to the C++ C<errno> value.  
667    
668      Could not open "/usr/spool/news/twitlog": 6.  This method traces an important message. If an RSS feed is configured
669    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
670    then the message will be echoed to the feed. In general, a tracing
671    destination of C<WARN> indicates that the caller is running as a web
672    service in a production environment; however, this is not a requirement.
673    
674    To force warnings into the RSS feed even when the tracing destination
675    is not C<WARN>, simply specify the C<Feed> tracing module. This can be
676    configured automatically when L</StandardSetup> is used.
677    
678    The L</Cluck> method calls this one for its final message. Since
679    L</Confess> calls L</Cluck>, this means that any error which is caught
680    and confessed will put something in the feed. This insures that someone
681    will be alerted relatively quickly when a failure occurs.
682    
683  =over 4  =over 4
684    
685  =item fileHandle  =item message
686    
687  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.  
688    
689  =item fileSpec  =back
690    
691  File name and mode, as per the PERL C<open> function.  =cut
692    
693  =item message (optional)  sub Warn {
694        # Get the parameters.
695        my ($message) = @_;
696        # Trace the message.
697        Trace($message);
698        # Check for feed forcing.
699        my $forceFeed = exists $Categories{feed};
700        # An error here would be disastrous. Note, however, that we aren't too worried
701        # about losing events. The error log is always available for the occasions where
702        # we mess up. Note that if debug mode is specified, we do this stuff even in a
703        # test environment.
704        eval {
705            # Do we need to put this in the RSS feed?
706            if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
707                # Yes. We now need to compute the date, the link, and the title.
708                # First, the date, in a very specific format.
709                my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
710                    (tz_local_offset() / 30);
711                # Environment data goes in here. We start with the date.
712                my $environment = "$date.  ";
713                # If we need to recap the message (because it's too long to be a title), we'll
714                # put it in here.
715                my $recap;
716                # Copy the message and remove excess space.
717                my $title = $message;
718                $title =~ s/\s+/ /gs;
719                # If it's too long, we have to split it up.
720                if (length $title > 60) {
721                    # Put the full message in the environment string.
722                    $recap = $title;
723                    # Excerpt it as the title.
724                    $title = substr($title, 0, 50) . "...";
725                }
726                # If we have a CGI object, then this is a web error. Otherwise, it's
727                # command-line.
728                if (defined $SavedCGI) {
729                    # We're in a web service. The environment is the user's IP, and the link
730                    # is the URL that got us here.
731                    my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
732                    $environment .= "Event Reported at IP address $key.";
733                    my $url = $SavedCGI->url(-full => 1, -query => 1);
734                    # We need the user agent string and (if available) the referrer.
735                    # The referrer will be the link.
736                    $environment .= "User Agent $ENV{HTTP_USER_AGENT}";
737                    if ($ENV{HTTP_REFERER}) {
738                        my $link = $ENV{HTTP_REFERER};
739                        $environment .= " referred from <a href=\"$link\">$link</a>.";
740                    } else {
741                        $environment .= " referrer unknown.";
742                    }
743                    # Close off the sentence with the original link.
744                    $environment .= " URL of error is <a href=\"$url\">$url</a>.";
745                } else {
746                    # No CGI object, so we're a command-line tool. Use the tracing
747                    # key and the PID as the user identifier, and add the command.
748                    my $key = EmergencyKey();
749                    $environment .= "Event Reported by $key Process $$.";
750                    if ($CommandLine) {
751                        # We're in a StandardSetup script, so we have the real command line.
752                        $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
753                    } elsif ($ENV{_}) {
754                        # We're in a BASH script, so the command has been stored in the _ variable.
755                        $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
756                    }
757                }
758                # Build a GUID. We use the current time, the title, and the process ID,
759                # then digest the result.
760                my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
761                # Finally, the description. This is a stack trace plus various environmental stuff.
762                my $stackTrace = "";
763                my @trace = LongMess();
764                # Only proceed if we got something back.
765                if (scalar(@trace) > 0) {
766                    $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
767                    $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
768                }
769                # We got the stack trace. Now it's time to put it all together.
770                # We have a goofy thing here in that we need to HTML-escape some sections of the description
771                # twice. They will be escaped once here, and then once when written by XML::Simple. They are
772                # unescaped once when processed by the RSS reader, and stuff in the description is treated as
773                # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
774                # our <br>s and <pre>s are used to format the description.
775                $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
776                my $description = "$recap$environment  $stackTrace";
777                # Okay, we have all the pieces. Create a hash of the new event.
778                my $newItem = { title => $title,
779                                description => $description,
780                                category => $LastCategory,
781                                pubDate => $date,
782                                guid => $guid,
783                               };
784                # We need XML capability for this.
785                require XML::Simple;
786                # The RSS document goes in here.
787                my $rss;
788                # Get the name of the RSS file. It's in the FIG temporary directory.
789                my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
790                # Does it exist?
791                if (-s $fileName) {
792                    # Slurp it in.
793                    $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
794                } else {
795                    my $size = -s $fileName;
796                    # Create an empty channel.
797                    $rss = {
798                        channel => {
799                            title => 'NMPDR Warning Feed',
800                            link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
801                            description => "Important messages regarding the status of the NMPDR.",
802                            generator => "NMPDR Trace Facility",
803                            docs => "http://blogs.law.harvard.edu/tech/rss",
804                            item => []
805                        },
806                    };
807                }
808                # Get the channel object.
809                my $channel = $rss->{channel};
810                # Update the last-build date.
811                $channel->{lastBuildDate} = $date;
812                # Get the item array.
813                my $items = $channel->{item};
814                # Insure it has only 100 entries.
815                while (scalar @{$items} > 100) {
816                    pop @{$items};
817                }
818                # Add our new item at the front.
819                unshift @{$items}, $newItem;
820                # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
821                # the requirements for those.
822                my $xml = XML::Simple::XMLout($rss, NoAttr => 1, RootName => undef, XmlDecl => '');
823                # Here we put in the root and declaration. The problem is that the root has to have the version attribute
824                # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
825                $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
826                # We don't use Open here because we can't afford an error.
827                if (open XMLOUT, ">$fileName") {
828                    print XMLOUT $xml;
829                    close XMLOUT;
830                }
831            }
832        };
833        if ($@) {
834            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
835            # (which is a good thing).
836            my $error = $@;
837            Trace("Feed Error: $error") if T(Feed => 0);
838        }
839    }
840    
841  Error message to use if the open fails. If omitted, a standard error message  =head3 Assert
 will be generated. In either case, the error information from the file system  
 is appended to the message. To specify a conditional open that does not throw  
 an error if it fails, use C<0>.  
842    
843  =item RETURN      Assert($condition1, $condition2, ... $conditionN);
844    
845  Returns the name of the file handle assigned to the file, or C<undef> if the  Return TRUE if all the conditions are true. This method can be used in conjunction with
846  open failed.  the OR operator and the L</Confess> method as a debugging assert.
847    So, for example
848    
849        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
850    
851    Will abort the program with a stack trace if the value of C<$recNum> is negative.
852    
853    =cut
854    sub Assert {
855        my $retVal = 1;
856        LOOP: for my $condition (@_) {
857            if (! $condition) {
858                $retVal = 0;
859                last LOOP;
860            }
861        }
862        return $retVal;
863    }
864    
865    =head3 Cluck
866    
867        Cluck($message);
868    
869    Trace the call stack. Note that for best results, you should qualify the call with a
870    trace condition. For example,
871    
872        Cluck("Starting record parse.") if T(3);
873    
874    will only trace the stack if the trace level for the package is 3 or more.
875    
876    =over 4
877    
878    =item message
879    
880    Message to include in the trace.
881    
882    =back
883    
884    =cut
885    
886    sub Cluck {
887        # Get the parameters.
888        my ($message) = @_;
889        # Trace what's happening.
890        Trace("Stack trace for event: $message");
891        # Get the stack trace.
892        my @trace = LongMess();
893        # Convert the trace to a series of messages.
894        for my $line (@trace) {
895            # Replace the tab at the beginning with spaces.
896            $line =~ s/^\t/    /;
897            # Trace the line.
898            Trace($line);
899        }
900        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
901        Warn($message);
902    }
903    
904    =head3 LongMess
905    
906        my @lines = Tracer::LongMess();
907    
908    Return a stack trace with all tracing methods removed. The return will be in the form of a list
909    of message strings.
910    
911    =cut
912    
913    sub LongMess {
914        # Declare the return variable.
915        my @retVal = ();
916        my $confession = longmess("");
917        for my $line (split /\s*\n/, $confession) {
918            unless ($line =~ /Tracer\.pm/) {
919                # Here we have a line worth keeping. Push it onto the result list.
920                push @retVal, $line;
921            }
922        }
923        # Return the result.
924        return @retVal;
925    }
926    
927    =head3 ScriptSetup (deprecated)
928    
929        my ($cgi, $varHash) = ScriptSetup($noTrace);
930    
931    Perform standard tracing and debugging setup for scripts. The value returned is
932    the CGI object followed by a pre-built variable hash. At the end of the script,
933    the client should call L</ScriptFinish> to output the web page.
934    
935    This method calls L</ETracing> to configure tracing, which allows the tracing
936    to be configured via the emergency tracing form on the debugging control panel.
937    Tracing will then be turned on automatically for all programs that use the L</ETracing>
938    method, which includes every program that uses this method or L</StandardSetup>.
939    
940    =over 4
941    
942    =item noTrace (optional)
943    
944    If specified, tracing will be suppressed. This is useful if the script wants to set up
945    tracing manually.
946    
947    =item RETURN
948    
949    Returns a two-element list consisting of a CGI query object and a variable hash for
950    the output page.
951    
952    =back
953    
954    =cut
955    
956    sub ScriptSetup {
957        # Get the parameters.
958        my ($noTrace) = @_;
959        # Get the CGI query object.
960        my $cgi = CGI->new();
961        # Set up tracing if it's not suppressed.
962        ETracing($cgi) unless $noTrace;
963        # Create the variable hash.
964        my $varHash = { results => '' };
965        # Return the query object and variable hash.
966        return ($cgi, $varHash);
967    }
968    
969    =head3 ETracing
970    
971        ETracing($parameter);
972    
973    Set up emergency tracing. Emergency tracing is tracing that is turned
974    on automatically for any program that calls this method. The emergency
975    tracing parameters are stored in a a file identified by a tracing key.
976    If this method is called with a CGI object, then the tracing key is
977    taken from a cookie. If it is called with no parameters, then the tracing
978    key is taken from an environment variable. If it is called with a string,
979    the tracing key is that string.
980    
981    =over 4
982    
983    =item parameter
984    
985    A parameter from which the tracing key is computed. If it is a scalar,
986    that scalar is used as the tracing key. If it is a CGI object, the
987    tracing key is taken from the C<IP> cookie. If it is omitted, the
988    tracing key is taken from the C<TRACING> environment variable. If it
989    is a CGI object and emergency tracing is not on, the C<Trace> and
990    C<TF> parameters will be used to determine the type of tracing.
991    
992    =back
993    
994    =cut
995    
996    sub ETracing {
997        # Get the parameter.
998        my ($parameter) = @_;
999        # Check for CGI mode.
1000        if (defined $parameter && ref $parameter eq 'CGI') {
1001            $SavedCGI = $parameter;
1002        } else {
1003            $SavedCGI = undef;
1004        }
1005        # Default to no tracing except errors.
1006        my ($tracing, $dest) = ("0", "WARN");
1007        # Check for emergency tracing.
1008        my $tkey = EmergencyKey($parameter);
1009        my $emergencyFile = EmergencyFileName($tkey);
1010        if (-e $emergencyFile) {
1011            # We have the file. Read in the data.
1012            my @tracing = GetFile($emergencyFile);
1013            # Pull off the time limit.
1014            my $expire = shift @tracing;
1015            # Convert it to seconds.
1016            $expire *= 3600;
1017            # Check the file data.
1018            my $stat = stat($emergencyFile);
1019            my ($now) = gettimeofday;
1020            if ($now - $stat->mtime > $expire) {
1021                # Delete the expired file.
1022                unlink $emergencyFile;
1023            } else {
1024                # Emergency tracing is on. Pull off the destination and
1025                # the trace level;
1026                $dest = shift @tracing;
1027                my $level = shift @tracing;
1028                # Convert the destination to a real tracing destination.
1029                # temp directory.
1030                $dest = EmergencyTracingDest($tkey, $dest);
1031                # Insure Tracer is specified.
1032                my %moduleHash = map { $_ => 1 } @tracing;
1033                $moduleHash{Tracer} = 1;
1034                # Set the trace parameter.
1035                $tracing = join(" ", $level, sort keys %moduleHash);
1036            }
1037        } elsif (defined $SavedCGI) {
1038            # There's no emergency tracing, but we have a CGI object, so check
1039            # for tracing from the form parameters.
1040            if ($SavedCGI->param('Trace')) {
1041                # Here the user has requested tracing via a form.
1042                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1043                $tracing = $SavedCGI->param('Trace') . " Tracer";
1044            }
1045        }
1046        # Setup the tracing we've determined from all the stuff above.
1047        TSetup($tracing, $dest);
1048        # Check to see if we're a web script.
1049        if (defined $SavedCGI) {
1050            # Yes we are. Trace the form and environment data.
1051            TraceParms($SavedCGI);
1052            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1053            # emitted by the script in its raw form.
1054            if (T(Raw => 3)) {
1055                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1056            }
1057        }
1058    }
1059    
1060    =head3 EmergencyFileName
1061    
1062        my $fileName = Tracer::EmergencyFileName($tkey);
1063    
1064    Return the emergency tracing file name. This is the file that specifies
1065    the tracing information.
1066    
1067    =over 4
1068    
1069    =item tkey
1070    
1071    Tracing key for the current program.
1072    
1073    =item RETURN
1074    
1075    Returns the name of the file to contain the emergency tracing information.
1076    
1077    =back
1078    
1079    =cut
1080    
1081    sub EmergencyFileName {
1082        # Get the parameters.
1083        my ($tkey) = @_;
1084        # Compute the emergency tracing file name.
1085        return "$FIG_Config::temp/Emergency$tkey.txt";
1086    }
1087    
1088    =head3 EmergencyFileTarget
1089    
1090        my $fileName = Tracer::EmergencyFileTarget($tkey);
1091    
1092    Return the emergency tracing target file name. This is the file that receives
1093    the tracing output for file-based tracing.
1094    
1095    =over 4
1096    
1097    =item tkey
1098    
1099    Tracing key for the current program.
1100    
1101    =item RETURN
1102    
1103    Returns the name of the file to contain the trace output.
1104    
1105    =back
1106    
1107    =cut
1108    
1109    sub EmergencyFileTarget {
1110        # Get the parameters.
1111        my ($tkey) = @_;
1112        # Compute the emergency tracing file name.
1113        return "$FIG_Config::temp/trace$tkey.log";
1114    }
1115    
1116    =head3 EmergencyTracingDest
1117    
1118        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1119    
1120    This method converts an emergency tracing destination to a real
1121    tracing destination. The main difference is that if the
1122    destination is C<FILE> or C<APPEND>, we convert it to file
1123    output. If the destination is C<DUAL>, we convert it to file
1124    and standard output.
1125    
1126    =over 4
1127    
1128    =item tkey
1129    
1130    Tracing key for this environment.
1131    
1132    =item myDest
1133    
1134    Destination from the emergency tracing file.
1135    
1136    =item RETURN
1137    
1138    Returns a destination that can be passed into L</TSetup>.
1139    
1140    =back
1141    
1142    =cut
1143    
1144    sub EmergencyTracingDest {
1145        # Get the parameters.
1146        my ($tkey, $myDest) = @_;
1147        # Declare the return variable.
1148        my $retVal = $myDest;
1149        # Process according to the destination value.
1150        if ($myDest eq 'FILE') {
1151            $retVal = ">" . EmergencyFileTarget($tkey);
1152        } elsif ($myDest eq 'APPEND') {
1153            $retVal = ">>" . EmergencyFileTarget($tkey);
1154        } elsif ($myDest eq 'DUAL') {
1155            $retVal = "+>" . EmergencyFileTarget($tkey);
1156        } elsif ($myDest eq 'WARN') {
1157            $retVal = "WARN";
1158        }
1159        # Return the result.
1160        return $retVal;
1161    }
1162    
1163    =head3 Emergency
1164    
1165        Emergency($key, $hours, $dest, $level, @modules);
1166    
1167    Turn on emergency tracing. This method is normally invoked over the web from
1168    a debugging console, but it can also be called by the C<trace.pl> script.
1169    The caller specifies the duration of the emergency in hours, the desired tracing
1170    destination, the trace level, and a list of the trace modules to activate.
1171    For the length of the duration, when a program in an environment with the
1172    specified tracing key active invokes a Sprout CGI script, tracing will be
1173    turned on automatically. See L</TSetup> for more about tracing setup and
1174    L</ETracing> for more about emergency tracing.
1175    
1176    =over 4
1177    
1178    =item tkey
1179    
1180    The tracing key. This is used to identify the control file and the trace file.
1181    
1182    =item hours
1183    
1184    Number of hours to keep emergency tracing alive.
1185    
1186    =item dest
1187    
1188    Tracing destination. If no path information is specified for a file
1189    destination, it is put in the FIG temporary directory.
1190    
1191    =item level
1192    
1193    Tracing level. A higher level means more trace messages.
1194    
1195    =item modules
1196    
1197    A list of the tracing modules to activate.
1198    
1199    =back
1200    
1201    =cut
1202    
1203    sub Emergency {
1204        # Get the parameters.
1205        my ($tkey, $hours, $dest, $level, @modules) = @_;
1206        # Create the emergency file.
1207        my $specFile = EmergencyFileName($tkey);
1208        my $outHandle = Open(undef, ">$specFile");
1209        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1210    }
1211    
1212    =head3 EmergencyKey
1213    
1214        my $tkey = EmergencyKey($parameter);
1215    
1216    Return the Key to be used for emergency tracing. This could be an IP address,
1217     a session ID, or a user name, depending on the environment.
1218    
1219    =over 4
1220    
1221    =item parameter
1222    
1223    Parameter defining the method for finding the tracing key. If it is a scalar,
1224    then it is presumed to be the tracing key itself. If it is a CGI object, then
1225    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1226    taken from the C<TRACING> environment variable.
1227    
1228    =item RETURN
1229    
1230    Returns the key to be used for labels in emergency tracing.
1231    
1232  =back  =back
1233    
1234  =cut  =cut
1235    
1236  sub Open {  sub EmergencyKey {
1237      # Get the parameters.      # Get the parameters.
1238      my ($fileHandle, $fileSpec, $message) = @_;      my ($parameter) = @_;
1239      # Attempt to open the file.      # Declare the return variable.
1240      my $rv = open $fileHandle, $fileSpec;      my $retVal;
1241      # If the open failed, generate an error message.      # Determine the parameter type.
1242      if (! $rv) {      if (! defined $parameter) {
1243          # Save the system error message.          # Here we're supposed to check the environment. If that fails, we
1244          my $sysMessage = $!;          # get the effective login ID.
1245          # See if we need a default message.          $retVal = $ENV{TRACING} || scalar getpwuid($<);
1246          if (!$message) {      } else {
1247              # Clean any obvious mode characters and leading spaces from the          my $ptype = ref $parameter;
1248              # filename.          if ($ptype eq 'CGI') {
1249              my ($fileName) = FindNamePart($fileSpec);              # Here we were invoked from a web page. Look for a cookie.
1250              $message = "Could not open \"$fileName\"";              $retVal = $parameter->cookie('IP');
1251            } elsif (! $ptype) {
1252                # Here the key was passed in.
1253                $retVal = $parameter;
1254            }
1255        }
1256        # If no luck finding a key, use the PID.
1257        if (! defined $retVal) {
1258            $retVal = $$;
1259        }
1260        # Return the result.
1261        return $retVal;
1262    }
1263    
1264    
1265    =head3 TraceParms
1266    
1267        Tracer::TraceParms($cgi);
1268    
1269    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1270    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1271    
1272    =over 4
1273    
1274    =item cgi
1275    
1276    CGI query object containing the parameters to trace.
1277    
1278    =back
1279    
1280    =cut
1281    
1282    sub TraceParms {
1283        # Get the parameters.
1284        my ($cgi) = @_;
1285        if (T(CGI => 2)) {
1286            # Here we trace the GET-style URL for the script.
1287            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1288        }
1289        if (T(CGI => 3)) {
1290            # Here we want to trace the parameter data.
1291            my @names = $cgi->param;
1292            for my $parmName (sort @names) {
1293                # Note we skip the Trace parameters, which are for our use only.
1294                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1295                    my @values = $cgi->param($parmName);
1296                    Trace("[CGI] $parmName = " . join(", ", @values));
1297                }
1298            }
1299            # Display the request method.
1300            my $method = $cgi->request_method();
1301            Trace("Method: $method");
1302        }
1303        if (T(CGI => 4)) {
1304            # Here we want the environment data too.
1305            for my $envName (sort keys %ENV) {
1306                Trace("[ENV] $envName = $ENV{$envName}");
1307            }
1308        }
1309    }
1310    
1311    =head3 TraceImages
1312    
1313        Tracer::TraceImages($htmlString);
1314    
1315    Trace information about all of an html document's images. The tracing
1316    will be for type "IMG" at level 3. The image's source string
1317    will be displayed. This is generally either the URL of the image or
1318    raw data for the image itself. If the source is too long, only the first 300
1319    characters will be shown at trace level 3. The entire source will be shown,
1320    however, at trace level 4. This method is not very smart, and might catch
1321    Javascript code, but it is still useful when debugging the arcane
1322    behavior of images in multiple browser environments.
1323    
1324    =over 4
1325    
1326    =item htmlString
1327    
1328    HTML text for an outgoing web page.
1329    
1330    =back
1331    
1332    =cut
1333    
1334    sub TraceImages {
1335        # Only proceed if we're at the proper trace level.
1336        if (T(IMG => 3)) {
1337            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1338            # into a variable called "$htmlString". This is because we expect html strings to be
1339            # long, and don't want to copy them any more than we have to.
1340            Trace(length($_[0]) . " characters in web page.");
1341            # Loop through the HTML, culling image tags.
1342            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1343                # Extract the source string and determine whether or not it's too long.
1344                my $srcString = $1;
1345                my $pos = pos($_[0]) - length($srcString);
1346                my $excess = length($srcString) - 300;
1347                # We'll put the display string in here.
1348                my $srcDisplay = $srcString;
1349                # If it's a data string, split it at the comma.
1350                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1351                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1352                # a long string, however, we only show the first 300 characters.
1353                if ($excess > 0 && ! T(IMG => 4)) {
1354                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1355                }
1356                # Output the trace message.
1357                Trace("Image tag at position $pos:\n$srcDisplay");
1358            }
1359        }
1360    }
1361    
1362    
1363    =head3 ScriptFinish (deprecated)
1364    
1365        ScriptFinish($webData, $varHash);
1366    
1367    Output a web page at the end of a script. Either the string to be output or the
1368    name of a template file can be specified. If the second parameter is omitted,
1369    it is assumed we have a string to be output; otherwise, it is assumed we have the
1370    name of a template file. The template should have the variable C<DebugData>
1371    specified in any form that invokes a standard script. If debugging mode is turned
1372    on, a form field will be put in that allows the user to enter tracing data.
1373    Trace messages will be placed immediately before the terminal C<BODY> tag in
1374    the output, formatted as a list.
1375    
1376    A typical standard script would loook like the following.
1377    
1378        BEGIN {
1379            # Print the HTML header.
1380            print "CONTENT-TYPE: text/html\n\n";
1381        }
1382        use Tracer;
1383        use CGI;
1384        use FIG;
1385        # ... more uses ...
1386    
1387        my ($cgi, $varHash) = ScriptSetup();
1388        eval {
1389            # ... get data from $cgi, put it in $varHash ...
1390        };
1391        if ($@) {
1392            Trace("Script Error: $@") if T(0);
1393        }
1394        ScriptFinish("Html/MyTemplate.html", $varHash);
1395    
1396    The idea here is that even if the script fails, you'll see trace messages and
1397    useful output.
1398    
1399    =over 4
1400    
1401    =item webData
1402    
1403    A string containing either the full web page to be written to the output or the
1404    name of a template file from which the page is to be constructed. If the name
1405    of a template file is specified, then the second parameter must be present;
1406    otherwise, it must be absent.
1407    
1408    =item varHash (optional)
1409    
1410    If specified, then a reference to a hash mapping variable names for a template
1411    to their values. The template file will be read into memory, and variable markers
1412    will be replaced by data in this hash reference.
1413    
1414    =back
1415    
1416    =cut
1417    
1418    sub ScriptFinish {
1419        # Get the parameters.
1420        my ($webData, $varHash) = @_;
1421        # Check for a template file situation.
1422        my $outputString;
1423        if (defined $varHash) {
1424            # Here we have a template file. We need to determine the template type.
1425            my $template;
1426            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1427                $template = "$FIG_Config::template_url/$webData";
1428            } else {
1429                $template = "<<$webData";
1430            }
1431            $outputString = PageBuilder::Build($template, $varHash, "Html");
1432        } else {
1433            # Here the user gave us a raw string.
1434            $outputString = $webData;
1435        }
1436        # Check for trace messages.
1437        if ($Destination ne "NONE" && $TraceLevel > 0) {
1438            # We have trace messages, so we want to put them at the end of the body. This
1439            # is either at the end of the whole string or at the beginning of the BODY
1440            # end-tag.
1441            my $pos = length $outputString;
1442            if ($outputString =~ m#</body>#gi) {
1443                $pos = (pos $outputString) - 7;
1444            }
1445            # If the trace messages were queued, we unroll them. Otherwise, we display the
1446            # destination.
1447            my $traceHtml;
1448            if ($Destination eq "QUEUE") {
1449                $traceHtml = QTrace('Html');
1450            } elsif ($Destination =~ /^>>(.+)$/) {
1451                # Here the tracing output it to a file. We code it as a hyperlink so the user
1452                # can copy the file name into the clipboard easily.
1453                my $actualDest = $1;
1454                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1455            } else {
1456                # Here we have one of the special destinations.
1457                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1458            }
1459            substr $outputString, $pos, 0, $traceHtml;
1460        }
1461        # Write the output string.
1462        print $outputString;
1463    }
1464    
1465    =head2 Command-Line Utility Methods
1466    
1467    =head3 SendSMS
1468    
1469        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1470    
1471    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1472    user name, password, and API ID for the relevant account in the hash reference variable
1473    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1474    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1475    is C<2561022>, then the FIG_Config file must contain
1476    
1477        $phone =  { user => 'BruceTheHumanPet',
1478                    password => 'silly',
1479                    api_id => '2561022' };
1480    
1481    The original purpose of this method was to insure Bruce would be notified immediately when the
1482    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1483    when you call this method.
1484    
1485    The message ID will be returned if successful, and C<undef> if an error occurs.
1486    
1487    =over 4
1488    
1489    =item phoneNumber
1490    
1491    Phone number to receive the message, in international format. A United States phone number
1492    would be prefixed by "1". A British phone number would be prefixed by "44".
1493    
1494    =item msg
1495    
1496    Message to send to the specified phone.
1497    
1498    =item RETURN
1499    
1500    Returns the message ID if successful, and C<undef> if the message could not be sent.
1501    
1502    =back
1503    
1504    =cut
1505    
1506    sub SendSMS {
1507        # Get the parameters.
1508        my ($phoneNumber, $msg) = @_;
1509        # Declare the return variable. If we do not change it, C<undef> will be returned.
1510        my $retVal;
1511        # Only proceed if we have phone support.
1512        if (! defined $FIG_Config::phone) {
1513            Trace("Phone support not present in FIG_Config.") if T(1);
1514        } else {
1515            # Get the phone data.
1516            my $parms = $FIG_Config::phone;
1517            # Get the Clickatell URL.
1518            my $url = "http://api.clickatell.com/http/";
1519            # Create the user agent.
1520            my $ua = LWP::UserAgent->new;
1521            # Request a Clickatell session.
1522            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1523                                         password => $parms->{password},
1524                                         api_id => $parms->{api_id},
1525                                         to => $phoneNumber,
1526                                         text => $msg});
1527            # Check for an error.
1528            if (! $resp->is_success) {
1529                Trace("Alert failed.") if T(1);
1530            } else {
1531                # Get the message ID.
1532                my $rstring = $resp->content;
1533                if ($rstring =~ /^ID:\s+(.*)$/) {
1534                    $retVal = $1;
1535                } else {
1536                    Trace("Phone attempt failed with $rstring") if T(1);
1537          }          }
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
1538      }      }
1539      # Return the file handle.      }
1540      return $fileHandle;      # Return the result.
1541        return $retVal;
1542  }  }
1543    
1544  =head3 FindNamePart  =head3 StandardSetup
1545    
1546  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>      my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1547    
1548  Extract the portion of a file specification that contains the file name.  This method performs standard command-line parsing and tracing setup. The return
1549    values are a hash of the command-line options and a list of the positional
1550    parameters. Tracing is automatically set up and the command-line options are
1551    validated.
1552    
1553  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
1554  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>.  
1555    
1556      >>/usr/fig/myfile.txt  The I<categories> parameter is the most obtuse. It is a reference to a list of
1557      </usr/fig/myfile.txt  special-purpose tracing categories. Most tracing categories are PERL package
1558      | sort -u > /usr/fig/myfile.txt  names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1559    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1560    
1561  If the method cannot find a file name using its normal methods, it will return the      ["Sprout", "SproutLoad", "ERDB"]
1562  whole incoming string.  
1563    This would cause trace messages in the specified three packages to appear in
1564    the output. There are two special tracing categories that are automatically
1565    handled by this method. In other words, if you used L</TSetup> you would need
1566    to include these categories manually, but if you use this method they are turned
1567    on automatically.
1568    
1569  =over 4  =over 4
1570    
1571  =item fileSpec  =item SQL
1572    
1573  File specification string from which the file name is to be extracted.  Traces SQL commands and activity.
1574    
1575  =item RETURN  =item Tracer
1576    
1577  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.  
1578    
1579  =back  =back
1580    
1581  =cut  C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1582  #: Return Type $;  The trace level is specified using the C<-trace> command-line option. For example,
1583  sub FindNamePart {  the following command line for C<TransactFeatures> turns on SQL tracing and runs
1584      # Get the parameters.  all tracing at level 3.
     my ($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, $len);  
 }  
1585    
1586  =head3 OpenDir      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1587    
1588  C<< my @files = OpenDir($dirName, $filtered, $flag); >>  Standard tracing is output to the standard output and echoed to the file
1589    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1590    process ID. You can also specify the C<user> parameter to put a user ID
1591    instead of a process ID in the trace file name. So, for example
1592    
1593  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.
1594  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,  
1595    
1596      my @files = OpenDir("/Volumes/fig/contigs", 1);      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1597    
1598  is effectively the same as  would send the trace output to C<traceBruce.log> in the temporary directory.
1599    
1600      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
1601      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  options, their default values, and an explanation of what they mean. Command-line
1602    options may be in the form of switches or keywords. In the case of a switch, the
1603    option value is 1 if it is specified and 0 if it is not specified. In the case
1604    of a keyword, the value is separated from the option name by an equal sign. You
1605    can see this last in the command-line example above.
1606    
1607  Similarly, the following code  You can specify a different default trace level by setting C<$options->{trace}>
1608    prior to calling this method.
1609    
1610      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  An example at this point would help. Consider, for example, the command-line utility
1611    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1612    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1613    the following code.
1614    
1615  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1616  automatically returns an empty list if the directory fails to open.                          { safe => [0, "use database transactions"],
1617                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1618                              start => [' ', "start with this genome"],
1619                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1620                            "<command> <transactionDirectory> <IDfile>",
1621                          @ARGV);
1622    
 =over 4  
1623    
1624  =item dirName  The call to C<ParseCommand> specifies the default values for the options and
1625    stores the actual options in a hash that is returned as C<$options>. The
1626    positional parameters are returned in C<@parameters>.
1627    
1628  Name of the directory to open.  The following is a sample command line for C<TransactFeatures>.
1629    
1630  =item filtered      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1631    
1632  TRUE if files whose names begin with a period (C<.>) should be automatically removed  Single and double hyphens are equivalent. So, you could also code the
1633  from the list, else FALSE.  above command as
1634    
1635  =item flag      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1636    
1637  TRUE if a failure to open is okay, else FALSE  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1638    parameters, and would find themselves in I<@parameters> after executing the
1639    above code fragment. The tracing would be set to level 2, and the categories
1640    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1641    and C<DocUtils> was included because it came in within the first parameter
1642    to this method. The I<$options> hash would be
1643    
1644  =back      { trace => 2, sql => 0, safe => 0,
1645          noAlias => 1, start => ' ', tblFiles => 0 }
1646    
1647  =cut  Use of C<StandardSetup> in this way provides a simple way of performing
1648  #: Return Type @;  standard tracing setup and command-line parsing. Note that the caller is
1649  sub OpenDir {  not even aware of the command-line switches C<-trace> and C<-sql>, which
1650      # Get the parameters.  are used by this method to control the tracing. If additional tracing features
1651      my ($dirName, $filtered, $flag) = @_;  need to be added in the future, they can be processed by this method without
1652      # 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 $dirName.");  
     }  
     # Return the result.  
     return @retVal;  
 }  
1653    
1654  =head3 SetLevel  If the C<background> option is specified on the command line, then the
1655    standard and error outputs will be directed to files in the temporary
1656    directory, using the same suffix as the trace file. So, if the command
1657    line specified
1658    
1659  C<< Tracer::SetLevel($newLevel); >>      -user=Bruce -background
1660    
1661  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
1662    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1663    simplify starting a command in the background.
1664    
1665  =over 4  The user name is also used as the tracing key for L</Emergency Tracing>.
1666    Specifying a value of C<E> for the trace level causes emergency tracing to
1667    be used instead of custom tracing. If the user name is not specified,
1668    the tracing key is taken from the C<Tracing> environment variable. If there
1669    is no value for that variable, the tracing key will be computed from the active
1670    login ID.
1671    
1672  =item newLevel  Since the default situation in StandardSetup is to trace to the standard
1673    output, errors that occur in command-line scripts will not generate
1674    RSS events. To force the events, use the C<warn> option.
1675    
1676  Proposed new trace level.      TransactFeatures -background -warn register ../xacts IDs.tbl
1677    
1678  =back  Finally, if the special option C<-help> is specified, the option
1679    names will be traced at level 0 and the program will exit without processing.
1680    This provides a limited help capability. For example, if the user enters
1681    
1682  =cut      TransactFeatures -help
1683    
1684  sub SetLevel {  he would see the following output.
     $TraceLevel = $_[0];  
 }  
1685    
1686  =head3 Now      TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1687            -trace    tracing level (default E)
1688            -sql      trace SQL commands
1689            -safe     use database transactions
1690            -noAlias  do not expect aliases in CHANGE transactions
1691            -start    start with this genome
1692            -tblFiles output TBL files containing the corrected IDs
1693    
1694  C<< my $string = Tracer::Now(); >>  The caller has the option of modifying the tracing scheme by placing a value
1695    for C<trace> in the incoming options hash. The default value can be overridden,
1696    or the tracing to the standard output can be turned off by suffixing a minus
1697    sign to the trace level. So, for example,
1698    
1699  Return a displayable time stamp containing the local time.      { trace => [0, "tracing level (default 0)"],
1700           ...
1701    
1702  =cut  would set the default trace level to 0 instead of E, while
1703    
1704  sub Now {      { trace => ["2-", "tracing level (default 2)"],
1705      my ($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 $retVal;  
 }  
1706    
1707  # Pad a number to 2 digits.  would set the default to 2, but trace only to the log file, not to the
1708  sub _p2 {  standard output.
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
 }  
1709    
1710  =head3 ParseTraceDate  The parameters to this method are as follows.
1711    
1712  C<< my $time = Tracer::ParseTraceDate($dateString); >>  =over 4
1713    
1714  Convert a date from the trace file into a PERL timestamp.  =item categories
1715    
1716  =over 4  Reference to a list of tracing category names. These should be names of
1717    packages whose internal workings will need to be debugged to get the
1718    command working.
1719    
1720    =item options
1721    
1722    Reference to a hash containing the legal options for the current command mapped
1723    to their default values and descriptions. The user can override the defaults
1724    by specifying the options as command-line switches prefixed by a hyphen.
1725    Tracing-related options may be added to this hash. If the C<-h> option is
1726    specified on the command line, the option descriptions will be used to
1727    explain the options. To turn off tracing to the standard output, add a
1728    minus sign to the value for C<trace> (see above).
1729    
1730    =item parmHelp
1731    
1732    A string that vaguely describes the positional parameters. This is used
1733    if the user specifies the C<-h> option.
1734    
1735  =item dateString  =item argv
1736    
1737  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
1738  L</Now> method.  precede the positional parameters and be prefixed by a hyphen.
1739    
1740  =item RETURN  =item RETURN
1741    
1742  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
1743  the time string is invalid.  maps the command-line option switches to their values. These will either be the
1744    default values or overrides specified on the command line. The remaining
1745    elements of the list are the position parameters, in order.
1746    
1747  =back  =back
1748    
1749  =cut  =cut
1750    
1751  sub ParseTraceDate {  sub StandardSetup {
1752      # Get the parameters.      # Get the parameters.
1753      my ($dateString) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
1754      # Declare the return variable.      # Get the default tracing key.
1755      my $retVal;      my $tkey = EmergencyKey();
1756      # Parse the date.      # Save the command line.
1757      if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {      $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1758          # Create a time object. Note we need to convert the day, month,      # Add the tracing options.
1759          # and year to a different base. Years count from 1900, and      if (! exists $options->{trace}) {
1760          # the internal month value is relocated to January = 0.          $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
         $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);  
1761      }      }
1762      # Return the result.      $options->{sql} = [0, "turn on SQL tracing"];
1763      return $retVal;      $options->{help} = [0, "display command-line options"];
1764        $options->{user} = [$tkey, "tracing key"];
1765        $options->{background} = [0, "spool standard and error output"];
1766        $options->{warn} = [0, "send errors to RSS feed"];
1767        # Create a parsing hash from the options hash. The parsing hash
1768        # contains the default values rather than the default value
1769        # and the description. While we're at it, we'll memorize the
1770        # length of the longest option name.
1771        my $longestName = 0;
1772        my %parseOptions = ();
1773        for my $key (keys %{$options}) {
1774            if (length $key > $longestName) {
1775                $longestName = length $key;
1776  }  }
1777            $parseOptions{$key} = $options->{$key}->[0];
1778  =head3 LogErrors      }
1779        # Parse the command line.
1780  C<< Tracer::LogErrors($fileName); >>      my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1781        # Get the logfile suffix.
1782  Route the standard error output to a log file.      my $suffix = $retOptions->{user};
1783        # Check for background mode.
1784  =over 4      if ($retOptions->{background}) {
1785            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1786  =item fileName          my $errFileName = "$FIG_Config::temp/err$suffix.log";
1787            open STDOUT, ">$outFileName";
1788  Name of the file to receive the error output.          open STDERR, ">$errFileName";
1789            # Check for phone support. If we have phone support and a phone number,
1790  =back          # we want to turn it on.
1791            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1792  =cut              $retOptions->{phone} = $ENV{PHONE};
1793            }
1794  sub LogErrors {      }
1795      # Get the file name.      # Now we want to set up tracing. First, we need to know if the user
1796      my ($fileName) = @_;      # wants emergency tracing.
1797      # Open the file as the standard error output.      if ($retOptions->{trace} eq 'E') {
1798      open STDERR, '>', $fileName;          ETracing($retOptions->{user});
1799        } else {
1800            # Here the tracing is controlled from the command line.
1801            my @cats = @{$categories};
1802            if ($retOptions->{sql}) {
1803                push @cats, "SQL";
1804            }
1805            if ($retOptions->{warn}) {
1806                push @cats, "Feed";
1807            }
1808            # Add the default categories.
1809            push @cats, "Tracer";
1810            # Next, we create the category string by joining the categories.
1811            my $cats = join(" ", @cats);
1812            # Check to determine whether or not the caller wants to turn off tracing
1813            # to the standard output.
1814            my $traceLevel = $retOptions->{trace};
1815            my $textOKFlag = 1;
1816            if ($traceLevel =~ /^(.)-/) {
1817                $traceLevel = $1;
1818                $textOKFlag = 0;
1819            }
1820            # Now we set up the trace mode.
1821            my $traceMode;
1822            # Verify that we can open a file in the FIG temporary directory.
1823            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1824            if (open TESTTRACE, ">$traceFileName") {
1825                # Here we can trace to a file.
1826                $traceMode = ">$traceFileName";
1827                if ($textOKFlag) {
1828                    # Echo to standard output if the text-OK flag is set.
1829                    $traceMode = "+$traceMode";
1830                }
1831                # Close the test file.
1832                close TESTTRACE;
1833            } else {
1834                # Here we can't trace to a file. Complain about this.
1835                warn "Could not open trace file $traceFileName: $!\n";
1836                # We trace to the standard output if it's
1837                # okay, and the error log otherwise.
1838                if ($textOKFlag) {
1839                    $traceMode = "TEXT";
1840                } else {
1841                    $traceMode = "WARN";
1842                }
1843            }
1844            # Now set up the tracing.
1845            TSetup("$traceLevel $cats", $traceMode);
1846        }
1847        # Check for the "help" option. If it is specified, dump the command-line
1848        # options and exit the program.
1849        if ($retOptions->{help}) {
1850            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1851            print "$1 [options] $parmHelp\n";
1852            for my $key (sort keys %{$options}) {
1853                my $name = Pad($key, $longestName, 0, ' ');
1854                my $desc = $options->{$key}->[1];
1855                if ($options->{$key}->[0]) {
1856                    $desc .= " (default " . $options->{$key}->[0] . ")";
1857                }
1858                print "  $name $desc\n";
1859            }
1860            exit(0);
1861        }
1862        # Trace the options, if applicable.
1863        if (T(3)) {
1864            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1865            Trace("Selected options: " . join(", ", sort @parms) . ".");
1866        }
1867        # Return the parsed parameters.
1868        return ($retOptions, @retParameters);
1869  }  }
1870    
1871  =head3 ReadOptions  =head3 ReadOptions
1872    
1873  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1874    
1875  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
1876  format  format
# Line 1069  Line 1931 
1931    
1932  =head3 GetOptions  =head3 GetOptions
1933    
1934  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1935    
1936  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
1937  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 1940 
1940    
1941  Consider the following example.  Consider the following example.
1942    
1943  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1944    
1945  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1946  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 1086  Line 1948 
1948  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1949  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1950    
1951  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1952    
1953  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1954    
# Line 1130  Line 1992 
1992    
1993  =head3 MergeOptions  =head3 MergeOptions
1994    
1995  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
1996    
1997  Merge default values into a hash table. This method looks at the key-value pairs in the  Merge default values into a hash table. This method looks at the key-value pairs in the
1998  second (default) hash, and if a matching key is not found in the first hash, the default  second (default) hash, and if a matching key is not found in the first hash, the default
# Line 1145  Line 2007 
2007    
2008  =item defaults  =item defaults
2009    
2010  Default values to be merged into the first hash table if they are not already present.  Default values to be merged into the first hash table if they are not already present.
2011    
2012  =back  =back
2013    
2014  =cut  =cut
2015    
2016  sub MergeOptions {  sub MergeOptions {
2017      # Get the parameters.      # Get the parameters.
2018      my ($table, $defaults) = @_;      my ($table, $defaults) = @_;
2019      # Loop through the defaults.      # Loop through the defaults.
2020      while (my ($key, $value) = each %{$defaults}) {      while (my ($key, $value) = each %{$defaults}) {
2021          if (!exists $table->{$key}) {          if (!exists $table->{$key}) {
2022              $table->{$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.");  
2023          }          }
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
2024      }      }
     # Return the computed result.  
     return $retVal;  
2025  }  }
2026    
2027  =head3 ParseCommand  =head3 ParseCommand
2028    
2029  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2030    
2031  Parse a command line consisting of a list of parameters. The initial parameters may be option  Parse a command line consisting of a list of parameters. The initial parameters may be option
2032  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2033  off and merged into a table of default options. The remainder of the command line is  off and merged into a table of default options. The remainder of the command line is
2034  returned as a list of positional arguments. For example, consider the following invocation.  returned as a list of positional arguments. For example, consider the following invocation.
2035    
2036  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2037    
2038  In this case, the list @words will be treated as a command line and there are two options available,  In this case, the list @words will be treated as a command line and there are two options available,
2039  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
2040    
2041  C<< -logFile=error.log apple orange rutabaga >>      -logFile=error.log apple orange rutabaga
2042    
2043  then at the end of the invocation, C<$options> will be  then at the end of the invocation, C<$options> will be
2044    
2045  C<< { errors => 0, logFile => 'error.log' } >>      { errors => 0, logFile => 'error.log' }
2046    
2047  and C<@arguments> will contain  and C<@arguments> will contain
2048    
2049  C<< apple orange rutabaga >>      apple orange rutabaga
2050    
2051  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2052  support for quote characters. Options can be specified with single or double hyphens.  support for quote characters. Options can be specified with single or double hyphens.
# Line 1356  Line 2097 
2097          push @retVal, UnEscape($inputParm);          push @retVal, UnEscape($inputParm);
2098      }      }
2099      # Return the results.      # Return the results.
2100      return ($optionTable, @retVal);      return ($optionTable, @retVal);
 }  
   
 =head3 Escape  
   
 C<< my $codedString = Tracer::Escape($realString); >>  
   
 Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  
 replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
 result is to reverse the effect of L</UnEscape>.  
   
 =over 4  
   
 =item realString  
   
 String to escape.  
   
 =item RETURN  
   
 Escaped equivalent of the real string.  
   
 =back  
   
 =cut  
   
 sub Escape {  
     # Get the parameter.  
     my ($realString) = @_;  
     # Initialize the return variable.  
     my $retVal = "";  
     # Loop through the parameter string, looking for sequences to escape.  
     while (length $realString > 0) {  
         # Look for the first sequence to escape.  
         if ($realString =~ /^(.*?)([\n\t\r\\])/) {  
             # Here we found it. The text preceding the sequence is in $1. The sequence  
             # itself is in $2. First, move the clear text to the return variable.  
             $retVal .= $1;  
             # Strip the processed section off the real string.  
             $realString = substr $realString, (length $2) + (length $1);  
             # Get the matched character.  
             my $char = $2;  
             # If we have a CR, we are done.  
             if ($char ne "\r") {  
                 # It's not a CR, so encode the escape sequence.  
                 $char =~ tr/\t\n/tn/;  
                 $retVal .= "\\" . $char;  
             }  
         } else {  
             # Here there are no more escape sequences. The rest of the string is  
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
         }  
     }  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 UnEscape  
   
 C<< my $realString = Tracer::UnEscape($codedString); >>  
   
 Replace escape sequences with their actual equivalents. C<\t> will be replaced by  
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
   
 =over 4  
   
 =item codedString  
   
 String to un-escape.  
   
 =item RETURN  
   
 Returns a copy of the original string with the escape sequences converted to their actual  
 values.  
   
 =back  
   
 =cut  
   
 sub UnEscape {  
     # Get the parameter.  
     my ($codedString) = @_;  
     # Initialize the return variable.  
     my $retVal = "";  
     # Only proceed if the incoming string is nonempty.  
     if (defined $codedString) {  
         # Loop through the parameter string, looking for escape sequences. We can't do  
         # translating because it causes problems with the escaped slash. ("\\t" becomes  
         # "\<tab>" no matter what we do.)  
         while (length $codedString > 0) {  
             # Look for the first escape sequence.  
             if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {  
                 # Here we found it. The text preceding the sequence is in $1. The sequence  
                 # itself is in $2. First, move the clear text to the return variable.  
                 $retVal .= $1;  
                 $codedString = substr $codedString, (2 + length $1);  
                 # Get the escape value.  
                 my $char = $2;  
                 # If we have a "\r", we are done.  
                 if ($char ne 'r') {  
                     # Here it's not an 'r', so we convert it.  
                     $char =~ tr/\\tn/\\\t\n/;  
                     $retVal .= $char;  
                 }  
             } else {  
                 # Here there are no more escape sequences. The rest of the string is  
                 # transferred unmodified.  
                 $retVal .= $codedString;  
                 $codedString = "";  
             }  
         }  
     }  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 ParseRecord  
   
 C<< my @fields = Tracer::ParseRecord($line); >>  
   
 Parse a tab-delimited data line. The data line is split into field values. Embedded tab  
 and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
 These will automatically be converted.  
   
 =over 4  
   
 =item line  
   
 Line of data containing the tab-delimited fields.  
   
 =item RETURN  
   
 Returns a list of the fields found in the data line.  
   
 =back  
   
 =cut  
   
 sub ParseRecord {  
     # Get the parameter.  
     my ($line) = @_;  
     # Remove the trailing new-line, if any.  
     chomp $line;  
     # Split the line read into pieces using the tab character.  
     my @retVal = split /\t/, $line;  
     # Trim and fix the escapes in each piece.  
     for my $value (@retVal) {  
         # Trim leading whitespace.  
         $value =~ s/^\s+//;  
         # Trim trailing whitespace.  
         $value =~ s/\s+$//;  
         # Delete the carriage returns.  
         $value =~ s/\r//g;  
         # Convert the escapes into their real values.  
         $value =~ s/\\t/"\t"/ge;  
         $value =~ s/\\n/"\n"/ge;  
     }  
     # Return the result.  
     return @retVal;  
 }  
   
 =head3 Merge  
   
 C<< my @mergedList = Tracer::Merge(@inputList); >>  
   
 Sort a list of strings and remove duplicates.  
   
 =over 4  
   
 =item inputList  
   
 List of scalars to sort and merge.  
   
 =item RETURN  
   
 Returns a list containing the same elements sorted in ascending order with duplicates  
 removed.  
   
 =back  
   
 =cut  
   
 sub Merge {  
     # Get the input list in sort order.  
     my @inputList = sort @_;  
     # Only proceed if the list has at least two elements.  
     if (@inputList > 1) {  
         # Now we want to move through the list splicing out duplicates.  
         my $i = 0;  
         while ($i < @inputList) {  
             # Get the current entry.  
             my $thisEntry = $inputList[$i];  
             # Find out how many elements duplicate the current entry.  
             my $j = $i + 1;  
             my $dup1 = $i + 1;  
             while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };  
             # If the number is nonzero, splice out the duplicates found.  
             if ($j > $dup1) {  
                 splice @inputList, $dup1, $j - $dup1;  
             }  
             # Now the element at position $dup1 is different from the element before it  
             # at position $i. We push $i forward one position and start again.  
             $i++;  
         }  
     }  
     # Return the merged list.  
     return @inputList;  
 }  
   
 =head3 Percent  
   
 C<< my $percent = Tracer::Percent($number, $base); >>  
   
 Returns the percent of the base represented by the given number. If the base  
 is zero, returns zero.  
   
 =over 4  
   
 =item number  
   
 Percent numerator.  
   
 =item base  
   
 Percent base.  
   
 =item RETURN  
   
 Returns the percentage of the base represented by the numerator.  
   
 =back  
   
 =cut  
   
 sub Percent {  
     # Get the parameters.  
     my ($number, $base) = @_;  
     # Declare the return variable.  
     my $retVal = 0;  
     # Compute the percent.  
     if ($base != 0) {  
         $retVal = $number * 100 / $base;  
     }  
     # Return the result.  
     return $retVal;  
2101  }  }
2102    
2103    
2104    =head2 File Utility Methods
2105    
2106  =head3 GetFile  =head3 GetFile
2107    
2108  C<< my @fileContents = Tracer::GetFile($fileName); >>      my @fileContents = Tracer::GetFile($fileName);
2109    
2110      or      or
2111    
2112  C<< my $fileContents = Tracer::GetFile($fileName); >>      my $fileContents = Tracer::GetFile($fileName);
2113    
2114  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
2115  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 2159 
2159    
2160  =head3 PutFile  =head3 PutFile
2161    
2162  C<< Tracer::PutFile($fileName, \@lines); >>      Tracer::PutFile($fileName, \@lines);
2163    
2164  Write out a file from a list of lines of text.  Write out a file from a list of lines of text.
2165    
# Line 1704  Line 2202 
2202      close $handle;      close $handle;
2203  }  }
2204    
2205  =head3 QTrace  =head3 ParseRecord
2206    
2207  C<< my $data = QTrace($format); >>      my @fields = Tracer::ParseRecord($line);
2208    
2209  Return the queued trace data in the specified format.  Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2210    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2211    These will automatically be converted.
2212    
2213  =over 4  =over 4
2214    
2215  =item format  =item line
2216    
2217  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Line of data containing the tab-delimited fields.
2218    
2219    =item RETURN
2220    
2221    Returns a list of the fields found in the data line.
2222    
2223  =back  =back
2224    
2225  =cut  =cut
2226    
2227  sub QTrace {  sub ParseRecord {
2228      # Get the parameter.      # Get the parameter.
2229      my ($format) = @_;      my ($line) = @_;
2230      # Create the return variable.      # Remove the trailing new-line, if any.
2231      my $retVal = "";      chomp $line;
2232      # Only proceed if there is an actual queue.      # Split the line read into pieces using the tab character.
2233      if (@Queue) {      my @retVal = split /\t/, $line;
2234          # Process according to the format.      # Trim and fix the escapes in each piece.
2235          if ($format =~ m/^HTML$/i) {      for my $value (@retVal) {
2236              # Convert the queue into an HTML list.          # Trim leading whitespace.
2237              $retVal = "<ul>\n";          $value =~ s/^\s+//;
2238              for my $line (@Queue) {          # Trim trailing whitespace.
2239                  my $escapedLine = CGI::escapeHTML($line);          $value =~ s/\s+$//;
2240                  $retVal .= "<li>$escapedLine</li>\n";          # Delete the carriage returns.
2241              }          $value =~ s/\r//g;
2242              $retVal .= "</ul>\n";          # Convert the escapes into their real values.
2243          } elsif ($format =~ m/^TEXT$/i) {          $value =~ s/\\t/"\t"/ge;
2244              # Convert the queue into a list of text lines.          $value =~ s/\\n/"\n"/ge;
             $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
2245      }      }
2246      # Return the formatted list.      # Return the result.
2247      return $retVal;      return @retVal;
2248  }  }
2249    
2250  =head3 Confess  =head3 Merge
2251    
2252  C<< Confess($message); >>      my @mergedList = Tracer::Merge(@inputList);
2253    
2254  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  
2255    
2256  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
2257    
2258  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item inputList
2259    
2260  =over 4  List of scalars to sort and merge.
2261    
2262  =item message  =item RETURN
2263    
2264  Message to include in the trace.  Returns a list containing the same elements sorted in ascending order with duplicates
2265    removed.
2266    
2267  =back  =back
2268    
2269  =cut  =cut
2270    
2271  sub Confess {  sub Merge {
2272      # Get the parameters.      # Get the input list in sort order.
2273      my ($message) = @_;      my @inputList = sort @_;
2274      # Trace the call stack.      # Only proceed if the list has at least two elements.
2275      Cluck($message);      if (@inputList > 1) {
2276      # Abort the program.          # Now we want to move through the list splicing out duplicates.
2277      croak(">>> $message");          my $i = 0;
2278            while ($i < @inputList) {
2279                # Get the current entry.
2280                my $thisEntry = $inputList[$i];
2281                # Find out how many elements duplicate the current entry.
2282                my $j = $i + 1;
2283                my $dup1 = $i + 1;
2284                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2285                # If the number is nonzero, splice out the duplicates found.
2286                if ($j > $dup1) {
2287                    splice @inputList, $dup1, $j - $dup1;
2288                }
2289                # Now the element at position $dup1 is different from the element before it
2290                # at position $i. We push $i forward one position and start again.
2291                $i++;
2292            }
2293        }
2294        # Return the merged list.
2295        return @inputList;
2296  }  }
2297    
2298  =head3 Assert  =head3 Open
2299    
2300  C<< Assert($condition1, $condition2, ... $conditionN); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2301    
2302  Return TRUE if all the conditions are true. This method can be used in conjunction with  Open a file.
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
2303    
2304  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2305    function. The mode is specified using Unix-like shell information. So, for
2306    example,
2307    
2308  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.");
2309    
2310  =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 $retVal;  
 }  
2311    
2312  =head3 Cluck      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2313    
2314  C<< Cluck($message); >>  would open a pipe that sorts the records written and removes duplicates. Note
2315    the use of file handle syntax in the Open call. To use anonymous file handles,
2316    code as follows.
2317    
2318  Trace the call stack. Note that for best results, you should qualify the call with a      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
 trace condition. For example,  
2319    
2320  C<< Cluck("Starting record parse.") if T(3); >>  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2321    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2322    failed open will throw an exception and the third parameter will be used to construct
2323    an error message. If the parameter is omitted, a standard message is constructed
2324    using the file spec.
2325    
2326  will only trace the stack if the trace level for the package is 3 or more.      Could not open "/usr/spool/news/twitlog"
2327    
2328    Note that the mode characters are automatically cleaned from the file name.
2329    The actual error message from the file system will be captured and appended to the
2330    message in any case.
2331    
2332        Could not open "/usr/spool/news/twitlog": file not found.
2333    
2334    In some versions of PERL the only error message we get is a number, which
2335    corresponds to the C++ C<errno> value.
2336    
2337        Could not open "/usr/spool/news/twitlog": 6.
2338    
2339  =over 4  =over 4
2340    
2341  =item message  =item fileHandle
2342    
2343  Message to include in the trace.  File handle. If this parameter is C<undef>, a file handle will be generated
2344    and returned as the value of this method.
2345    
2346    =item fileSpec
2347    
2348    File name and mode, as per the PERL C<open> function.
2349    
2350    =item message (optional)
2351    
2352    Error message to use if the open fails. If omitted, a standard error message
2353    will be generated. In either case, the error information from the file system
2354    is appended to the message. To specify a conditional open that does not throw
2355    an error if it fails, use C<0>.
2356    
2357    =item RETURN
2358    
2359    Returns the name of the file handle assigned to the file, or C<undef> if the
2360    open failed.
2361    
2362  =back  =back
2363    
2364  =cut  =cut
2365    
2366  sub Cluck {  sub Open {
2367      # Get the parameters.      # Get the parameters.
2368      my ($message) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2369      # Trace what's happening.      # Attempt to open the file.
2370      Trace("Stack trace for event: $message");      my $rv = open $fileHandle, $fileSpec;
2371      my $confession = longmess($message);      # If the open failed, generate an error message.
2372      # Convert the confession to a series of trace messages. Note we skip any      if (! $rv) {
2373      # messages relating to calls into Tracer.          # Save the system error message.
2374      for my $line (split /\s*\n/, $confession) {          my $sysMessage = $!;
2375          Trace($line) if ($line !~ /Tracer\.pm/);          # See if we need a default message.
2376            if (!$message) {
2377                # Clean any obvious mode characters and leading spaces from the
2378                # filename.
2379                my ($fileName) = FindNamePart($fileSpec);
2380                $message = "Could not open \"$fileName\"";
2381            }
2382            # Terminate with an error using the supplied message and the
2383            # error message from the file system.
2384            Confess("$message: $!");
2385      }      }
2386        # Return the file handle.
2387        return $fileHandle;
2388  }  }
2389    
2390  =head3 Min  =head3 FindNamePart
2391    
2392  C<< my $min = Min($value1, $value2, ... $valueN); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2393    
2394  Return the minimum argument. The arguments are treated as numbers.  Extract the portion of a file specification that contains the file name.
2395    
2396    A file specification is the string passed to an C<open> call. It specifies the file
2397    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2398    method assumes that the file name is whatever follows the first angle bracket
2399    sequence.  So, for example, in the following strings the file name is
2400    C</usr/fig/myfile.txt>.
2401    
2402        >>/usr/fig/myfile.txt
2403        </usr/fig/myfile.txt
2404        | sort -u > /usr/fig/myfile.txt
2405    
2406    If the method cannot find a file name using its normal methods, it will return the
2407    whole incoming string.
2408    
2409  =over 4  =over 4
2410    
2411  =item $value1, $value2, ... $valueN  =item fileSpec
2412    
2413  List of numbers to compare.  File specification string from which the file name is to be extracted.
2414    
2415  =item RETURN  =item RETURN
2416    
2417  Returns the lowest number in the list.  Returns a three-element list. The first element contains the file name portion of
2418    the specified string, or the whole string if a file name cannot be found via normal
2419    methods. The second element contains the start position of the file name portion and
2420    the third element contains the length.
2421    
2422    =back
2423    
2424    =cut
2425    #: Return Type $;
2426    sub FindNamePart {
2427        # Get the parameters.
2428        my ($fileSpec) = @_;
2429        # Default to the whole input string.
2430        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2431        # Parse out the file name if we can.
2432        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2433            $retVal = $2;
2434            $len = length $retVal;
2435            $pos = (length $fileSpec) - (length $3) - $len;
2436        }
2437        # Return the result.
2438        return ($retVal, $pos, $len);
2439    }
2440    
2441    =head3 OpenDir
2442    
2443        my @files = OpenDir($dirName, $filtered, $flag);
2444    
2445    Open a directory and return all the file names. This function essentially performs
2446    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2447    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2448    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2449    filtered out of the return list. If the directory does not open and I<$flag> is not
2450    set, an exception is thrown. So, for example,
2451    
2452  =back      my @files = OpenDir("/Volumes/fig/contigs", 1);
2453    
2454  =cut  is effectively the same as
2455    
2456  sub Min {      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2457      # Get the parameters. Note that we prime the return value with the first parameter.      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
     my ($retVal, @values) = @_;  
     # Loop through the remaining parameters, looking for the lowest.  
     for my $value (@values) {  
         if ($value < $retVal) {  
             $retVal = $value;  
         }  
     }  
     # Return the minimum found.  
     return $retVal;  
 }  
2458    
2459  =head3 Max  Similarly, the following code
2460    
2461  C<< my $max = Max($value1, $value2, ... $valueN); >>      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2462    
2463  Return the maximum argument. The arguments are treated as numbers.  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2464    automatically returns an empty list if the directory fails to open.
2465    
2466  =over 4  =over 4
2467    
2468  =item $value1, $value2, ... $valueN  =item dirName
2469    
2470  List of numbers to compare.  Name of the directory to open.
2471    
2472  =item RETURN  =item filtered
2473    
2474  Returns the highest number in the list.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2475    from the list, else FALSE.
2476    
2477    =item flag
2478    
2479    TRUE if a failure to open is okay, else FALSE
2480    
2481  =back  =back
2482    
2483  =cut  =cut
2484    #: Return Type @;
2485  sub Max {  sub OpenDir {
2486      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2487      my ($retVal, @values) = @_;      my ($dirName, $filtered, $flag) = @_;
2488      # Loop through the remaining parameters, looking for the highest.      # Declare the return variable.
2489      for my $value (@values) {      my @retVal = ();
2490          if ($value > $retVal) {      # Open the directory.
2491              $retVal = $value;      if (opendir(my $dirHandle, $dirName)) {
2492            # The directory opened successfully. Get the appropriate list according to the
2493            # strictures of the filter parameter.
2494            if ($filtered) {
2495                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2496            } else {
2497                @retVal = readdir $dirHandle;
2498          }          }
2499        } elsif (! $flag) {
2500            # Here the directory would not open and it's considered an error.
2501            Confess("Could not open directory $dirName.");
2502      }      }
2503      # Return the maximum found.      # Return the result.
2504      return $retVal;      return @retVal;
2505  }  }
2506    
 =head3 AddToListMap  
   
 C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>  
2507    
2508  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  =head3 Insure
 is created for the key. Otherwise, the new value is pushed onto the list.  
2509    
2510  =over 4      Insure($dirName, $chmod);
2511    
2512  =item hash  Insure a directory is present.
2513    
2514  Reference to the target hash.  =over 4
2515    
2516  =item key  =item dirName
2517    
2518  Key for which the value is to be added.  Name of the directory to check. If it does not exist, it will be created.
2519    
2520  =item value1, value2, ... valueN  =item chmod (optional)
2521    
2522  List of values to add to the key's value list.  Security privileges to be given to the directory if it is created.
2523    
2524  =back  =back
2525    
2526  =cut  =cut
2527    
2528  sub AddToListMap {  sub Insure {
2529      # Get the parameters.      my ($dirName, $chmod) = @_;
2530      my ($hash, $key, @values) = @_;      if (! -d $dirName) {
2531      # Process according to whether or not the key already has a value.          Trace("Creating $dirName directory.") if T(2);
2532      if (! exists $hash->{$key}) {          eval {
2533          $hash->{$key} = [@values];              mkpath $dirName;
2534      } else {              # If we have permissions specified, set them here.
2535          push @{$hash->{$key}}, @values;              if (defined($chmod)) {
2536                    chmod $chmod, $dirName;
2537      }      }
2538            };
2539            if ($@) {
2540                Confess("Error creating $dirName: $@");
2541  }  }
   
 =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.");  
2542      }      }
     # Return the determination indicator.  
     return $retVal;  
2543  }  }
2544    
2545  =head3 Strip  =head3 ChDir
2546    
2547  C<< my $string = Tracer::Strip($line); >>      ChDir($dirName);
2548    
2549  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.  
2550    
2551  =over 4  =over 4
2552    
2553  =item line  =item dirName
   
 Line of text to be stripped.  
   
 =item RETURN  
2554    
2555  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.
2556    
2557  =back  =back
2558    
2559  =cut  =cut
2560    
2561  sub Strip {  sub ChDir {
2562      # Get a copy of the parameter string.      my ($dirName) = @_;
2563      my ($string) = @_;      if (! -d $dirName) {
2564      my $retVal = (defined $string ? $string : "");          Confess("Cannot change to directory $dirName: no such directory.");
2565      # Strip the line terminator characters.      } else {
2566      $retVal =~ s/(\r|\n)+$//g;          Trace("Changing to directory $dirName.") if T(File => 4);
2567      # Return the result.          my $okFlag = chdir $dirName;
2568      return $retVal;          if (! $okFlag) {
2569                Confess("Error switching to directory $dirName.");
2570            }
2571        }
2572  }  }
2573    
2574  =head3 Pad  =head3 SetPermissions
2575    
2576  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2577    
2578  Pad a string to a specified length. The pad character will be a  Set the permissions for a directory and all the files and folders inside it.
2579  space, and the padding will be on the right side unless specified  In addition, the group ownership will be changed to the specified value.
2580  in the third parameter.  
2581    This method is more vulnerable than most to permission and compatability
2582    problems, so it does internal error recovery.
2583    
2584  =over 4  =over 4
2585    
2586  =item string  =item dirName
2587    
2588  String to be padded.  Name of the directory to process.
2589    
2590  =item len  =item group
2591    
2592  Desired length of the padded string.  Name of the group to be assigned.
2593    
2594  =item left (optional)  =item mask
2595    
2596  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  Permission mask. Bits that are C<1> in this mask will be ORed into the
2597    permission bits of any file or directory that does not already have them
2598    set to 1.
2599    
2600  =item padChar (optional)  =item otherMasks
2601    
2602  Character to use for padding. The default is a space.  Map of search patterns to permission masks. If a directory name matches
2603    one of the patterns, that directory and all its members and subdirectories
2604    will be assigned the new pattern. For example, the following would
2605    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2606    
2607  =item RETURN      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2608    
2609  Returns a copy of the original string with the pad character added to the  The list is ordered, so the following would use 0777 for C<tmp1> and
2610  specified end so that it achieves the desired length.  0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2611    
2612        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2613                                                       '^tmp' => 0666);
2614    
2615    Note that the pattern matches are all case-insensitive, and only directory
2616    names are matched, not file names.
2617    
2618  =back  =back
2619    
2620  =cut  =cut
2621    
2622  sub Pad {  sub SetPermissions {
2623      # Get the parameters.      # Get the parameters.
2624      my ($string, $len, $left, $padChar) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2625      # Compute the padding character.      # Set up for error recovery.
2626      if (! defined $padChar) {      eval {
2627          $padChar = " ";          # Switch to the specified directory.
2628            ChDir($dirName);
2629            # Get the group ID.
2630            my $gid = getgrnam($group);
2631            # Get the mask for tracing.
2632            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2633            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2634            my $fixCount = 0;
2635            my $lookCount = 0;
2636            # @dirs will be a stack of directories to be processed.
2637            my @dirs = (getcwd());
2638            while (scalar(@dirs) > 0) {
2639                # Get the current directory.
2640                my $dir = pop @dirs;
2641                # Check for a match to one of the specified directory names. To do
2642                # that, we need to pull the individual part of the name off of the
2643                # whole path.
2644                my $simpleName = $dir;
2645                if ($dir =~ m!/([^/]+)$!) {
2646                    $simpleName = $1;
2647      }      }
2648      # Compute the number of spaces needed.              Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2649      my $needed = $len - length $string;              # Search for a match.
2650      # Copy the string into the return variable.              my $match = 0;
2651      my $retVal = $string;              my $i;
2652      # Only proceed if padding is needed.              for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2653      if ($needed > 0) {                  my $pattern = $otherMasks[$i];
2654          # Create the pad string.                  if ($simpleName =~ /$pattern/i) {
2655          my $pad = $padChar x $needed;                      $match = 1;
2656          # Affix it to the return value.                  }
2657          if ($left) {              }
2658              $retVal = $pad . $retVal;              # Check for a match. Note we use $i-1 because the loop added 2
2659                # before terminating due to the match.
2660                if ($match && $otherMasks[$i-1] != $mask) {
2661                    # This directory matches one of the incoming patterns, and it's
2662                    # a different mask, so we process it recursively with that mask.
2663                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2664          } else {          } else {
2665              $retVal .= $pad;                  # Here we can process normally. Get all of the non-hidden members.
2666                    my @submems = OpenDir($dir, 1);
2667                    for my $submem (@submems) {
2668                        # Get the full name.
2669                        my $thisMem = "$dir/$submem";
2670                        Trace("Checking member $thisMem.") if T(4);
2671                        $lookCount++;
2672                        if ($lookCount % 1000 == 0) {
2673                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2674                        }
2675                        # Fix the group.
2676                        chown -1, $gid, $thisMem;
2677                        # Insure this member is not a symlink.
2678                        if (! -l $thisMem) {
2679                            # Get its info.
2680                            my $fileInfo = stat $thisMem;
2681                            # Only proceed if we got the info. Otherwise, it's a hard link
2682                            # and we want to skip it anyway.
2683                            if ($fileInfo) {
2684                                my $fileMode = $fileInfo->mode;
2685                                if (($fileMode & $mask) != $mask) {
2686                                    # Fix this member.
2687                                    $fileMode |= $mask;
2688                                    chmod $fileMode, $thisMem;
2689                                    $fixCount++;
2690                                }
2691                                # If it's a subdirectory, stack it.
2692                                if (-d $thisMem) {
2693                                    push @dirs, $thisMem;
2694          }          }
2695      }      }
     # Return the result.  
     return $retVal;  
2696  }  }
   
 =head3 EOF  
   
 This is a constant that is lexically greater than any useful string.  
   
 =cut  
   
 sub EOF {  
     return "\xFF\xFF\xFF\xFF\xFF";  
2697  }  }
   
 =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) {  
         $commandString =~ s!^\./!!;  
2698      }      }
2699      # Activate the command and return the result.          }
2700      return `$commandString`;          Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2701        };
2702        # Check for an error.
2703        if ($@) {
2704            Confess("SetPermissions error: $@");
2705        }
2706  }  }
2707    
2708  =head3 ScriptSetup  =head3 GetLine
   
 C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  
2709    
2710  Perform standard tracing and debugging setup for scripts. The value returned is      my @data = Tracer::GetLine($handle);
 the CGI object followed by a pre-built variable hash. At the end of the script,  
 the client should call L</ScriptFinish> to output the web page.  
2711    
2712  This method calls L</ETracing> to configure tracing, which allows the tracing  Read a line of data from a tab-delimited file.
 to be configured via the emergency tracing form on the debugging control panel.  
 Tracing will then be turned on automatically for all programs that use the L</ETracing>  
 method, which includes every program that uses this method or L</StandardSetup>.  
2713    
2714  =over 4  =over 4
2715    
2716  =item noTrace (optional)  =item handle
2717    
2718  If specified, tracing will be suppressed. This is useful if the script wants to set up  Open file handle from which to read.
 tracing manually.  
2719    
2720  =item RETURN  =item RETURN
2721    
2722  Returns a two-element list consisting of a CGI query object and a variable hash for  Returns a list of the fields in the record read. The fields are presumed to be
2723  the output page.  tab-delimited. If we are at the end of the file, then an empty list will be
2724    returned. If an empty line is read, a single list item consisting of a null
2725    string will be returned.
2726    
2727  =back  =back
2728    
2729  =cut  =cut
2730    
2731  sub ScriptSetup {  sub GetLine {
2732      # Get the parameters.      # Get the parameters.
2733      my ($noTrace) = @_;      my ($handle) = @_;
2734      # Get the CGI query object.      # Declare the return variable.
2735      my $cgi = CGI->new();      my @retVal = ();
2736      # Set up tracing if it's not suppressed.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2737      ETracing($cgi) unless $noTrace;      # Read from the file.
2738      # Create the variable hash.      my $line = <$handle>;
2739      my $varHash = { results => '' };      # Only proceed if we found something.
2740      # Return the query object and variable hash.      if (defined $line) {
2741      return ($cgi, $varHash);          # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2742            # upload control and have a nonstandard EOL combination.
2743            $line =~ s/(\r|\n)+$//;
2744            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2745            if (T(File => 4)) {
2746                my $escapedLine = $line;
2747                $escapedLine =~ s/\n/\\n/g;
2748                $escapedLine =~ s/\r/\\r/g;
2749                $escapedLine =~ s/\t/\\t/g;
2750                Trace("Line read: -->$escapedLine<--");
2751  }  }
2752            # If the line is empty, return a single empty string; otherwise, parse
2753  =head3 ETracing          # it into fields.
2754            if ($line eq "") {
2755  C<< ETracing($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 $emergencyFile;  
2756          } else {          } else {
2757              # Emergency tracing is on. Pull off the destination and              push @retVal, split /\t/,$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 = $cgi->param('Trace') . " Tracer";  
         }  
2758      }      }
2759      # Setup the tracing we've determined from all the stuff above.      } else {
2760      TSetup($tracing, $dest);          # Trace the reason the read failed.
2761      # 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);  
2762      }      }
2763        # Return the result.
2764        return @retVal;
2765  }  }
2766    
2767  =head3 EmergencyFileName  =head3 PutLine
2768    
2769  C<< my $fileName = Tracer::EmergencyFileName($tkey); >>      Tracer::PutLine($handle, \@fields, $eol);
2770    
2771  Return the emergency tracing file name. This is the file that specifies  Write a line of data to a tab-delimited file. The specified field values will be
2772  the tracing information.  output in tab-separated form, with a trailing new-line.
2773    
2774  =over 4  =over 4
2775    
2776  =item tkey  =item handle
2777    
2778  Tracing key for the current program.  Output file handle.
2779    
2780  =item RETURN  =item fields
2781    
2782  Returns the name of the file to contain the emergency tracing information.  List of field values.
2783    
2784    =item eol (optional)
2785    
2786    End-of-line character (default is "\n").
2787    
2788  =back  =back
2789    
2790  =cut  =cut
2791    
2792  sub EmergencyFileName {  sub PutLine {
2793      # Get the parameters.      # Get the parameters.
2794      my ($tkey) = @_;      my ($handle, $fields, $eol) = @_;
2795      # Compute the emergency tracing file name.      # Write the data.
2796      return "$FIG_Config::temp/Emergency$tkey.txt";      print $handle join("\t", @{$fields}) . ($eol || "\n");
2797  }  }
2798    
 =head3 EmergencyFileTarget  
   
 C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>  
2799    
2800  Return the emergency tracing target file name. This is the file that receives  =head3 PrintLine
 the tracing output for file-based tracing.  
2801    
2802  =over 4      Tracer::PrintLine($line);
2803    
2804  =item tkey  Print a line of text with a trailing new-line.
2805    
2806  Tracing key for the current program.  =over 4
2807    
2808  =item RETURN  =item line
2809    
2810  Returns the name of the file to contain the trace output.  Line of text to print.
2811    
2812  =back  =back
2813    
2814  =cut  =cut
2815    
2816  sub EmergencyFileTarget {  sub PrintLine {
2817      # Get the parameters.      # Get the parameters.
2818      my ($tkey) = @_;      my ($line) = @_;
2819      # Compute the emergency tracing file name.      # Print the line.
2820      return "$FIG_Config::temp/trace$tkey.log";      print "$line\n";
2821  }  }
2822    
 =head3 EmergencyTracingDest  
2823    
2824  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>  =head2 Other Useful Methods
2825    
2826  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.  
2827    
2828  =over 4      my $listValue = Tracer::ParseParm($string);
2829    
2830  =item tkey  Convert a parameter into a list reference. If the parameter is undefined,
2831    an undefined value will be returned. Otherwise, it will be parsed as a
2832    comma-separated list of values.
2833    
2834  Tracing key for this environment.  =over 4
2835    
2836  =item myDest  =item string
2837    
2838  Destination from the emergency tracing file.  Incoming string.
2839    
2840  =item RETURN  =item RETURN
2841    
2842  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
2843    was undefined.
2844    
2845  =back  =back
2846    
2847  =cut  =cut
2848    
2849  sub EmergencyTracingDest {  sub ParseParm {
2850      # Get the parameters.      # Get the parameters.
2851      my ($tkey, $myDest) = @_;      my ($string) = @_;
2852      # Declare the return variable.      # Declare the return variable.
2853      my $retVal = $myDest;      my $retVal;
2854      # Process according to the destination value.      # Check for data.
2855      if ($myDest eq 'FILE') {      if (defined $string) {
2856          $retVal = ">" . EmergencyFileTarget($tkey);          # We have some, so split it into a list.
2857      } elsif ($myDest eq 'APPEND') {          $retVal = [ split /\s*,\s*/, $string];
         $retVal = ">>" . EmergencyFileTarget($tkey);  
     } elsif ($myDest eq 'DUAL') {  
         $retVal = "+>" . EmergencyFileTarget($tkey);  
2858      }      }
2859      # Return the result.      # Return the result.
2860      return $retVal;      return $retVal;
2861  }  }
2862    
2863  =head3 Emergency  =head3 Now
   
 C<< Emergency($key, $hours, $dest, $level, @modules); >>  
2864    
2865  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.  
2866    
2867  =over 4  Return a displayable time stamp containing the local time. Whatever format this
2868    method produces must be parseable by L</ParseDate>.
2869    
2870  =item tkey  =cut
2871    
2872  The tracing key. This is used to identify the control file and the trace file.  sub Now {
2873        return DisplayTime(time);
2874    }
2875    
2876  =item hours  =head3 DisplayTime
2877    
2878  Number of hours to keep emergency tracing alive.      my $string = Tracer::DisplayTime($time);
2879    
2880  =item dest  Convert a time value to a displayable time stamp. Whatever format this
2881    method produces must be parseable by L</ParseDate>.
2882    
2883  Tracing destination. If no path information is specified for a file  =over 4
 destination, it is put in the FIG temporary directory.  
2884    
2885  =item level  =item time
2886    
2887  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.
2888    
2889  =item modules  =item RETURN
2890    
2891  A list of the tracing modules to activate.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2892    
2893  =back  =back
2894    
2895  =cut  =cut
2896    
2897  sub Emergency {  sub DisplayTime {
2898      # Get the parameters.      my ($time) = @_;
2899      my ($tkey, $hours, $dest, $level, @modules) = @_;      my $retVal = "(n/a)";
2900      # Create the emergency file.      if (defined $time) {
2901      my $specFile = EmergencyFileName($tkey);          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2902      my $outHandle = Open(undef, ">$specFile");          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2903      print $outHandle join("\n", $hours, $dest, $level, @modules, "");                    _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2904        }
2905        return $retVal;
2906  }  }
2907    
2908  =head3 EmergencyKey  # Pad a number to 2 digits.
2909    sub _p2 {
2910        my ($value) = @_;
2911        $value = "0$value" if ($value < 10);
2912        return $value;
2913    }
2914    
2915  C<< my $tkey = EmergencyKey($parameter); >>  =head3 Escape
2916    
2917  Return the Key to be used for emergency tracing. This could be an IP address,      my $codedString = Tracer::Escape($realString);
2918   a session ID, or a user name, depending on the environment.  
2919    Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2920    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2921    result is to reverse the effect of L</UnEscape>.
2922    
2923  =over 4  =over 4
2924    
2925  =item parameter  =item realString
2926    
2927  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.  
2928    
2929  =item RETURN  =item RETURN
2930    
2931  Returns the key to be used for labels in emergency tracing.  Escaped equivalent of the real string.
2932    
2933  =back  =back
2934    
2935  =cut  =cut
2936    
2937  sub EmergencyKey {  sub Escape {
2938      # Get the parameters.      # Get the parameter.
2939      my ($parameter) = @_;      my ($realString) = @_;
2940      # Declare the return variable.      # Initialize the return variable.
2941      my $retVal;      my $retVal = "";
2942      # Determine the parameter type.      # Loop through the parameter string, looking for sequences to escape.
2943      if (! defined $parameter) {      while (length $realString > 0) {
2944          # Here we're supposed to check the environment.          # Look for the first sequence to escape.
2945          $retVal = $ENV{TRACING};          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2946      } else {              # Here we found it. The text preceding the sequence is in $1. The sequence
2947          my $ptype = ref $parameter;              # itself is in $2. First, move the clear text to the return variable.
2948          if ($ptype eq 'CGI') {              $retVal .= $1;
2949              # Here we were invoked from a web page. Look for a cookie.              # Strip the processed section off the real string.
2950              $retVal = $parameter->cookie('IP');              $realString = substr $realString, (length $2) + (length $1);
2951          } elsif (! $ptype) {              # Get the matched character.
2952              # Here the key was passed in.              my $char = $2;
2953              $retVal = $parameter;              # If we have a CR, we are done.
2954                if ($char ne "\r") {
2955                    # It's not a CR, so encode the escape sequence.
2956                    $char =~ tr/\t\n/tn/;
2957                    $retVal .= "\\" . $char;
2958          }          }
2959            } else {
2960                # Here there are no more escape sequences. The rest of the string is
2961                # transferred unmodified.
2962                $retVal .= $realString;
2963                $realString = "";
2964      }      }
     # If no luck finding a key, use the PID.  
     if (! defined $retVal) {  
         $retVal = $$;  
2965      }      }
2966      # Return the result.      # Return the result.
2967      return $retVal;      return $retVal;
2968  }  }
2969    
2970    =head3 UnEscape
2971    
2972  =head3 TraceParms      my $realString = Tracer::UnEscape($codedString);
   
 C<< Tracer::TraceParms($cgi); >>  
2973    
2974  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2975  at level CGI => 4.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2976    be deleted.
2977    
2978  =over 4  =over 4
2979    
2980  =item cgi  =item codedString
2981    
2982  CGI query object containing the parameters to trace.  String to un-escape.
2983    
2984    =item RETURN
2985    
2986    Returns a copy of the original string with the escape sequences converted to their actual
2987    values.
2988    
2989  =back  =back
2990    
2991  =cut  =cut
2992    
2993  sub TraceParms {  sub UnEscape {
2994      # Get the parameters.      # Get the parameter.
2995      my ($cgi) = @_;      my ($codedString) = @_;
2996      if (T(CGI => 3)) {      # Initialize the return variable.
2997          # Here we want to trace the parameter data.      my $retVal = "";
2998          my @names = $cgi->param;      # Only proceed if the incoming string is nonempty.
2999          for my $parmName (sort @names) {      if (defined $codedString) {
3000              # Note we skip the Trace parameters, which are for our use only.          # Loop through the parameter string, looking for escape sequences. We can't do
3001              if ($parmName ne 'Trace' && $parmName ne 'TF') {          # translating because it causes problems with the escaped slash. ("\\t" becomes
3002                  my @values = $cgi->param($parmName);          # "\<tab>" no matter what we do.)
3003                  Trace("CGI: $parmName = " . join(", ", @values));          while (length $codedString > 0) {
3004              }              # Look for the first escape sequence.
3005                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
3006                    # Here we found it. The text preceding the sequence is in $1. The sequence
3007                    # itself is in $2. First, move the clear text to the return variable.
3008                    $retVal .= $1;
3009                    $codedString = substr $codedString, (2 + length $1);
3010                    # Get the escape value.
3011                    my $char = $2;
3012                    # If we have a "\r", we are done.
3013                    if ($char ne 'r') {
3014                        # Here it's not an 'r', so we convert it.
3015                        $char =~ tr/\\tn/\\\t\n/;
3016                        $retVal .= $char;
3017          }          }
3018          # Display the request method.              } else {
3019          my $method = $cgi->request_method();                  # Here there are no more escape sequences. The rest of the string is
3020          Trace("Method: $method");                  # transferred unmodified.
3021                    $retVal .= $codedString;
3022                    $codedString = "";
3023      }      }
     if (T(CGI => 4)) {  
         # Here we want the environment data too.  
         for my $envName (sort keys %ENV) {  
             Trace("ENV: $envName = $ENV{$envName}");  
3024          }          }
3025      }      }
3026        # Return the result.
3027        return $retVal;
3028  }  }
3029    
3030  =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.  
3031    
3032  A typical standard script would loook like the following.      my $percent = Tracer::Percent($number, $base);
3033    
3034      BEGIN {  Returns the percent of the base represented by the given number. If the base
3035          # Print the HTML header.  is zero, returns zero.
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
3036    
3037      my ($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", $varHash);  
3038    
3039  The idea here is that even if the script fails, you'll see trace messages and  =item number
 useful output.  
3040    
3041  =over 4  Percent numerator.
3042    
3043  =item webData  =item base
3044    
3045  A string containing either the full web page to be written to the output or the  Percent base.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3046    
3047  =item varHash (optional)  =item RETURN
3048    
3049  If specified, then a reference to a hash mapping variable names for a template  Returns the percentage of the base represented by the numerator.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3050    
3051  =back  =back
3052    
3053  =cut  =cut
3054    
3055  sub ScriptFinish {  sub Percent {
3056      # Get the parameters.      # Get the parameters.
3057      my ($webData, $varHash) = @_;      my ($number, $base) = @_;
3058      # Check for a template file situation.      # Declare the return variable.
3059      my $outputString;      my $retVal = 0;
3060      if (defined $varHash) {      # Compute the percent.
3061          # Here we have a template file. We need to determine the template type.      if ($base != 0) {
3062          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;  
3063      }      }
3064      # Write the output string.      # Return the result.
3065      print $outputString;      return $retVal;
3066  }  }
3067    
3068  =head3 Insure  =head3 Constrain
3069    
3070  C<< Insure($dirName); >>      my $constrained = Constrain($value, $min, $max);
3071    
3072  Insure a directory is present.  Modify a numeric value to bring it to a point in between a maximum and a minimum.
3073    
3074  =over 4  =over 4
3075    
3076  =item dirName  =item value
3077    
3078  Name of the directory to check. If it does not exist, it will be created.  Value to constrain.
3079    
3080    =item min (optional)
3081    
3082    Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3083    
3084    =item max (optional)
3085    
3086    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3087    
3088    =item RETURN
3089    
3090    Returns the incoming value, constrained according to the other parameters.
3091    
3092  =back  =back
3093    
3094  =cut  =cut
3095    
3096  sub Insure {  sub Constrain {
3097      my ($dirName) = @_;      # Get the parameters.
3098      if (! -d $dirName) {      my ($value, $min, $max) = @_;
3099          Trace("Creating $dirName directory.") if T(File => 2);      # Declare the return variable.
3100          eval { mkpath $dirName; };      my $retVal = $value;
3101          if ($@) {      # Apply the minimum constraint.
3102              Confess("Error creating $dirName: $@");      if (defined $min && $retVal < $min) {
3103          }          $retVal = $min;
3104        }
3105        # Apply the maximum constraint.
3106        if (defined $max && $retVal > $max) {
3107            $retVal = $max;
3108      }      }
3109        # Return the result.
3110        return $retVal;
3111  }  }
3112    
3113  =head3 ChDir  =head3 Min
3114    
3115  C<< ChDir($dirName); >>      my $min = Min($value1, $value2, ... $valueN);
3116    
3117  Change to the specified directory.  Return the minimum argument. The arguments are treated as numbers.
3118    
3119  =over 4  =over 4
3120    
3121  =item dirName  =item $value1, $value2, ... $valueN
3122    
3123  Name of the directory to which we want to change.  List of numbers to compare.
3124    
3125    =item RETURN
3126    
3127    Returns the lowest number in the list.
3128    
3129  =back  =back
3130    
3131  =cut  =cut
3132    
3133  sub ChDir {  sub Min {
3134      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
3135      if (! -d $dirName) {      my ($retVal, @values) = @_;
3136          Confess("Cannot change to directory $dirName: no such directory.");      # Loop through the remaining parameters, looking for the lowest.
3137      } else {      for my $value (@values) {
3138          Trace("Changing to directory $dirName.") if T(File => 4);          if ($value < $retVal) {
3139          my $okFlag = chdir $dirName;              $retVal = $value;
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
3140          }          }
3141      }      }
3142        # Return the minimum found.
3143        return $retVal;
3144  }  }
3145    
3146  =head3 SendSMS  =head3 Max
3147    
3148  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>      my $max = Max($value1, $value2, ... $valueN);
3149    
3150  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  Return the maximum argument. The arguments are treated as numbers.
 user name, password, and API ID for the relevant account in the hash reference variable  
 I<$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  
3151    
3152      $phone =  { user => 'BruceTheHumanPet',  =over 4
                 password => 'silly',  
                 api_id => '2561022' };  
3153    
3154  The original purpose of this method was to insure Bruce would be notified immediately when the  =item $value1, $value2, ... $valueN
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3155    
3156  The message ID will be returned if successful, and C<undef> if an error occurs.  List of numbers to compare.
3157    
3158  =over 4  =item RETURN
3159    
3160  =item phoneNumber  Returns the highest number in the list.
3161    
3162  Phone number to receive the message, in international format. A United States phone number  =back
 would be prefixed by "1". A British phone number would be prefixed by "44".  
3163    
3164  =item msg  =cut
3165    
3166  Message to send to the specified phone.  sub Max {
3167        # Get the parameters. Note that we prime the return value with the first parameter.
3168        my ($retVal, @values) = @_;
3169        # Loop through the remaining parameters, looking for the highest.
3170        for my $value (@values) {
3171            if ($value > $retVal) {
3172                $retVal = $value;
3173            }
3174        }
3175        # Return the maximum found.
3176        return $retVal;
3177    }
3178    
3179    
3180    =head3 Strip
3181    
3182        my $string = Tracer::Strip($line);
3183    
3184    Strip all line terminators off a string. This is necessary when dealing with files
3185    that may have been transferred back and forth several times among different
3186    operating environments.
3187    
3188    =over 4
3189    
3190    =item line
3191    
3192    Line of text to be stripped.
3193    
3194  =item RETURN  =item RETURN
3195    
3196  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.
3197    
3198  =back  =back
3199    
3200  =cut  =cut
3201    
3202  sub SendSMS {  sub Strip {
3203      # Get the parameters.      # Get a copy of the parameter string.
3204      my ($phoneNumber, $msg) = @_;      my ($string) = @_;
3205      # Declare the return variable. If we do not change it, C<undef> will be returned.      my $retVal = (defined $string ? $string : "");
3206      my $retVal;      # Strip the line terminator characters.
3207      # 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);  
             }  
         }  
     }  
3208      # Return the result.      # Return the result.
3209      return $retVal;      return $retVal;
3210  }  }
3211    
3212  =head3 CommaFormat  =head3 Pad
3213    
3214  C<< my $formatted = Tracer::CommaFormat($number); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3215    
3216  Insert commas into a number.  Pad a string to a specified length. The pad character will be a
3217    space, and the padding will be on the right side unless specified
3218    in the third parameter.
3219    
3220  =over 4  =over 4
3221    
3222  =item number  =item string
3223    
3224  A sequence of digits.  String to be padded.
3225    
3226    =item len
3227    
3228    Desired length of the padded string.
3229    
3230    =item left (optional)
3231    
3232    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3233    
3234    =item padChar (optional)
3235    
3236    Character to use for padding. The default is a space.
3237    
3238  =item RETURN  =item RETURN
3239    
3240  Returns the same digits with commas strategically inserted.  Returns a copy of the original string with the pad character added to the
3241    specified end so that it achieves the desired length.
3242    
3243  =back  =back
3244    
3245  =cut  =cut
3246    
3247  sub CommaFormat {  sub Pad {
3248      # Get the parameters.      # Get the parameters.
3249      my ($number) = @_;      my ($string, $len, $left, $padChar) = @_;
3250      # Pad the length up to a multiple of three.      # Compute the padding character.
3251      my $padded = "$number";      if (! defined $padChar) {
3252      $padded = " " . $padded while length($padded) % 3 != 0;          $padChar = " ";
3253      # This is a fancy PERL trick. The parentheses in the SPLIT pattern      }
3254      # cause the delimiters to be included in the output stream. The      # Compute the number of spaces needed.
3255      # GREP removes the empty strings in between the delimiters.      my $needed = $len - length $string;
3256      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));      # Copy the string into the return variable.
3257      # Clean out the spaces.      my $retVal = $string;
3258      $retVal =~ s/ //g;      # Only proceed if padding is needed.
3259        if ($needed > 0) {
3260            # Create the pad string.
3261            my $pad = $padChar x $needed;
3262            # Affix it to the return value.
3263            if ($left) {
3264                $retVal = $pad . $retVal;
3265            } else {
3266                $retVal .= $pad;
3267            }
3268        }
3269      # Return the result.      # Return the result.
3270      return $retVal;      return $retVal;
3271  }  }
 =head3 SetPermissions  
3272    
3273  C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  =head3 EOF
3274    
3275    This is a constant that is lexically greater than any useful string.
3276    
3277  Set the permissions for a directory and all the files and folders inside it.  =cut
 In addition, the group ownership will be changed to the specified value.  
3278    
3279  This method is more vulnerable than most to permission and compatability  sub EOF {
3280  problems, so it does internal error recovery.      return "\xFF\xFF\xFF\xFF\xFF";
3281    }
3282    
3283    =head3 TICK
3284    
3285        my @results = TICK($commandString);
3286    
3287    Perform a back-tick operation on a command. If this is a Windows environment, any leading
3288    dot-slash (C<./> will be removed. So, for example, if you were doing
3289    
3290        `./protein.cgi`
3291    
3292    from inside a CGI script, it would work fine in Unix, but would issue an error message
3293    in Windows complaining that C<'.'> is not a valid command. If instead you code
3294    
3295        TICK("./protein.cgi")
3296    
3297    it will work correctly in both environments.
3298    
3299  =over 4  =over 4
3300    
3301  =item dirName  =item commandString
3302    
3303  Name of the directory to process.  The command string to pass to the system.
3304    
3305  =item group  =item RETURN
3306    
3307    Returns the standard output from the specified command, as a list.
3308    
3309    =back
3310    
3311    =cut
3312    #: Return Type @;
3313    sub TICK {
3314        # Get the parameters.
3315        my ($commandString) = @_;
3316        # Chop off the dot-slash if this is Windows.
3317        if ($FIG_Config::win_mode) {
3318            $commandString =~ s!^\./!!;
3319        }
3320        # Activate the command and return the result.
3321        return `$commandString`;
3322    }
3323    
 Name of the group to be assigned.  
3324    
3325  =item mask  =head3 CommaFormat
3326    
3327  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.  
3328    
3329  =item otherMasks  Insert commas into a number.
3330    
3331  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>.  
3332    
3333      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  =item number
3334    
3335  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>.  
3336    
3337      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  =item RETURN
                                                    '^tmp' => 0666);  
3338    
3339  Note that the pattern matches are all case-insensitive, and only directory  Returns the same digits with commas strategically inserted.
 names are matched, not file names.  
3340    
3341  =back  =back
3342    
3343  =cut  =cut
3344    
3345  sub SetPermissions {  sub CommaFormat {
3346      # Get the parameters.      # Get the parameters.
3347      my ($dirName, $group, $mask, @otherMasks) = @_;      my ($number) = @_;
3348      # Set up for error recovery.      # Pad the length up to a multiple of three.
3349      eval {      my $padded = "$number";
3350          # Switch to the specified directory.      $padded = " " . $padded wh