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revision 1.86, Fri May 18 19:27:17 2007 UTC revision 1.99, Wed May 7 23:00:16 2008 UTC
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1  #  # -*- perl -*-
2    ########################################################################
3  # Copyright (c) 2003-2006 University of Chicago and Fellowship  # Copyright (c) 2003-2006 University of Chicago and Fellowship
4  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
5  #  #
# Line 13  Line 14 
14  # at info@ci.uchicago.edu or the Fellowship for Interpretation of  # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15  # Genomes at veronika@thefig.info or download a copy from  # Genomes at veronika@thefig.info or download a copy from
16  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
17  #  ########################################################################
18    
19  package Tracer;  package Tracer;
20    
21      require Exporter;      require Exporter;
22      @ISA = ('Exporter');      @ISA = ('Exporter');
23      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn);
24      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
25      use strict;      use strict;
26      use Carp qw(longmess croak);      use Carp qw(longmess croak carp);
27      use CGI;      use CGI;
28      use Cwd;      use Cwd;
29      use FIG_Config;      use FIG_Config;
# Line 35  Line 36 
36      use Time::HiRes 'gettimeofday';      use Time::HiRes 'gettimeofday';
37      use URI::Escape;      use URI::Escape;
38      use Time::Local;      use Time::Local;
39        use POSIX qw(strftime);
40        use Time::Zone;
41    
42    
43  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
44    
# Line 159  Line 163 
163    
164  Sometimes, you need a way for tracing to happen automatically without putting parameters  Sometimes, you need a way for tracing to happen automatically without putting parameters
165  in a form or on the command line. Emergency tracing does this. You invoke emergency tracing  in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
166  from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.  from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
167  Emergency tracing requires you specify a tracing key. For command-line tools, the key is  that you specify a tracing key. For command-line tools, the key is
168  taken from the C<TRACING> environment variable. For web services, the key is taken from  taken from the C<TRACING> environment variable. For web services, the key is taken from
169  a cookie. Either way, the key tells the tracing facility who you are, so that you control  a cookie. Either way, the key tells the tracing facility who you are, so that you control
170  the tracing in your environment without stepping on other users.  the tracing in your environment without stepping on other users.
# Line 183  Line 187 
187    
188  The web script will look for the tracing key in the cookies, and the command-line  The web script will look for the tracing key in the cookies, and the command-line
189  script will look for it in the C<TRACING> environment variable. If you are  script will look for it in the C<TRACING> environment variable. If you are
190  using the L</StandardScript> or L</StandardSetup> methods, emergency tracing  using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
191  will be configured automatically.  will be configured automatically.
192    
 NOTE: to configure emergency tracing from the command line instead of the Debugging  
 Control Panel (see below), use the C<trace.pl> script.  
   
 =head3 Debugging Control Panel  
   
 The debugging control panel provides several tools to assist in development of  
 SEED and Sprout software. You access the debugging control panel from the URL  
 C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,  
 for example, the panel access point for the development NMPDR system is  
 C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to  
 find out what the password is. From this page, you can also specify a tracing  
 key. If you don't specify a key, one will be generated for you.  
   
 =head4 Emergency Tracing Form  
   
 At the bottom of the debugging control panel is a form that allows you to  
 specify a trace level and tracing categories. Special and common categories  
 are listed with check boxes. You can hold your mouse over a check box to see  
 what its category does. In general, however, a category name is the same as  
 the name of the package in which the trace message occurs.  
   
 Additional categories can be entered in an input box, delimited by spaces or commas.  
   
 The B<Activate> button turns on Emergency tracing at the level you specify with the  
 specified categories active. The B<Terminate> button turns tracing off. The  
 B<Show File> button displays the current contents of the trace file. The tracing  
 form at the bottom of the control panel is designed for emergency tracing, so it  
 will only affect programs that call L</ETracing>, L</StandardScript>,  
 or L</StandardSetup>.  
   
 =head4 Script Form  
   
 The top form of the debugging control panel allows you to enter a tiny script and  
 have the output generated in a formatted table. Certain object variables are  
 predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),  
 and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.  
   
 The last line of the script must be a scalar, but it can be a reference to a hash,  
 a list, a list of lists, and various other combinations. If you select the appropriate  
 data type in the dropdown box, the output will be formatted accordingly. The form  
 also has controls for specifying tracing. These controls override any emergency  
 tracing in effect.  
   
 =head4 Database Query Forms  
   
 The forms between the script form and the emergency tracing form allow you to  
 make queries against the database. The FIG query form allows simple queries against  
 a single FIG table. The Sprout query form uses the B<GetAll> method to do a  
 multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>  
 package, and it takes five parameters.  
   
     GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);  
   
 Each of the five parameters corresponds to a text box on the query form:  
   
 =over 4  
   
 =item Objects  
   
 Comma-separated list containing the names of the entity and relationship objects to be retrieved.  
   
 =item Filter  
   
 WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  
 be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form  
 B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a  
 field, I<objectName> is the name of the entity or relationship object containing the field, and  
 I<number> is the 1-based position of the object in the object list. Any parameters  
 specified in the filter clause should be specified in the B<Params> field.  
 The fields in a filter clause can come from primary entity relations,  
 relationship relations, or secondary entity relations; however, all of the  
 entities and relationships involved must be included in the list of object names.  
   
 =item Params  
   
 List of the parameters to be substituted in for the parameters marks in the filter clause. This  
 is a comma-separated list without any quoting or escaping.  
   
 =item fields  
   
 Comma-separated list of the fields to be returned in each element of the list returned. Fields  
 are specified in the same manner as in the filter clause.  
   
 =item count  
   
 Maximum number of records to return. If omitted or 0, all available records will be returned.  
   
 =back  
   
 B<GetAll> automatically joins together the entities and relationships listed in the object  
 names. This simplifies the coding of the filter clause, but it means that some queries are  
 not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation  
 that has yet to be addressed.  
   
193  =cut  =cut
194    
195  # Declare the configuration variables.  # Declare the configuration variables.
196    
197  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
198  my $TeeFlag = 0;            # TRUE if output is going to a file and to the  my $TeeFlag = 0;            # TRUE if output is going to a file and to the
199                              # standard output                              # standard output
200  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
201                              # hash of active category names                              # hash of active category names
202    my @LevelNames = qw(error warn notice info detail);
203  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
204                              # messages                              # messages
205  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
206  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
207    my $LastLevel = 0;          # level of the last test call
208  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
209  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
210    my $SavedCGI;               # CGI object passed to ETracing
211    umask 2;                    # Fix the damn umask so everything is group-writable.
212    
213    =head2 Tracing Methods
214    
215    =head3 Setups
216    
217        my $count = Tracer::Setups();
218    
219    Return the number of times L</TSetup> has been called.
220    
221    This method allows for the creation of conditional tracing setups where, for example, we
222    may want to set up tracing if nobody else has done it before us.
223    
224    =cut
225    
226  =head2 Public Methods  sub Setups {
227        return $SetupCount;
228    }
229    
230  =head3 TSetup  =head3 TSetup
231    
232  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
233    
234  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
235  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 350  Line 279 
279          }          }
280      }      }
281      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
282      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
283      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
284        # the standard output (tee mode).
285      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
286          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
287              $TeeFlag = 1;              $TeeFlag = 1;
288              $target = substr($target, 1);              $target = substr($target, 1);
289          }          }
290          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
291                # We need to initialize the file (which clears it).
292              open TRACEFILE, $target;              open TRACEFILE, $target;
293              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
294              close TRACEFILE;              close TRACEFILE;
295                # Set to append mode now that the file has been cleared.
296              $Destination = ">$target";              $Destination = ">$target";
297          } else {          } else {
298              $Destination = $target;              $Destination = $target;
# Line 372  Line 304 
304      $SetupCount++;      $SetupCount++;
305  }  }
306    
307  =head3 StandardSetup  =head3 SetLevel
308    
309  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
310    
311  This method performs standard command-line parsing and tracing setup. The return  Modify the trace level. A higher trace level will cause more messages to appear.
 values are a hash of the command-line options and a list of the positional  
 parameters. Tracing is automatically set up and the command-line options are  
 validated.  
312    
313  This is a complex method that does a lot of grunt work. The parameters can  =over 4
 be more easily understood, however, once they are examined individually.  
314    
315  The I<categories> parameter is the most obtuse. It is a reference to a list of  =item newLevel
 special-purpose tracing categories. Most tracing categories are PERL package  
 names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,  
 B<ERDB>, and B<SproutLoad> packages, you would specify the categories  
316    
317      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
318    
319  This would cause trace messages in the specified three packages to appear in  =back
 the output. There are two special tracing categories that are automatically  
 handled by this method. In other words, if you used L</TSetup> you would need  
 to include these categories manually, but if you use this method they are turned  
 on automatically.  
320    
321  =over 4  =cut
322    
323  =item SQL  sub SetLevel {
324        $TraceLevel = $_[0];
325    }
326    
327  Traces SQL commands and activity.  =head3 ParseDate
328    
329  =item Tracer      my $time = Tracer::ParseDate($dateString);
330    
331  Traces error messages and call stacks.  Convert a date into a PERL time number. This method expects a date-like string
332    and parses it into a number. The string must be vaguely date-like or it will
333    return an undefined value. Our requirement is that a month and day be
334    present and that three pieces of the date string (time of day, month and day,
335    year) be separated by likely delimiters, such as spaces, commas, and such-like.
336    
337  =back  If a time of day is present, it must be in military time with two digits for
338    everything but the hour.
339    
340  C<SQL> is only turned on if the C<-sql> option is specified in the command line.  The year must be exactly four digits.
 The trace level is specified using the C<-trace> command-line option. For example,  
 the following command line for C<TransactFeatures> turns on SQL tracing and runs  
 all tracing at level 3.  
341    
342      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  Additional stuff can be in the string. We presume it's time zones or weekdays or something
343    equally innocuous. This means, however, that a sufficiently long sentence with date-like
344    parts in it may be interpreted as a date. Hopefully this will not be a problem.
345    
346  Standard tracing is output to the standard output and echoed to the file  It should be guaranteed that this method will parse the output of the L</Now> function.
 C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the  
 process ID. You can also specify the C<user> parameter to put a user ID  
 instead of a process ID in the trace file name. So, for example  
347    
348  The default trace level is 2. To get all messages, specify a trace level of 4.  The parameters are as follows.
 For a genome-by-genome update, use 3.  
349    
350      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  =over 4
351    
352  would send the trace output to C<traceBruce.log> in the temporary directory.  =item dateString
353    
354  The I<options> parameter is a reference to a hash containing the command-line  The date string to convert.
 options, their default values, and an explanation of what they mean. Command-line  
 options may be in the form of switches or keywords. In the case of a switch, the  
 option value is 1 if it is specified and 0 if it is not specified. In the case  
 of a keyword, the value is separated from the option name by an equal sign. You  
 can see this last in the command-line example above.  
355    
356  You can specify a different default trace level by setting C<$options->{trace}>  =item RETURN
 prior to calling this method.  
357    
358  An example at this point would help. Consider, for example, the command-line utility  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
359  C<TransactFeatures>. It accepts a list of positional parameters plus the options  the date string is invalid. A valid date string must contain a month and day.
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
360    
361      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  =back
                         { safe => [0, "use database transactions"],  
                           noAlias => [0, "do not expect aliases in CHANGE transactions"],  
                           start => [' ', "start with this genome"],  
                           tblFiles => [0, "output TBL files containing the corrected IDs"] },  
                         "<command> <transactionDirectory> <IDfile>",  
                       @ARGV);  
362    
363    =cut
364    
365  The call to C<ParseCommand> specifies the default values for the options and  # Universal month conversion table.
366  stores the actual options in a hash that is returned as C<$options>. The  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
367  positional parameters are returned in C<@parameters>.                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
368                                Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
369                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
370                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
371                                Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
372                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
373                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
374                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
375                                Oct =>  9, October  =>   9, '10' =>  9,
376                                Nov => 10, November =>  10, '11' => 10,
377                                Dec => 11, December =>  11, '12' => 11
378                            };
379    
380  The following is a sample command line for C<TransactFeatures>.  sub ParseDate {
381        # Get the parameters.
382        my ($dateString) = @_;
383        # Declare the return variable.
384        my $retVal;
385        # Find the month and day of month. There are two ways that can happen. We check for the
386        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
387        # won't be fooled into thinking the month is Sunday.
388        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
389            my ($mon, $mday) = (MONTHS->{$1}, $2);
390            # Insist that the month and day are valid.
391            if (defined($mon) && $2 >= 1 && $2 <= 31) {
392                # Find the time.
393                my ($hour, $min, $sec) = (0, 0, 0);
394                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
395                    ($hour, $min, $sec) = ($1, $2, $3);
396                }
397                # Find the year.
398                my $year;
399                if ($dateString =~ /\b(\d{4})\b/) {
400                    $year = $1;
401                } else {
402                    # Get the default year, which is this one. Note we must convert it to
403                    # the four-digit value expected by "timelocal".
404                    (undef, undef, undef, undef, undef, $year) = localtime();
405                    $year += 1900;
406                }
407                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
408            }
409        }
410        # Return the result.
411        return $retVal;
412    }
413    
414      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  =head3 LogErrors
415    
416  Single and double hyphens are equivalent. So, you could also code the      Tracer::LogErrors($fileName);
 above command as  
417    
418      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl  Route the standard error output to a log file.
419    
420  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  =over 4
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
421    
422      { trace => 2, sql => 0, safe => 0,  =item fileName
       noAlias => 1, start => ' ', tblFiles => 0 }  
423    
424  Use of C<StandardSetup> in this way provides a simple way of performing  Name of the file to receive the error output.
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
425    
426  If the C<background> option is specified on the command line, then the  =back
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
427    
428      -user=Bruce -background  =cut
429    
430  then the trace output would go to C<traceBruce.log>, the standard output to  sub LogErrors {
431  C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to      # Get the file name.
432  simplify starting a command in the background.      my ($fileName) = @_;
433        # Open the file as the standard error output.
434        open STDERR, '>', $fileName;
435    }
436    
437  The user name is also used as the tracing key for L</Emergency Tracing>.  =head3 Trace
 Specifying a value of C<E> for the trace level causes emergency tracing to  
 be used instead of custom tracing. If the user name is not specified,  
 the tracing key is taken from the C<Tracing> environment variable. If there  
 is no value for that variable, the tracing key will be computed from the PID.  
438    
439  Finally, if the special option C<-help> is specified, the option      Trace($message);
 names will be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
440    
441      TransactFeatures -help  Write a trace message to the target location specified in L</TSetup>. If there has not been
442    any prior call to B<TSetup>.
443    
444  he would see the following output.  =over 4
445    
446      TransactFeatures [options] <command> <transactionDirectory> <IDfile>  =item message
         -trace    tracing level (default E)  
         -sql      trace SQL commands  
         -safe     use database transactions  
         -noAlias  do not expect aliases in CHANGE transactions  
         -start    start with this genome  
         -tblFiles output TBL files containing the corrected IDs  
447    
448  The caller has the option of modifying the tracing scheme by placing a value  Message to write.
 for C<trace> in the incoming options hash. The default value can be overridden,  
 or the tracing to the standard output can be turned off by suffixing a minus  
 sign to the trace level. So, for example,  
449    
450      { trace => [0, "tracing level (default 0)"],  =back
        ...  
451    
452  would set the default trace level to 0 instead of E, while  =cut
453    
454      { trace => ["2-", "tracing level (default 2)"],  sub Trace {
455         ...      # Get the parameters.
456        my ($message) = @_;
457        # Strip off any line terminators at the end of the message. We will add
458        # new-line stuff ourselves.
459        my $stripped = Strip($message);
460        # Compute the caller information.
461        my ($callPackage, $callFile, $callLine) = caller();
462        my $callFileTitle = basename($callFile);
463        # Check the caller.
464        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
465        # Get the timestamp.
466        my $timeStamp = Now();
467        # Build the prefix.
468        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
469        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
470        # Format the message.
471        my $formatted = "$prefix $stripped";
472        # Process according to the destination.
473        if ($Destination eq "TEXT") {
474            # Write the message to the standard output.
475            print "$formatted\n";
476        } elsif ($Destination eq "ERROR") {
477            # Write the message to the error output. Here, we want our prefix fields.
478            print STDERR "$formatted\n";
479        } elsif ($Destination eq "WARN") {
480            # Emit the message to the standard error output. It is presumed that the
481            # error logger will add its own prefix fields, the notable exception being
482            # the caller info.
483            print STDERR "$callerInfo$stripped\n";
484        } elsif ($Destination eq "QUEUE") {
485            # Push the message into the queue.
486            push @Queue, "$formatted";
487        } elsif ($Destination eq "HTML") {
488            # Convert the message to HTML and write it to the standard output.
489            my $escapedMessage = CGI::escapeHTML($stripped);
490            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
491        } elsif ($Destination =~ m/^>>/) {
492            # Write the trace message to an output file.
493            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
494            print TRACING "$formatted\n";
495            close TRACING;
496            # If the Tee flag is on, echo it to the standard output.
497            if ($TeeFlag) {
498                print "$formatted\n";
499            }
500        }
501    }
502    
503  would set the default to 2, but trace only to the log file, not to the  =head3 T
 standard output.  
504    
505  The parameters to this method are as follows.      my $switch = T($category, $traceLevel);
506    
507  =over 4      or
508    
509  =item categories      my $switch = T($traceLevel);
510    
511  Reference to a list of tracing category names. These should be names of  Return TRUE if the trace level is at or above a specified value and the specified category
512  packages whose internal workings will need to be debugged to get the  is active, else FALSE. If no category is specified, the caller's package name is used.
 command working.  
513    
514  =item options  =over 4
515    
516  Reference to a hash containing the legal options for the current command mapped  =item category
 to their default values and descriptions. The user can override the defaults  
 by specifying the options as command-line switches prefixed by a hyphen.  
 Tracing-related options may be added to this hash. If the C<-h> option is  
 specified on the command line, the option descriptions will be used to  
 explain the options. To turn off tracing to the standard output, add a  
 minus sign to the value for C<trace> (see above).  
517    
518  =item parmHelp  Category to which the message belongs. If not specified, the caller's package name is
519    used.
520    
521    =item traceLevel
522    
523    Relevant tracing level.
524    
525    =item RETURN
526    
527    TRUE if a message at the specified trace level would appear in the trace, else FALSE.
528    
529    =back
530    
531    =cut
532    
533    sub T {
534        # Declare the return variable.
535        my $retVal = 0;
536        # Only proceed if tracing is turned on.
537        if ($Destination ne "NONE") {
538            # Get the parameters.
539            my ($category, $traceLevel) = @_;
540            if (!defined $traceLevel) {
541                # Here we have no category, so we need to get the calling package.
542                # The calling package is normally the first parameter. If it is
543                # omitted, the first parameter will be the tracelevel. So, the
544                # first thing we do is shift the so-called category into the
545                # $traceLevel variable where it belongs.
546                $traceLevel = $category;
547                my ($package, $fileName, $line) = caller;
548                # If there is no calling package, we default to "main".
549                if (!$package) {
550                    $category = "main";
551                } else {
552                    my @cats = split /::/, $package;
553                    $category = $cats[$#cats];
554                }
555            }
556            # Save the category name and level.
557            $LastCategory = $category;
558            $LastLevel = $traceLevel;
559            # Convert it to lower case before we hash it.
560            $category = lc $category;
561            # Use the category and tracelevel to compute the result.
562            if (ref $traceLevel) {
563                Confess("Bad trace level.");
564            } elsif (ref $TraceLevel) {
565                Confess("Bad trace config.");
566            }
567            $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
568        }
569        # Return the computed result.
570        return $retVal;
571    }
572    
573    =head3 QTrace
574    
575        my $data = QTrace($format);
576    
577    Return the queued trace data in the specified format.
578    
579    =over 4
580    
581    =item format
582    
583    C<html> to format the data as an HTML list, C<text> to format it as straight text.
584    
585    =back
586    
587    =cut
588    
589    sub QTrace {
590        # Get the parameter.
591        my ($format) = @_;
592        # Create the return variable.
593        my $retVal = "";
594        # Only proceed if there is an actual queue.
595        if (@Queue) {
596            # Process according to the format.
597            if ($format =~ m/^HTML$/i) {
598                # Convert the queue into an HTML list.
599                $retVal = "<ul>\n";
600                for my $line (@Queue) {
601                    my $escapedLine = CGI::escapeHTML($line);
602                    $retVal .= "<li>$escapedLine</li>\n";
603                }
604                $retVal .= "</ul>\n";
605            } elsif ($format =~ m/^TEXT$/i) {
606                # Convert the queue into a list of text lines.
607                $retVal = join("\n", @Queue) . "\n";
608            }
609            # Clear the queue.
610            @Queue = ();
611        }
612        # Return the formatted list.
613        return $retVal;
614    }
615    
616    =head3 Confess
617    
618        Confess($message);
619    
620    Trace the call stack and abort the program with the specified message. When used with
621    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
622    So, for example
623    
624        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
625    
626    Will abort the program with a stack trace if the value of C<$recNum> is negative.
627    
628    =over 4
629    
630    =item message
631    
632    Message to include in the trace.
633    
634    =back
635    
636    =cut
637    
638    sub Confess {
639        # Get the parameters.
640        my ($message) = @_;
641        # Set up the category and level.
642        $LastCategory = "(confess)";
643        $LastLevel = 0;
644        if (! defined($FIG_Config::no_tool_hdr)) {
645            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
646            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
647            # Only proceed if the tool header file is actually present.
648            if (-f $toolHeaderFile) {
649                my $fh;
650                if (open $fh, "<$toolHeaderFile") {
651                    my @lines = <$fh>;
652                    Trace("Tool header has " . scalar(@lines) . " lines.");
653                }
654            }
655        }
656        # Trace the call stack.
657        Cluck($message);
658        # Abort the program.
659        croak(">>> $message");
660    }
661    
662    =head3 Warn
663    
664        Warn($message);
665    
666    This method traces an important message. If an RSS feed is configured
667    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
668    then the message will be echoed to the feed. In general, a tracing
669    destination of C<WARN> indicates that the caller is running as a web
670    service in a production environment; however, this is not a requirement.
671    
672    The L</Cluck> method calls this one for its final message. Since
673    L</Confess> calls L</Cluck>, this means that any error which is caught
674    and confessed will put something in the feed. This insures that someone
675    will be alerted relatively quickly when a failure occurs.
676    
677    =over 4
678    
679    =item message
680    
681    Message to be traced.
682    
683    =back
684    
685    =cut
686    
687    sub Warn {
688        # Get the parameters.
689        my ($message) = @_;
690        # Trace the message.
691        Trace($message);
692        # An error here would be disastrous. Note, however, that we aren't too worried
693        # about losing events. The error log is always available for the occasions where
694        # we mess up.
695        eval {
696            # Do we need to put this in the RSS feed?
697            if ($FIG_Config::error_feed && $Destination eq 'WARN') {
698                # Yes. We now need to compute the date, the link, and the title.
699                # First, the date, in a very specific format.
700                my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
701                    (tz_local_offset() / 30);
702                # We'll put the link and title in here.
703                my ($link, $title);
704                # Environment data goes in here.
705                my $environment;
706                # HTML-escape the message.
707                my $escaped = CGI::escapeHTML($message);
708                # If we have a CGI object, then this is a web error. Otherwise, it's
709                # command-line.
710                if (defined $SavedCGI) {
711                    # We're in a web service. The title is the user's IP, and the link
712                    # is the URL that got us here.
713                    my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
714                    $title = "Event Reported at IP address $key: $escaped";
715                    $link = $SavedCGI->url(-full => 1, -query => 1);
716                    # We need the user agent string.
717                    $environment = "User Agent $ENV{HTTP_USER_AGENT}."
718                } else {
719                    # No CGI object, so we're a command-line tool. Use the tracing
720                    # key and the PID as the user identifier.
721                    my $key = EmergencyKey();
722                    $title = "Event Reported by $key Process $$: $escaped";
723                    # Set the link to the development NMPDR. There is really no good
724                    # choice here.
725                    $link = "http://$FIG_Config::dev_server";
726                    # We need the command
727                    $environment = "Command $ENV{_}.";
728                }
729                # Build a GUID. We use the current time, the title, and the process ID,
730                # then digest the result.
731                my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
732                # Finally, the description. This is a stack trace plus various environmental stuff.
733                my @trace = LongMess();
734                my $trace = join "; ", @trace;
735                my $description = CGI::escapeHTML("$environment Stack trace: $trace");
736                # Okay, we have all the pieces. Create a hash of the new event.
737                my $newItem = { title => $title,
738                                description => $description,
739                                link => $link,
740                                category => $LastCategory,
741                                pubDate => $date,
742                                guid => $guid,
743                               };
744                # We need XML capability for this.
745                require XML::Simple;
746                # The RSS document goes in here.
747                my $rss;
748                # Get the name of the RSS file. It's in the FIG temporary directory.
749                my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
750                # Does it exist?
751                if (-s $fileName) {
752                    # Slurp it in.
753                    $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
754                } else {
755                    my $size = -s $fileName;
756                    # Create an empty channel.
757                    $rss = {
758                        channel => {
759                            title => 'NMPDR Warning Feed',
760                            link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
761                            description => "Important messages regarding the status of the NMPDR.",
762                            generator => "NMPDR Trace Facility",
763                            docs => "http://blogs.law.harvard.edu/tech/rss",
764                            item => []
765                        },
766                    };
767                }
768                # Get the channel object.
769                my $channel = $rss->{channel};
770                # Update the last-build date.
771                $channel->{lastBuildDate} = $date;
772                # Get the item array.
773                my $items = $channel->{item};
774                # Insure it has only 100 entries.
775                while (scalar @{$items} > 100) {
776                    pop @{$items};
777                }
778                # Add our new item at the front.
779                unshift @{$items}, $newItem;
780                # Replace the file.
781                my $xml = XML::Simple::XMLout($rss, NoAttr => 1, RootName => 'rss', XmlDecl => '<?xml version="1.0" encoding="utf-8"?>',
782                                              NoEscape => 1);
783                # We don't use Open here because we can't afford an error.
784                if (open XMLOUT, ">$fileName") {
785                    print XMLOUT $xml;
786                    close XMLOUT;
787                }
788            }
789        };
790        # There's no "if ($@)" here, because putting an error message in the log
791        # saying that we missed putting an error message in the feed of messages
792        # in the log is not going to help anybody.
793    }
794    
795    =head3 Assert
796    
797        Assert($condition1, $condition2, ... $conditionN);
798    
799    Return TRUE if all the conditions are true. This method can be used in conjunction with
800    the OR operator and the L</Confess> method as a debugging assert.
801    So, for example
802    
803        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
804    
805    Will abort the program with a stack trace if the value of C<$recNum> is negative.
806    
807    =cut
808    sub Assert {
809        my $retVal = 1;
810        LOOP: for my $condition (@_) {
811            if (! $condition) {
812                $retVal = 0;
813                last LOOP;
814            }
815        }
816        return $retVal;
817    }
818    
819    =head3 Cluck
820    
821        Cluck($message);
822    
823    Trace the call stack. Note that for best results, you should qualify the call with a
824    trace condition. For example,
825    
826        Cluck("Starting record parse.") if T(3);
827    
828    will only trace the stack if the trace level for the package is 3 or more.
829    
830    =over 4
831    
832    =item message
833    
834    Message to include in the trace.
835    
836    =back
837    
838    =cut
839    
840    sub Cluck {
841        # Get the parameters.
842        my ($message) = @_;
843        # Trace what's happening.
844        Trace("Stack trace for event: $message");
845        # Get the stack trace.
846        my @trace = LongMess();
847        # Convert the trace to a series of messages.
848        for my $line (@trace) {
849            # Replace the tab at the beginning with spaces.
850            $line =~ s/^\t/    /;
851            # Trace the line.
852            Trace($line);
853        }
854        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
855        Warn($message);
856    }
857    
858    =head3 LongMess
859    
860        my @lines = Tracer::LongMess();
861    
862    Return a stack trace with all tracing methods removed. The return will be in the form of a list
863    of message strings.
864    
865    =cut
866    
867    sub LongMess {
868        # Declare the return variable.
869        my @retVal = ();
870        my $confession = longmess("");
871        for my $line (split /\s*\n/, $confession) {
872            unless ($line =~ /Tracer\.pm/) {
873                # Here we have a line worth keeping. Push it onto the result list.
874                push @retVal, $line;
875            }
876        }
877        # Return the result.
878        return @retVal;
879    }
880    
881    =head3 ScriptSetup (deprecated)
882    
883        my ($cgi, $varHash) = ScriptSetup($noTrace);
884    
885    Perform standard tracing and debugging setup for scripts. The value returned is
886    the CGI object followed by a pre-built variable hash. At the end of the script,
887    the client should call L</ScriptFinish> to output the web page.
888    
889    This method calls L</ETracing> to configure tracing, which allows the tracing
890    to be configured via the emergency tracing form on the debugging control panel.
891    Tracing will then be turned on automatically for all programs that use the L</ETracing>
892    method, which includes every program that uses this method or L</StandardSetup>.
893    
894    =over 4
895    
896    =item noTrace (optional)
897    
898    If specified, tracing will be suppressed. This is useful if the script wants to set up
899    tracing manually.
900    
901    =item RETURN
902    
903    Returns a two-element list consisting of a CGI query object and a variable hash for
904    the output page.
905    
906    =back
907    
908    =cut
909    
910    sub ScriptSetup {
911        # Get the parameters.
912        my ($noTrace) = @_;
913        # Get the CGI query object.
914        my $cgi = CGI->new();
915        # Set up tracing if it's not suppressed.
916        ETracing($cgi) unless $noTrace;
917        # Create the variable hash.
918        my $varHash = { results => '' };
919        # Return the query object and variable hash.
920        return ($cgi, $varHash);
921    }
922    
923    =head3 ETracing
924    
925        ETracing($parameter);
926    
927    Set up emergency tracing. Emergency tracing is tracing that is turned
928    on automatically for any program that calls this method. The emergency
929    tracing parameters are stored in a a file identified by a tracing key.
930    If this method is called with a CGI object, then the tracing key is
931    taken from a cookie. If it is called with no parameters, then the tracing
932    key is taken from an environment variable. If it is called with a string,
933    the tracing key is that string.
934    
935    =over 4
936    
937    =item parameter
938    
939    A parameter from which the tracing key is computed. If it is a scalar,
940    that scalar is used as the tracing key. If it is a CGI object, the
941    tracing key is taken from the C<IP> cookie. If it is omitted, the
942    tracing key is taken from the C<TRACING> environment variable. If it
943    is a CGI object and emergency tracing is not on, the C<Trace> and
944    C<TF> parameters will be used to determine the type of tracing.
945    
946    =back
947    
948    =cut
949    
950    sub ETracing {
951        # Get the parameter.
952        my ($parameter) = @_;
953        # Check for CGI mode.
954        if (defined $parameter && ref $parameter eq 'CGI') {
955            $SavedCGI = $parameter;
956        } else {
957            $SavedCGI = undef;
958        }
959        # Default to no tracing except errors.
960        my ($tracing, $dest) = ("0", "WARN");
961        # Check for emergency tracing.
962        my $tkey = EmergencyKey($parameter);
963        my $emergencyFile = EmergencyFileName($tkey);
964        if (-e $emergencyFile) {
965            # We have the file. Read in the data.
966            my @tracing = GetFile($emergencyFile);
967            # Pull off the time limit.
968            my $expire = shift @tracing;
969            # Convert it to seconds.
970            $expire *= 3600;
971            # Check the file data.
972            my $stat = stat($emergencyFile);
973            my ($now) = gettimeofday;
974            if ($now - $stat->mtime > $expire) {
975                # Delete the expired file.
976                unlink $emergencyFile;
977            } else {
978                # Emergency tracing is on. Pull off the destination and
979                # the trace level;
980                $dest = shift @tracing;
981                my $level = shift @tracing;
982                # Convert the destination to a real tracing destination.
983                # temp directory.
984                $dest = EmergencyTracingDest($tkey, $dest);
985                # Insure Tracer is specified.
986                my %moduleHash = map { $_ => 1 } @tracing;
987                $moduleHash{Tracer} = 1;
988                # Set the trace parameter.
989                $tracing = join(" ", $level, sort keys %moduleHash);
990            }
991        } elsif (defined $SavedCGI) {
992            # There's no emergency tracing, but we have a CGI object, so check
993            # for tracing from the form parameters.
994            if ($SavedCGI->param('Trace')) {
995                # Here the user has requested tracing via a form.
996                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
997                $tracing = $SavedCGI->param('Trace') . " Tracer";
998            }
999        }
1000        # Setup the tracing we've determined from all the stuff above.
1001        TSetup($tracing, $dest);
1002        # Check to see if we're a web script.
1003        if (defined $SavedCGI) {
1004            # Yes we are. Trace the form and environment data.
1005            TraceParms($SavedCGI);
1006            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1007            # emitted by the script in its raw form.
1008            if (T(Raw => 3)) {
1009                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1010            }
1011        }
1012    }
1013    
1014  A string that vaguely describes the positional parameters. This is used  =head3 EmergencyFileName
 if the user specifies the C<-h> option.  
1015    
1016  =item argv      my $fileName = Tracer::EmergencyFileName($tkey);
1017    
1018  List of command line parameters, including the option switches, which must  Return the emergency tracing file name. This is the file that specifies
1019  precede the positional parameters and be prefixed by a hyphen.  the tracing information.
1020    
1021    =over 4
1022    
1023    =item tkey
1024    
1025    Tracing key for the current program.
1026    
1027  =item RETURN  =item RETURN
1028    
1029  Returns a list. The first element of the list is the reference to a hash that  Returns the name of the file to contain the emergency tracing information.
 maps the command-line option switches to their values. These will either be the  
 default values or overrides specified on the command line. The remaining  
 elements of the list are the position parameters, in order.  
1030    
1031  =back  =back
1032    
1033  =cut  =cut
1034    
1035  sub StandardSetup {  sub EmergencyFileName {
1036      # Get the parameters.      # Get the parameters.
1037      my ($categories, $options, $parmHelp, @argv) = @_;      my ($tkey) = @_;
1038      # Get the default tracing key.      # Compute the emergency tracing file name.
1039      my $tkey = EmergencyKey();      return "$FIG_Config::temp/Emergency$tkey.txt";
     # Add the tracing options.  
     if (! exists $options->{trace}) {  
         $options->{trace} = ['2', "tracing level (E for emergency tracing)"];  
1040      }      }
1041      $options->{sql} = [0, "turn on SQL tracing"];  
1042      $options->{help} = [0, "display command-line options"];  =head3 EmergencyFileTarget
1043      $options->{user} = [$tkey, "tracing key"];  
1044      $options->{background} = [0, "spool standard and error output"];      my $fileName = Tracer::EmergencyFileTarget($tkey);
1045      # Create a parsing hash from the options hash. The parsing hash  
1046      # contains the default values rather than the default value  Return the emergency tracing target file name. This is the file that receives
1047      # and the description. While we're at it, we'll memorize the  the tracing output for file-based tracing.
1048      # length of the longest option name.  
1049      my $longestName = 0;  =over 4
1050      my %parseOptions = ();  
1051      for my $key (keys %{$options}) {  =item tkey
1052          if (length $key > $longestName) {  
1053              $longestName = length $key;  Tracing key for the current program.
1054    
1055    =item RETURN
1056    
1057    Returns the name of the file to contain the trace output.
1058    
1059    =back
1060    
1061    =cut
1062    
1063    sub EmergencyFileTarget {
1064        # Get the parameters.
1065        my ($tkey) = @_;
1066        # Compute the emergency tracing file name.
1067        return "$FIG_Config::temp/trace$tkey.log";
1068          }          }
1069          $parseOptions{$key} = $options->{$key}->[0];  
1070    =head3 EmergencyTracingDest
1071    
1072        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1073    
1074    This method converts an emergency tracing destination to a real
1075    tracing destination. The main difference is that if the
1076    destination is C<FILE> or C<APPEND>, we convert it to file
1077    output. If the destination is C<DUAL>, we convert it to file
1078    and standard output.
1079    
1080    =over 4
1081    
1082    =item tkey
1083    
1084    Tracing key for this environment.
1085    
1086    =item myDest
1087    
1088    Destination from the emergency tracing file.
1089    
1090    =item RETURN
1091    
1092    Returns a destination that can be passed into L</TSetup>.
1093    
1094    =back
1095    
1096    =cut
1097    
1098    sub EmergencyTracingDest {
1099        # Get the parameters.
1100        my ($tkey, $myDest) = @_;
1101        # Declare the return variable.
1102        my $retVal = $myDest;
1103        # Process according to the destination value.
1104        if ($myDest eq 'FILE') {
1105            $retVal = ">" . EmergencyFileTarget($tkey);
1106        } elsif ($myDest eq 'APPEND') {
1107            $retVal = ">>" . EmergencyFileTarget($tkey);
1108        } elsif ($myDest eq 'DUAL') {
1109            $retVal = "+>" . EmergencyFileTarget($tkey);
1110        } elsif ($myDest eq 'WARN') {
1111            $retVal = "WARN";
1112      }      }
1113      # Parse the command line.      # Return the result.
1114      my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);      return $retVal;
     # Get the logfile suffix.  
     my $suffix = $retOptions->{user};  
     # Check for background mode.  
     if ($retOptions->{background}) {  
         my $outFileName = "$FIG_Config::temp/out$suffix.log";  
         my $errFileName = "$FIG_Config::temp/err$suffix.log";  
         open STDOUT, ">$outFileName";  
         open STDERR, ">$errFileName";  
1115      }      }
1116      # Now we want to set up tracing. First, we need to know if the user  
1117      # wants emergency tracing.  =head3 Emergency
1118      if ($retOptions->{trace} eq 'E') {  
1119          ETracing($retOptions->{user});      Emergency($key, $hours, $dest, $level, @modules);
1120    
1121    Turn on emergency tracing. This method is normally invoked over the web from
1122    a debugging console, but it can also be called by the C<trace.pl> script.
1123    The caller specifies the duration of the emergency in hours, the desired tracing
1124    destination, the trace level, and a list of the trace modules to activate.
1125    For the length of the duration, when a program in an environment with the
1126    specified tracing key active invokes a Sprout CGI script, tracing will be
1127    turned on automatically. See L</TSetup> for more about tracing setup and
1128    L</ETracing> for more about emergency tracing.
1129    
1130    =over 4
1131    
1132    =item tkey
1133    
1134    The tracing key. This is used to identify the control file and the trace file.
1135    
1136    =item hours
1137    
1138    Number of hours to keep emergency tracing alive.
1139    
1140    =item dest
1141    
1142    Tracing destination. If no path information is specified for a file
1143    destination, it is put in the FIG temporary directory.
1144    
1145    =item level
1146    
1147    Tracing level. A higher level means more trace messages.
1148    
1149    =item modules
1150    
1151    A list of the tracing modules to activate.
1152    
1153    =back
1154    
1155    =cut
1156    
1157    sub Emergency {
1158        # Get the parameters.
1159        my ($tkey, $hours, $dest, $level, @modules) = @_;
1160        # Create the emergency file.
1161        my $specFile = EmergencyFileName($tkey);
1162        my $outHandle = Open(undef, ">$specFile");
1163        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1164    }
1165    
1166    =head3 EmergencyKey
1167    
1168        my $tkey = EmergencyKey($parameter);
1169    
1170    Return the Key to be used for emergency tracing. This could be an IP address,
1171     a session ID, or a user name, depending on the environment.
1172    
1173    =over 4
1174    
1175    =item parameter
1176    
1177    Parameter defining the method for finding the tracing key. If it is a scalar,
1178    then it is presumed to be the tracing key itself. If it is a CGI object, then
1179    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1180    taken from the C<TRACING> environment variable.
1181    
1182    =item RETURN
1183    
1184    Returns the key to be used for labels in emergency tracing.
1185    
1186    =back
1187    
1188    =cut
1189    
1190    sub EmergencyKey {
1191        # Get the parameters.
1192        my ($parameter) = @_;
1193        # Declare the return variable.
1194        my $retVal;
1195        # Determine the parameter type.
1196        if (! defined $parameter) {
1197            # Here we're supposed to check the environment. If that fails, we
1198            # get the effective login ID.
1199            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1200      } else {      } else {
1201          # Here the tracing is controlled from the command line.          my $ptype = ref $parameter;
1202          my @cats = @{$categories};          if ($ptype eq 'CGI') {
1203          if ($retOptions->{sql}) {              # Here we were invoked from a web page. Look for a cookie.
1204              push @cats, "SQL";              $retVal = $parameter->cookie('IP');
1205            } elsif (! $ptype) {
1206                # Here the key was passed in.
1207                $retVal = $parameter;
1208            }
1209        }
1210        # If no luck finding a key, use the PID.
1211        if (! defined $retVal) {
1212            $retVal = $$;
1213        }
1214        # Return the result.
1215        return $retVal;
1216    }
1217    
1218    
1219    =head3 TraceParms
1220    
1221        Tracer::TraceParms($cgi);
1222    
1223    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1224    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1225    
1226    =over 4
1227    
1228    =item cgi
1229    
1230    CGI query object containing the parameters to trace.
1231    
1232    =back
1233    
1234    =cut
1235    
1236    sub TraceParms {
1237        # Get the parameters.
1238        my ($cgi) = @_;
1239        if (T(CGI => 2)) {
1240            # Here we trace the GET-style URL for the script.
1241            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1242          }          }
1243          # Add the default categories.      if (T(CGI => 3)) {
1244          push @cats, "Tracer";          # Here we want to trace the parameter data.
1245          # Next, we create the category string by joining the categories.          my @names = $cgi->param;
1246          my $cats = join(" ", @cats);          for my $parmName (sort @names) {
1247          # Check to determine whether or not the caller wants to turn off tracing              # Note we skip the Trace parameters, which are for our use only.
1248          # to the standard output.              if ($parmName ne 'Trace' && $parmName ne 'TF') {
1249          my $traceLevel = $retOptions->{trace};                  my @values = $cgi->param($parmName);
1250          my $textOKFlag = 1;                  Trace("[CGI] $parmName = " . join(", ", @values));
         if ($traceLevel =~ /^(.)-/) {  
             $traceLevel = $1;  
             $textOKFlag = 0;  
1251          }          }
         # 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";  
1252              }              }
1253              # Close the test file.          # Display the request method.
1254              close TESTTRACE;          my $method = $cgi->request_method();
1255          } else {          Trace("Method: $method");
             # Here we can't trace to a file. We trace to the standard output if it's  
             # okay, and the error log otherwise.  
             if ($textOKFlag) {  
                 $traceMode = "TEXT";  
             } else {  
                 $traceMode = "WARN";  
1256              }              }
1257        if (T(CGI => 4)) {
1258            # Here we want the environment data too.
1259            for my $envName (sort keys %ENV) {
1260                Trace("[ENV] $envName = $ENV{$envName}");
1261          }          }
         # Now set up the tracing.  
         TSetup("$traceLevel $cats", $traceMode);  
1262      }      }
     # Check for the "h" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($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] . ")";  
1263              }              }
1264              print "  $name $desc\n";  
1265    =head3 TraceImages
1266    
1267        Tracer::TraceImages($htmlString);
1268    
1269    Trace information about all of an html document's images. The tracing
1270    will be for type "IMG" at level 3. The image's source string
1271    will be displayed. This is generally either the URL of the image or
1272    raw data for the image itself. If the source is too long, only the first 300
1273    characters will be shown at trace level 3. The entire source will be shown,
1274    however, at trace level 4. This method is not very smart, and might catch
1275    Javascript code, but it is still useful when debugging the arcane
1276    behavior of images in multiple browser environments.
1277    
1278    =over 4
1279    
1280    =item htmlString
1281    
1282    HTML text for an outgoing web page.
1283    
1284    =back
1285    
1286    =cut
1287    
1288    sub TraceImages {
1289        # Only proceed if we're at the proper trace level.
1290        if (T(IMG => 3)) {
1291            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1292            # into a variable called "$htmlString". This is because we expect html strings to be
1293            # long, and don't want to copy them any more than we have to.
1294            Trace(length($_[0]) . " characters in web page.");
1295            # Loop through the HTML, culling image tags.
1296            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1297                # Extract the source string and determine whether or not it's too long.
1298                my $srcString = $1;
1299                my $pos = pos($_[0]) - length($srcString);
1300                my $excess = length($srcString) - 300;
1301                # We'll put the display string in here.
1302                my $srcDisplay = $srcString;
1303                # If it's a data string, split it at the comma.
1304                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1305                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1306                # a long string, however, we only show the first 300 characters.
1307                if ($excess > 0 && ! T(IMG => 4)) {
1308                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1309          }          }
1310          exit(0);              # Output the trace message.
1311                Trace("Image tag at position $pos:\n$srcDisplay");
1312      }      }
     # Trace the options, if applicable.  
     if (T(3)) {  
         my @parms = grep { $retOptions->{$_} } keys %{$retOptions};  
         Trace("Selected options: " . join(", ", sort @parms) . ".");  
1313      }      }
     # Return the parsed parameters.  
     return ($retOptions, @retParameters);  
1314  }  }
1315    
 =head3 Setups  
1316    
1317  C<< my $count = Tracer::Setups(); >>  =head3 ScriptFinish (deprecated)
1318    
1319  Return the number of times L</TSetup> has been called.      ScriptFinish($webData, $varHash);
1320    
1321  This method allows for the creation of conditional tracing setups where, for example, we  Output a web page at the end of a script. Either the string to be output or the
1322  may want to set up tracing if nobody else has done it before us.  name of a template file can be specified. If the second parameter is omitted,
1323    it is assumed we have a string to be output; otherwise, it is assumed we have the
1324    name of a template file. The template should have the variable C<DebugData>
1325    specified in any form that invokes a standard script. If debugging mode is turned
1326    on, a form field will be put in that allows the user to enter tracing data.
1327    Trace messages will be placed immediately before the terminal C<BODY> tag in
1328    the output, formatted as a list.
1329    
1330  =cut  A typical standard script would loook like the following.
1331    
1332  sub Setups {      BEGIN {
1333      return $SetupCount;          # Print the HTML header.
1334            print "CONTENT-TYPE: text/html\n\n";
1335  }  }
1336        use Tracer;
1337        use CGI;
1338        use FIG;
1339        # ... more uses ...
1340    
1341  =head3 Open      my ($cgi, $varHash) = ScriptSetup();
1342        eval {
1343            # ... get data from $cgi, put it in $varHash ...
1344        };
1345        if ($@) {
1346            Trace("Script Error: $@") if T(0);
1347        }
1348        ScriptFinish("Html/MyTemplate.html", $varHash);
1349    
1350  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  The idea here is that even if the script fails, you'll see trace messages and
1351    useful output.
1352    
1353  Open a file.  =over 4
1354    
1355  The I<$fileSpec> is essentially the second argument of the PERL C<open>  =item webData
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
1356    
1357      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  A string containing either the full web page to be written to the output or the
1358    name of a template file from which the page is to be constructed. If the name
1359    of a template file is specified, then the second parameter must be present;
1360    otherwise, it must be absent.
1361    
1362  would open for output appended to the specified file, and  =item varHash (optional)
1363    
1364      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  If specified, then a reference to a hash mapping variable names for a template
1365    to their values. The template file will be read into memory, and variable markers
1366    will be replaced by data in this hash reference.
1367    
1368  would open a pipe that sorts the records written and removes duplicates. Note  =back
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
1369    
1370      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =cut
1371    
1372  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  sub ScriptFinish {
1373  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a      # Get the parameters.
1374  failed open will throw an exception and the third parameter will be used to construct      my ($webData, $varHash) = @_;
1375  an error message. If the parameter is omitted, a standard message is constructed      # Check for a template file situation.
1376  using the file spec.      my $outputString;
1377        if (defined $varHash) {
1378            # Here we have a template file. We need to determine the template type.
1379            my $template;
1380            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1381                $template = "$FIG_Config::template_url/$webData";
1382            } else {
1383                $template = "<<$webData";
1384            }
1385            $outputString = PageBuilder::Build($template, $varHash, "Html");
1386        } else {
1387            # Here the user gave us a raw string.
1388            $outputString = $webData;
1389        }
1390        # Check for trace messages.
1391        if ($Destination ne "NONE" && $TraceLevel > 0) {
1392            # We have trace messages, so we want to put them at the end of the body. This
1393            # is either at the end of the whole string or at the beginning of the BODY
1394            # end-tag.
1395            my $pos = length $outputString;
1396            if ($outputString =~ m#</body>#gi) {
1397                $pos = (pos $outputString) - 7;
1398            }
1399            # If the trace messages were queued, we unroll them. Otherwise, we display the
1400            # destination.
1401            my $traceHtml;
1402            if ($Destination eq "QUEUE") {
1403                $traceHtml = QTrace('Html');
1404            } elsif ($Destination =~ /^>>(.+)$/) {
1405                # Here the tracing output it to a file. We code it as a hyperlink so the user
1406                # can copy the file name into the clipboard easily.
1407                my $actualDest = $1;
1408                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1409            } else {
1410                # Here we have one of the special destinations.
1411                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1412            }
1413            substr $outputString, $pos, 0, $traceHtml;
1414        }
1415        # Write the output string.
1416        print $outputString;
1417    }
1418    
1419      Could not open "/usr/spool/news/twitlog"  =head2 Command-Line Utility Methods
1420    
1421  Note that the mode characters are automatically cleaned from the file name.  =head3 SendSMS
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
1422    
1423      Could not open "/usr/spool/news/twitlog": file not found.      my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1424    
1425  In some versions of PERL the only error message we get is a number, which  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1426  corresponds to the C++ C<errno> value.  user name, password, and API ID for the relevant account in the hash reference variable
1427    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1428    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1429    is C<2561022>, then the FIG_Config file must contain
1430    
1431      Could not open "/usr/spool/news/twitlog": 6.      $phone =  { user => 'BruceTheHumanPet',
1432                    password => 'silly',
1433                    api_id => '2561022' };
1434    
1435  =over 4  The original purpose of this method was to insure Bruce would be notified immediately when the
1436    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1437    when you call this method.
1438    
1439  =item fileHandle  The message ID will be returned if successful, and C<undef> if an error occurs.
1440    
1441  File handle. If this parameter is C<undef>, a file handle will be generated  =over 4
 and returned as the value of this method.  
1442    
1443  =item fileSpec  =item phoneNumber
1444    
1445  File name and mode, as per the PERL C<open> function.  Phone number to receive the message, in international format. A United States phone number
1446    would be prefixed by "1". A British phone number would be prefixed by "44".
1447    
1448  =item message (optional)  =item msg
1449    
1450  Error message to use if the open fails. If omitted, a standard error message  Message to send to the specified phone.
 will be generated. In either case, the error information from the file system  
 is appended to the message. To specify a conditional open that does not throw  
 an error if it fails, use C<0>.  
1451    
1452  =item RETURN  =item RETURN
1453    
1454  Returns the name of the file handle assigned to the file, or C<undef> if the  Returns the message ID if successful, and C<undef> if the message could not be sent.
 open failed.  
1455    
1456  =back  =back
1457    
1458  =cut  =cut
1459    
1460  sub Open {  sub SendSMS {
1461      # Get the parameters.      # Get the parameters.
1462      my ($fileHandle, $fileSpec, $message) = @_;      my ($phoneNumber, $msg) = @_;
1463      # Attempt to open the file.      # Declare the return variable. If we do not change it, C<undef> will be returned.
1464      my $rv = open $fileHandle, $fileSpec;      my $retVal;
1465      # If the open failed, generate an error message.      # Only proceed if we have phone support.
1466      if (! $rv) {      if (! defined $FIG_Config::phone) {
1467          # Save the system error message.          Trace("Phone support not present in FIG_Config.") if T(1);
1468          my $sysMessage = $!;      } else {
1469          # See if we need a default message.          # Get the phone data.
1470          if (!$message) {          my $parms = $FIG_Config::phone;
1471              # Clean any obvious mode characters and leading spaces from the          # Get the Clickatell URL.
1472              # filename.          my $url = "http://api.clickatell.com/http/";
1473              my ($fileName) = FindNamePart($fileSpec);          # Create the user agent.
1474              $message = "Could not open \"$fileName\"";          my $ua = LWP::UserAgent->new;
1475            # Request a Clickatell session.
1476            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1477                                         password => $parms->{password},
1478                                         api_id => $parms->{api_id},
1479                                         to => $phoneNumber,
1480                                         text => $msg});
1481            # Check for an error.
1482            if (! $resp->is_success) {
1483                Trace("Alert failed.") if T(1);
1484            } else {
1485                # Get the message ID.
1486                my $rstring = $resp->content;
1487                if ($rstring =~ /^ID:\s+(.*)$/) {
1488                    $retVal = $1;
1489                } else {
1490                    Trace("Phone attempt failed with $rstring") if T(1);
1491          }          }
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
1492      }      }
1493      # Return the file handle.      }
1494      return $fileHandle;      # Return the result.
1495        return $retVal;
1496  }  }
1497    
1498  =head3 FindNamePart  =head3 StandardSetup
1499    
1500  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>      my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1501    
1502  Extract the portion of a file specification that contains the file name.  This method performs standard command-line parsing and tracing setup. The return
1503    values are a hash of the command-line options and a list of the positional
1504    parameters. Tracing is automatically set up and the command-line options are
1505    validated.
1506    
1507  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
1508  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>.  
1509    
1510      >>/usr/fig/myfile.txt  The I<categories> parameter is the most obtuse. It is a reference to a list of
1511      </usr/fig/myfile.txt  special-purpose tracing categories. Most tracing categories are PERL package
1512      | sort -u > /usr/fig/myfile.txt  names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1513    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1514    
1515  If the method cannot find a file name using its normal methods, it will return the      ["Sprout", "SproutLoad", "ERDB"]
1516  whole incoming string.  
1517    This would cause trace messages in the specified three packages to appear in
1518    the output. There are two special tracing categories that are automatically
1519    handled by this method. In other words, if you used L</TSetup> you would need
1520    to include these categories manually, but if you use this method they are turned
1521    on automatically.
1522    
1523  =over 4  =over 4
1524    
1525  =item fileSpec  =item SQL
1526    
1527  File specification string from which the file name is to be extracted.  Traces SQL commands and activity.
1528    
1529  =item RETURN  =item Tracer
1530    
1531  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.  
1532    
1533  =back  =back
1534    
1535  =cut  C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1536  #: Return Type $;  The trace level is specified using the C<-trace> command-line option. For example,
1537  sub FindNamePart {  the following command line for C<TransactFeatures> turns on SQL tracing and runs
1538      # Get the parameters.  all tracing at level 3.
     my ($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, $len);  
 }  
1539    
1540  =head3 OpenDir      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1541    
1542  C<< my @files = OpenDir($dirName, $filtered, $flag); >>  Standard tracing is output to the standard output and echoed to the file
1543    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1544    process ID. You can also specify the C<user> parameter to put a user ID
1545    instead of a process ID in the trace file name. So, for example
1546    
1547  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.
1548  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,  
1549    
1550      my @files = OpenDir("/Volumes/fig/contigs", 1);      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1551    
1552  is effectively the same as  would send the trace output to C<traceBruce.log> in the temporary directory.
1553    
1554      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
1555      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  options, their default values, and an explanation of what they mean. Command-line
1556    options may be in the form of switches or keywords. In the case of a switch, the
1557    option value is 1 if it is specified and 0 if it is not specified. In the case
1558    of a keyword, the value is separated from the option name by an equal sign. You
1559    can see this last in the command-line example above.
1560    
1561  Similarly, the following code  You can specify a different default trace level by setting C<$options->{trace}>
1562    prior to calling this method.
1563    
1564      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  An example at this point would help. Consider, for example, the command-line utility
1565    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1566    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1567    the following code.
1568    
1569  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1570  automatically returns an empty list if the directory fails to open.                          { safe => [0, "use database transactions"],
1571                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1572                              start => [' ', "start with this genome"],
1573                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1574                            "<command> <transactionDirectory> <IDfile>",
1575                          @ARGV);
1576    
 =over 4  
1577    
1578  =item dirName  The call to C<ParseCommand> specifies the default values for the options and
1579    stores the actual options in a hash that is returned as C<$options>. The
1580    positional parameters are returned in C<@parameters>.
1581    
1582  Name of the directory to open.  The following is a sample command line for C<TransactFeatures>.
1583    
1584  =item filtered      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1585    
1586  TRUE if files whose names begin with a period (C<.>) should be automatically removed  Single and double hyphens are equivalent. So, you could also code the
1587  from the list, else FALSE.  above command as
1588    
1589  =item flag      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1590    
1591  TRUE if a failure to open is okay, else FALSE  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1592    parameters, and would find themselves in I<@parameters> after executing the
1593    above code fragment. The tracing would be set to level 2, and the categories
1594    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1595    and C<DocUtils> was included because it came in within the first parameter
1596    to this method. The I<$options> hash would be
1597    
1598  =back      { trace => 2, sql => 0, safe => 0,
1599          noAlias => 1, start => ' ', tblFiles => 0 }
1600    
1601  =cut  Use of C<StandardSetup> in this way provides a simple way of performing
1602  #: Return Type @;  standard tracing setup and command-line parsing. Note that the caller is
1603  sub OpenDir {  not even aware of the command-line switches C<-trace> and C<-sql>, which
1604      # Get the parameters.  are used by this method to control the tracing. If additional tracing features
1605      my ($dirName, $filtered, $flag) = @_;  need to be added in the future, they can be processed by this method without
1606      # 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 $dirName.");  
     }  
     # Return the result.  
     return @retVal;  
 }  
1607    
1608  =head3 SetLevel  If the C<background> option is specified on the command line, then the
1609    standard and error outputs will be directed to files in the temporary
1610    directory, using the same suffix as the trace file. So, if the command
1611    line specified
1612    
1613  C<< Tracer::SetLevel($newLevel); >>      -user=Bruce -background
1614    
1615  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
1616    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1617    simplify starting a command in the background.
1618    
1619  =over 4  The user name is also used as the tracing key for L</Emergency Tracing>.
1620    Specifying a value of C<E> for the trace level causes emergency tracing to
1621    be used instead of custom tracing. If the user name is not specified,
1622    the tracing key is taken from the C<Tracing> environment variable. If there
1623    is no value for that variable, the tracing key will be computed from the PID.
1624    
1625  =item newLevel  Finally, if the special option C<-help> is specified, the option
1626    names will be traced at level 0 and the program will exit without processing.
1627    This provides a limited help capability. For example, if the user enters
1628    
1629  Proposed new trace level.      TransactFeatures -help
1630    
1631  =back  he would see the following output.
1632    
1633  =cut      TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1634            -trace    tracing level (default E)
1635            -sql      trace SQL commands
1636            -safe     use database transactions
1637            -noAlias  do not expect aliases in CHANGE transactions
1638            -start    start with this genome
1639            -tblFiles output TBL files containing the corrected IDs
1640    
1641  sub SetLevel {  The caller has the option of modifying the tracing scheme by placing a value
1642      $TraceLevel = $_[0];  for C<trace> in the incoming options hash. The default value can be overridden,
1643  }  or the tracing to the standard output can be turned off by suffixing a minus
1644    sign to the trace level. So, for example,
1645    
1646  =head3 Now      { trace => [0, "tracing level (default 0)"],
1647           ...
1648    
1649    would set the default trace level to 0 instead of E, while
1650    
1651  C<< my $string = Tracer::Now(); >>      { trace => ["2-", "tracing level (default 2)"],
1652           ...
1653    
1654  Return a displayable time stamp containing the local time.  would set the default to 2, but trace only to the log file, not to the
1655    standard output.
1656    
1657  =cut  The parameters to this method are as follows.
1658    
1659  sub Now {  =over 4
     my ($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 $retVal;  
 }  
1660    
1661  # Pad a number to 2 digits.  =item categories
1662  sub _p2 {  
1663      my ($value) = @_;  Reference to a list of tracing category names. These should be names of
1664      $value = "0$value" if ($value < 10);  packages whose internal workings will need to be debugged to get the
1665      return $value;  command working.
 }  
1666    
1667  =head3 ParseTraceDate  =item options
1668    
1669  C<< my $time = Tracer::ParseTraceDate($dateString); >>  Reference to a hash containing the legal options for the current command mapped
1670    to their default values and descriptions. The user can override the defaults
1671    by specifying the options as command-line switches prefixed by a hyphen.
1672    Tracing-related options may be added to this hash. If the C<-h> option is
1673    specified on the command line, the option descriptions will be used to
1674    explain the options. To turn off tracing to the standard output, add a
1675    minus sign to the value for C<trace> (see above).
1676    
1677  Convert a date from the trace file into a PERL timestamp.  =item parmHelp
1678    
1679  =over 4  A string that vaguely describes the positional parameters. This is used
1680    if the user specifies the C<-h> option.
1681    
1682  =item dateString  =item argv
1683    
1684  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
1685  L</Now> method.  precede the positional parameters and be prefixed by a hyphen.
1686    
1687  =item RETURN  =item RETURN
1688    
1689  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
1690  the time string is invalid.  maps the command-line option switches to their values. These will either be the
1691    default values or overrides specified on the command line. The remaining
1692    elements of the list are the position parameters, in order.
1693    
1694  =back  =back
1695    
1696  =cut  =cut
1697    
1698  sub ParseTraceDate {  sub StandardSetup {
1699      # Get the parameters.      # Get the parameters.
1700      my ($dateString) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
1701      # Declare the return variable.      # Get the default tracing key.
1702      my $retVal;      my $tkey = EmergencyKey();
1703      # Parse the date.      # Add the tracing options.
1704      if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {      if (! exists $options->{trace}) {
1705          # Create a time object. Note we need to convert the day, month,          $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
         # and year to a different base. Years count from 1900, and  
         # the internal month value is relocated to January = 0.  
         $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);  
1706      }      }
1707      # Return the result.      $options->{sql} = [0, "turn on SQL tracing"];
1708      return $retVal;      $options->{help} = [0, "display command-line options"];
1709        $options->{user} = [$tkey, "tracing key"];
1710        $options->{background} = [0, "spool standard and error output"];
1711        # Create a parsing hash from the options hash. The parsing hash
1712        # contains the default values rather than the default value
1713        # and the description. While we're at it, we'll memorize the
1714        # length of the longest option name.
1715        my $longestName = 0;
1716        my %parseOptions = ();
1717        for my $key (keys %{$options}) {
1718            if (length $key > $longestName) {
1719                $longestName = length $key;
1720  }  }
1721            $parseOptions{$key} = $options->{$key}->[0];
1722  =head3 LogErrors      }
1723        # Parse the command line.
1724  C<< Tracer::LogErrors($fileName); >>      my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1725        # Get the logfile suffix.
1726  Route the standard error output to a log file.      my $suffix = $retOptions->{user};
1727        # Check for background mode.
1728  =over 4      if ($retOptions->{background}) {
1729            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1730  =item fileName          my $errFileName = "$FIG_Config::temp/err$suffix.log";
1731            open STDOUT, ">$outFileName";
1732  Name of the file to receive the error output.          open STDERR, ">$errFileName";
1733            # Check for phone support. If we have phone support and a phone number,
1734  =back          # we want to turn it on.
1735            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1736  =cut              $retOptions->{phone} = $ENV{PHONE};
1737            }
1738  sub LogErrors {      }
1739      # Get the file name.      # Now we want to set up tracing. First, we need to know if the user
1740      my ($fileName) = @_;      # wants emergency tracing.
1741      # Open the file as the standard error output.      if ($retOptions->{trace} eq 'E') {
1742      open STDERR, '>', $fileName;          ETracing($retOptions->{user});
1743        } else {
1744            # Here the tracing is controlled from the command line.
1745            my @cats = @{$categories};
1746            if ($retOptions->{sql}) {
1747                push @cats, "SQL";
1748            }
1749            # Add the default categories.
1750            push @cats, "Tracer";
1751            # Next, we create the category string by joining the categories.
1752            my $cats = join(" ", @cats);
1753            # Check to determine whether or not the caller wants to turn off tracing
1754            # to the standard output.
1755            my $traceLevel = $retOptions->{trace};
1756            my $textOKFlag = 1;
1757            if ($traceLevel =~ /^(.)-/) {
1758                $traceLevel = $1;
1759                $textOKFlag = 0;
1760            }
1761            # Now we set up the trace mode.
1762            my $traceMode;
1763            # Verify that we can open a file in the FIG temporary directory.
1764            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1765            if (open TESTTRACE, ">$traceFileName") {
1766                # Here we can trace to a file.
1767                $traceMode = ">$traceFileName";
1768                if ($textOKFlag) {
1769                    # Echo to standard output if the text-OK flag is set.
1770                    $traceMode = "+$traceMode";
1771                }
1772                # Close the test file.
1773                close TESTTRACE;
1774            } else {
1775                # Here we can't trace to a file. Complain about this.
1776                warn "Could not open trace file $traceFileName: $!\n";
1777                # We trace to the standard output if it's
1778                # okay, and the error log otherwise.
1779                if ($textOKFlag) {
1780                    $traceMode = "TEXT";
1781                } else {
1782                    $traceMode = "WARN";
1783                }
1784            }
1785            # Now set up the tracing.
1786            TSetup("$traceLevel $cats", $traceMode);
1787        }
1788        # Check for the "help" option. If it is specified, dump the command-line
1789        # options and exit the program.
1790        if ($retOptions->{help}) {
1791            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1792            print "$1 [options] $parmHelp\n";
1793            for my $key (sort keys %{$options}) {
1794                my $name = Pad($key, $longestName, 0, ' ');
1795                my $desc = $options->{$key}->[1];
1796                if ($options->{$key}->[0]) {
1797                    $desc .= " (default " . $options->{$key}->[0] . ")";
1798                }
1799                print "  $name $desc\n";
1800            }
1801            exit(0);
1802        }
1803        # Trace the options, if applicable.
1804        if (T(3)) {
1805            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1806            Trace("Selected options: " . join(", ", sort @parms) . ".");
1807        }
1808        # Return the parsed parameters.
1809        return ($retOptions, @retParameters);
1810  }  }
1811    
1812  =head3 ReadOptions  =head3 ReadOptions
1813    
1814  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1815    
1816  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
1817  format  format
# Line 1069  Line 1872 
1872    
1873  =head3 GetOptions  =head3 GetOptions
1874    
1875  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1876    
1877  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
1878  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 1881 
1881    
1882  Consider the following example.  Consider the following example.
1883    
1884  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1885    
1886  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1887  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 1086  Line 1889 
1889  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1890  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1891    
1892  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1893    
1894  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1895    
# Line 1130  Line 1933 
1933    
1934  =head3 MergeOptions  =head3 MergeOptions
1935    
1936  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
1937    
1938  Merge default values into a hash table. This method looks at the key-value pairs in the  Merge default values into a hash table. This method looks at the key-value pairs in the
1939  second (default) hash, and if a matching key is not found in the first hash, the default  second (default) hash, and if a matching key is not found in the first hash, the default
# Line 1146  Line 1949 
1949  =item defaults  =item defaults
1950    
1951  Default values to be merged into the first hash table if they are not already present.  Default values to be merged into the first hash table if they are not already present.
1952    
1953  =back  =back
1954    
1955  =cut  =cut
1956    
1957  sub MergeOptions {  sub MergeOptions {
1958      # Get the parameters.      # Get the parameters.
1959      my ($table, $defaults) = @_;      my ($table, $defaults) = @_;
1960      # Loop through the defaults.      # Loop through the defaults.
1961      while (my ($key, $value) = each %{$defaults}) {      while (my ($key, $value) = each %{$defaults}) {
1962          if (!exists $table->{$key}) {          if (!exists $table->{$key}) {
1963              $table->{$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.");  
1964          }          }
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
1965      }      }
     # Return the computed result.  
     return $retVal;  
1966  }  }
1967    
1968  =head3 ParseCommand  =head3 ParseCommand
1969    
1970  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1971    
1972  Parse a command line consisting of a list of parameters. The initial parameters may be option  Parse a command line consisting of a list of parameters. The initial parameters may be option
1973  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1974  off and merged into a table of default options. The remainder of the command line is  off and merged into a table of default options. The remainder of the command line is
1975  returned as a list of positional arguments. For example, consider the following invocation.  returned as a list of positional arguments. For example, consider the following invocation.
1976    
1977  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1978    
1979  In this case, the list @words will be treated as a command line and there are two options available,  In this case, the list @words will be treated as a command line and there are two options available,
1980  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
1981    
1982  C<< -logFile=error.log apple orange rutabaga >>      -logFile=error.log apple orange rutabaga
1983    
1984  then at the end of the invocation, C<$options> will be  then at the end of the invocation, C<$options> will be
1985    
1986  C<< { errors => 0, logFile => 'error.log' } >>      { errors => 0, logFile => 'error.log' }
1987    
1988  and C<@arguments> will contain  and C<@arguments> will contain
1989    
1990  C<< apple orange rutabaga >>      apple orange rutabaga
1991    
1992  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1993  support for quote characters. Options can be specified with single or double hyphens.  support for quote characters. Options can be specified with single or double hyphens.
# Line 1356  Line 2038 
2038          push @retVal, UnEscape($inputParm);          push @retVal, UnEscape($inputParm);
2039      }      }
2040      # Return the results.      # Return the results.
2041      return ($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 $retVal;  
2042  }  }
2043    
2044    
2045    =head2 File Utility Methods
2046    
2047  =head3 GetFile  =head3 GetFile
2048    
2049  C<< my @fileContents = Tracer::GetFile($fileName); >>      my @fileContents = Tracer::GetFile($fileName);
2050    
2051      or      or
2052    
2053  C<< my $fileContents = Tracer::GetFile($fileName); >>      my $fileContents = Tracer::GetFile($fileName);
2054    
2055  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
2056  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 2100 
2100    
2101  =head3 PutFile  =head3 PutFile
2102    
2103  C<< Tracer::PutFile($fileName, \@lines); >>      Tracer::PutFile($fileName, \@lines);
2104    
2105  Write out a file from a list of lines of text.  Write out a file from a list of lines of text.
2106    
# Line 1704  Line 2143 
2143      close $handle;      close $handle;
2144  }  }
2145    
2146  =head3 QTrace  =head3 ParseRecord
2147    
2148  C<< my $data = QTrace($format); >>      my @fields = Tracer::ParseRecord($line);
2149    
2150  Return the queued trace data in the specified format.  Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2151    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2152    These will automatically be converted.
2153    
2154  =over 4  =over 4
2155    
2156  =item format  =item line
2157    
2158  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Line of data containing the tab-delimited fields.
2159    
2160    =item RETURN
2161    
2162    Returns a list of the fields found in the data line.
2163    
2164  =back  =back
2165    
2166  =cut  =cut
2167    
2168  sub QTrace {  sub ParseRecord {
2169      # Get the parameter.      # Get the parameter.
2170      my ($format) = @_;      my ($line) = @_;
2171      # Create the return variable.      # Remove the trailing new-line, if any.
2172      my $retVal = "";      chomp $line;
2173      # Only proceed if there is an actual queue.      # Split the line read into pieces using the tab character.
2174      if (@Queue) {      my @retVal = split /\t/, $line;
2175          # Process according to the format.      # Trim and fix the escapes in each piece.
2176          if ($format =~ m/^HTML$/i) {      for my $value (@retVal) {
2177              # Convert the queue into an HTML list.          # Trim leading whitespace.
2178              $retVal = "<ul>\n";          $value =~ s/^\s+//;
2179              for my $line (@Queue) {          # Trim trailing whitespace.
2180                  my $escapedLine = CGI::escapeHTML($line);          $value =~ s/\s+$//;
2181                  $retVal .= "<li>$escapedLine</li>\n";          # Delete the carriage returns.
2182              }          $value =~ s/\r//g;
2183              $retVal .= "</ul>\n";          # Convert the escapes into their real values.
2184          } elsif ($format =~ m/^TEXT$/i) {          $value =~ s/\\t/"\t"/ge;
2185              # Convert the queue into a list of text lines.          $value =~ s/\\n/"\n"/ge;
             $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
2186      }      }
2187      # Return the formatted list.      # Return the result.
2188      return $retVal;      return @retVal;
2189  }  }
2190    
2191  =head3 Confess  =head3 Merge
2192    
2193  C<< Confess($message); >>      my @mergedList = Tracer::Merge(@inputList);
2194    
2195  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  
2196    
2197  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
2198    
2199  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item inputList
2200    
2201  =over 4  List of scalars to sort and merge.
2202    
2203  =item message  =item RETURN
2204    
2205  Message to include in the trace.  Returns a list containing the same elements sorted in ascending order with duplicates
2206    removed.
2207    
2208  =back  =back
2209    
2210  =cut  =cut
2211    
2212  sub Confess {  sub Merge {
2213      # Get the parameters.      # Get the input list in sort order.
2214      my ($message) = @_;      my @inputList = sort @_;
2215      # Trace the call stack.      # Only proceed if the list has at least two elements.
2216      Cluck($message);      if (@inputList > 1) {
2217      # Abort the program.          # Now we want to move through the list splicing out duplicates.
2218      croak(">>> $message");          my $i = 0;
2219            while ($i < @inputList) {
2220                # Get the current entry.
2221                my $thisEntry = $inputList[$i];
2222                # Find out how many elements duplicate the current entry.
2223                my $j = $i + 1;
2224                my $dup1 = $i + 1;
2225                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2226                # If the number is nonzero, splice out the duplicates found.
2227                if ($j > $dup1) {
2228                    splice @inputList, $dup1, $j - $dup1;
2229                }
2230                # Now the element at position $dup1 is different from the element before it
2231                # at position $i. We push $i forward one position and start again.
2232                $i++;
2233            }
2234        }
2235        # Return the merged list.
2236        return @inputList;
2237  }  }
2238    
2239  =head3 Assert  =head3 Open
2240    
2241  C<< Assert($condition1, $condition2, ... $conditionN); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2242    
2243  Return TRUE if all the conditions are true. This method can be used in conjunction with  Open a file.
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
2244    
2245  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2246    function. The mode is specified using Unix-like shell information. So, for
2247    example,
2248    
2249  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.");
2250    
2251  =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 $retVal;  
 }  
2252    
2253  =head3 Cluck      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2254    
2255  C<< Cluck($message); >>  would open a pipe that sorts the records written and removes duplicates. Note
2256    the use of file handle syntax in the Open call. To use anonymous file handles,
2257    code as follows.
2258    
2259  Trace the call stack. Note that for best results, you should qualify the call with a      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
 trace condition. For example,  
2260    
2261  C<< Cluck("Starting record parse.") if T(3); >>  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2262    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2263    failed open will throw an exception and the third parameter will be used to construct
2264    an error message. If the parameter is omitted, a standard message is constructed
2265    using the file spec.
2266    
2267  will only trace the stack if the trace level for the package is 3 or more.      Could not open "/usr/spool/news/twitlog"
2268    
2269    Note that the mode characters are automatically cleaned from the file name.
2270    The actual error message from the file system will be captured and appended to the
2271    message in any case.
2272    
2273        Could not open "/usr/spool/news/twitlog": file not found.
2274    
2275    In some versions of PERL the only error message we get is a number, which
2276    corresponds to the C++ C<errno> value.
2277    
2278        Could not open "/usr/spool/news/twitlog": 6.
2279    
2280  =over 4  =over 4
2281    
2282  =item message  =item fileHandle
2283    
2284  Message to include in the trace.  File handle. If this parameter is C<undef>, a file handle will be generated
2285    and returned as the value of this method.
2286    
2287    =item fileSpec
2288    
2289    File name and mode, as per the PERL C<open> function.
2290    
2291    =item message (optional)
2292    
2293    Error message to use if the open fails. If omitted, a standard error message
2294    will be generated. In either case, the error information from the file system
2295    is appended to the message. To specify a conditional open that does not throw
2296    an error if it fails, use C<0>.
2297    
2298    =item RETURN
2299    
2300    Returns the name of the file handle assigned to the file, or C<undef> if the
2301    open failed.
2302    
2303  =back  =back
2304    
2305  =cut  =cut
2306    
2307  sub Cluck {  sub Open {
2308      # Get the parameters.      # Get the parameters.
2309      my ($message) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2310      # Trace what's happening.      # Attempt to open the file.
2311      Trace("Stack trace for event: $message");      my $rv = open $fileHandle, $fileSpec;
2312      my $confession = longmess($message);      # If the open failed, generate an error message.
2313      # Convert the confession to a series of trace messages. Note we skip any      if (! $rv) {
2314      # messages relating to calls into Tracer.          # Save the system error message.
2315      for my $line (split /\s*\n/, $confession) {          my $sysMessage = $!;
2316          Trace($line) if ($line !~ /Tracer\.pm/);          # See if we need a default message.
2317            if (!$message) {
2318                # Clean any obvious mode characters and leading spaces from the
2319                # filename.
2320                my ($fileName) = FindNamePart($fileSpec);
2321                $message = "Could not open \"$fileName\"";
2322            }
2323            # Terminate with an error using the supplied message and the
2324            # error message from the file system.
2325            Confess("$message: $!");
2326      }      }
2327        # Return the file handle.
2328        return $fileHandle;
2329  }  }
2330    
2331  =head3 Min  =head3 FindNamePart
2332    
2333  C<< my $min = Min($value1, $value2, ... $valueN); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2334    
2335  Return the minimum argument. The arguments are treated as numbers.  Extract the portion of a file specification that contains the file name.
2336    
2337    A file specification is the string passed to an C<open> call. It specifies the file
2338    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2339    method assumes that the file name is whatever follows the first angle bracket
2340    sequence.  So, for example, in the following strings the file name is
2341    C</usr/fig/myfile.txt>.
2342    
2343        >>/usr/fig/myfile.txt
2344        </usr/fig/myfile.txt
2345        | sort -u > /usr/fig/myfile.txt
2346    
2347    If the method cannot find a file name using its normal methods, it will return the
2348    whole incoming string.
2349    
2350  =over 4  =over 4
2351    
2352  =item $value1, $value2, ... $valueN  =item fileSpec
2353    
2354  List of numbers to compare.  File specification string from which the file name is to be extracted.
2355    
2356  =item RETURN  =item RETURN
2357    
2358  Returns the lowest number in the list.  Returns a three-element list. The first element contains the file name portion of
2359    the specified string, or the whole string if a file name cannot be found via normal
2360    methods. The second element contains the start position of the file name portion and
2361    the third element contains the length.
2362    
2363    =back
2364    
2365    =cut
2366    #: Return Type $;
2367    sub FindNamePart {
2368        # Get the parameters.
2369        my ($fileSpec) = @_;
2370        # Default to the whole input string.
2371        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2372        # Parse out the file name if we can.
2373        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2374            $retVal = $2;
2375            $len = length $retVal;
2376            $pos = (length $fileSpec) - (length $3) - $len;
2377        }
2378        # Return the result.
2379        return ($retVal, $pos, $len);
2380    }
2381    
2382    =head3 OpenDir
2383    
2384        my @files = OpenDir($dirName, $filtered, $flag);
2385    
2386    Open a directory and return all the file names. This function essentially performs
2387    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2388    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2389    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2390    filtered out of the return list. If the directory does not open and I<$flag> is not
2391    set, an exception is thrown. So, for example,
2392    
2393  =back      my @files = OpenDir("/Volumes/fig/contigs", 1);
2394    
2395  =cut  is effectively the same as
2396    
2397  sub Min {      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2398      # 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;  
 }  
2399    
2400  =head3 Max  Similarly, the following code
2401    
2402  C<< my $max = Max($value1, $value2, ... $valueN); >>      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2403    
2404  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
2405    automatically returns an empty list if the directory fails to open.
2406    
2407  =over 4  =over 4
2408    
2409  =item $value1, $value2, ... $valueN  =item dirName
2410    
2411  List of numbers to compare.  Name of the directory to open.
2412    
2413  =item RETURN  =item filtered
2414    
2415  Returns the highest number in the list.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2416    from the list, else FALSE.
2417    
2418    =item flag
2419    
2420    TRUE if a failure to open is okay, else FALSE
2421    
2422  =back  =back
2423    
2424  =cut  =cut
2425    #: Return Type @;
2426  sub Max {  sub OpenDir {
2427      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2428      my ($retVal, @values) = @_;      my ($dirName, $filtered, $flag) = @_;
2429      # Loop through the remaining parameters, looking for the highest.      # Declare the return variable.
2430      for my $value (@values) {      my @retVal = ();
2431          if ($value > $retVal) {      # Open the directory.
2432              $retVal = $value;      if (opendir(my $dirHandle, $dirName)) {
2433            # The directory opened successfully. Get the appropriate list according to the
2434            # strictures of the filter parameter.
2435            if ($filtered) {
2436                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2437            } else {
2438                @retVal = readdir $dirHandle;
2439          }          }
2440        } elsif (! $flag) {
2441            # Here the directory would not open and it's considered an error.
2442            Confess("Could not open directory $dirName.");
2443      }      }
2444      # Return the maximum found.      # Return the result.
2445      return $retVal;      return @retVal;
2446  }  }
2447    
 =head3 AddToListMap  
   
 C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>  
2448    
2449  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  =head3 Insure
 is created for the key. Otherwise, the new value is pushed onto the list.  
2450    
2451  =over 4      Insure($dirName, $chmod);
2452    
2453  =item hash  Insure a directory is present.
2454    
2455  Reference to the target hash.  =over 4
2456    
2457  =item key  =item dirName
2458    
2459  Key for which the value is to be added.  Name of the directory to check. If it does not exist, it will be created.
2460    
2461  =item value1, value2, ... valueN  =item chmod (optional)
2462    
2463  List of values to add to the key's value list.  Security privileges to be given to the directory if it is created.
2464    
2465  =back  =back
2466    
2467  =cut  =cut
2468    
2469  sub AddToListMap {  sub Insure {
2470      # Get the parameters.      my ($dirName, $chmod) = @_;
2471      my ($hash, $key, @values) = @_;      if (! -d $dirName) {
2472      # Process according to whether or not the key already has a value.          Trace("Creating $dirName directory.") if T(2);
2473      if (! exists $hash->{$key}) {          eval {
2474          $hash->{$key} = [@values];              mkpath $dirName;
2475      } else {              # If we have permissions specified, set them here.
2476          push @{$hash->{$key}}, @values;              if (defined($chmod)) {
2477                    chmod $chmod, $dirName;
2478      }      }
2479            };
2480            if ($@) {
2481                Confess("Error creating $dirName: $@");
2482  }  }
   
 =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.");  
2483      }      }
     # Return the determination indicator.  
     return $retVal;  
2484  }  }
2485    
2486  =head3 Strip  =head3 ChDir
2487    
2488  C<< my $string = Tracer::Strip($line); >>      ChDir($dirName);
2489    
2490  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.  
2491    
2492  =over 4  =over 4
2493    
2494  =item line  =item dirName
   
 Line of text to be stripped.  
   
 =item RETURN  
2495    
2496  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.
2497    
2498  =back  =back
2499    
2500  =cut  =cut
2501    
2502  sub Strip {  sub ChDir {
2503      # Get a copy of the parameter string.      my ($dirName) = @_;
2504      my ($string) = @_;      if (! -d $dirName) {
2505      my $retVal = (defined $string ? $string : "");          Confess("Cannot change to directory $dirName: no such directory.");
2506      # Strip the line terminator characters.      } else {
2507      $retVal =~ s/(\r|\n)+$//g;          Trace("Changing to directory $dirName.") if T(File => 4);
2508      # Return the result.          my $okFlag = chdir $dirName;
2509      return $retVal;          if (! $okFlag) {
2510                Confess("Error switching to directory $dirName.");
2511            }
2512        }
2513  }  }
2514    
2515  =head3 Pad  =head3 SetPermissions
2516    
2517  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2518    
2519  Pad a string to a specified length. The pad character will be a  Set the permissions for a directory and all the files and folders inside it.
2520  space, and the padding will be on the right side unless specified  In addition, the group ownership will be changed to the specified value.
2521  in the third parameter.  
2522    This method is more vulnerable than most to permission and compatability
2523    problems, so it does internal error recovery.
2524    
2525  =over 4  =over 4
2526    
2527  =item string  =item dirName
2528    
2529  String to be padded.  Name of the directory to process.
2530    
2531  =item len  =item group
2532    
2533  Desired length of the padded string.  Name of the group to be assigned.
2534    
2535  =item left (optional)  =item mask
2536    
2537  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  Permission mask. Bits that are C<1> in this mask will be ORed into the
2538    permission bits of any file or directory that does not already have them
2539    set to 1.
2540    
2541  =item padChar (optional)  =item otherMasks
2542    
2543  Character to use for padding. The default is a space.  Map of search patterns to permission masks. If a directory name matches
2544    one of the patterns, that directory and all its members and subdirectories
2545    will be assigned the new pattern. For example, the following would
2546    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2547    
2548  =item RETURN      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2549    
2550  Returns a copy of the original string with the pad character added to the  The list is ordered, so the following would use 0777 for C<tmp1> and
2551  specified end so that it achieves the desired length.  0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2552    
2553        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2554                                                       '^tmp' => 0666);
2555    
2556    Note that the pattern matches are all case-insensitive, and only directory
2557    names are matched, not file names.
2558    
2559  =back  =back
2560    
2561  =cut  =cut
2562    
2563  sub Pad {  sub SetPermissions {
2564      # Get the parameters.      # Get the parameters.
2565      my ($string, $len, $left, $padChar) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2566      # Compute the padding character.      # Set up for error recovery.
2567      if (! defined $padChar) {      eval {
2568          $padChar = " ";          # Switch to the specified directory.
2569            ChDir($dirName);
2570            # Get the group ID.
2571            my $gid = getgrnam($group);
2572            # Get the mask for tracing.
2573            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2574            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2575            my $fixCount = 0;
2576            my $lookCount = 0;
2577            # @dirs will be a stack of directories to be processed.
2578            my @dirs = (getcwd());
2579            while (scalar(@dirs) > 0) {
2580                # Get the current directory.
2581                my $dir = pop @dirs;
2582                # Check for a match to one of the specified directory names. To do
2583                # that, we need to pull the individual part of the name off of the
2584                # whole path.
2585                my $simpleName = $dir;
2586                if ($dir =~ m!/([^/]+)$!) {
2587                    $simpleName = $1;
2588      }      }
2589      # Compute the number of spaces needed.              Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2590      my $needed = $len - length $string;              # Search for a match.
2591      # Copy the string into the return variable.              my $match = 0;
2592      my $retVal = $string;              my $i;
2593      # Only proceed if padding is needed.              for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2594      if ($needed > 0) {                  my $pattern = $otherMasks[$i];
2595          # Create the pad string.                  if ($simpleName =~ /$pattern/i) {
2596          my $pad = $padChar x $needed;                      $match = 1;
2597          # Affix it to the return value.                  }
2598          if ($left) {              }
2599              $retVal = $pad . $retVal;              # Check for a match. Note we use $i-1 because the loop added 2
2600                # before terminating due to the match.
2601                if ($match && $otherMasks[$i-1] != $mask) {
2602                    # This directory matches one of the incoming patterns, and it's
2603                    # a different mask, so we process it recursively with that mask.
2604                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2605          } else {          } else {
2606              $retVal .= $pad;                  # Here we can process normally. Get all of the non-hidden members.
2607                    my @submems = OpenDir($dir, 1);
2608                    for my $submem (@submems) {
2609                        # Get the full name.
2610                        my $thisMem = "$dir/$submem";
2611                        Trace("Checking member $thisMem.") if T(4);
2612                        $lookCount++;
2613                        if ($lookCount % 1000 == 0) {
2614                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2615                        }
2616                        # Fix the group.
2617                        chown -1, $gid, $thisMem;
2618                        # Insure this member is not a symlink.
2619                        if (! -l $thisMem) {
2620                            # Get its info.
2621                            my $fileInfo = stat $thisMem;
2622                            # Only proceed if we got the info. Otherwise, it's a hard link
2623                            # and we want to skip it anyway.
2624                            if ($fileInfo) {
2625                                my $fileMode = $fileInfo->mode;
2626                                if (($fileMode & $mask) != $mask) {
2627                                    # Fix this member.
2628                                    $fileMode |= $mask;
2629                                    chmod $fileMode, $thisMem;
2630                                    $fixCount++;
2631                                }
2632                                # If it's a subdirectory, stack it.
2633                                if (-d $thisMem) {
2634                                    push @dirs, $thisMem;
2635          }          }
2636      }      }
     # Return the result.  
     return $retVal;  
2637  }  }
   
 =head3 EOF  
   
 This is a constant that is lexically greater than any useful string.  
   
 =cut  
   
 sub EOF {  
     return "\xFF\xFF\xFF\xFF\xFF";  
2638  }  }
   
 =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) {  
         $commandString =~ s!^\./!!;  
2639      }      }
2640      # Activate the command and return the result.          }
2641      return `$commandString`;          Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2642        };
2643        # Check for an error.
2644        if ($@) {
2645            Confess("SetPermissions error: $@");
2646        }
2647  }  }
2648    
2649  =head3 ScriptSetup  =head3 GetLine
   
 C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  
2650    
2651  Perform standard tracing and debugging setup for scripts. The value returned is      my @data = Tracer::GetLine($handle);
 the CGI object followed by a pre-built variable hash. At the end of the script,  
 the client should call L</ScriptFinish> to output the web page.  
2652    
2653  This method calls L</ETracing> to configure tracing, which allows the tracing  Read a line of data from a tab-delimited file.
 to be configured via the emergency tracing form on the debugging control panel.  
 Tracing will then be turned on automatically for all programs that use the L</ETracing>  
 method, which includes every program that uses this method or L</StandardSetup>.  
2654    
2655  =over 4  =over 4
2656    
2657  =item noTrace (optional)  =item handle
2658    
2659  If specified, tracing will be suppressed. This is useful if the script wants to set up  Open file handle from which to read.
 tracing manually.  
2660    
2661  =item RETURN  =item RETURN
2662    
2663  Returns a two-element list consisting of a CGI query object and a variable hash for  Returns a list of the fields in the record read. The fields are presumed to be
2664  the output page.  tab-delimited. If we are at the end of the file, then an empty list will be
2665    returned. If an empty line is read, a single list item consisting of a null
2666    string will be returned.
2667    
2668  =back  =back
2669    
2670  =cut  =cut
2671    
2672  sub ScriptSetup {  sub GetLine {
2673      # Get the parameters.      # Get the parameters.
2674      my ($noTrace) = @_;      my ($handle) = @_;
2675      # Get the CGI query object.      # Declare the return variable.
2676      my $cgi = CGI->new();      my @retVal = ();
2677      # Set up tracing if it's not suppressed.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2678      ETracing($cgi) unless $noTrace;      # Read from the file.
2679      # Create the variable hash.      my $line = <$handle>;
2680      my $varHash = { results => '' };      # Only proceed if we found something.
2681      # Return the query object and variable hash.      if (defined $line) {
2682      return ($cgi, $varHash);          # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2683            # upload control and have a nonstandard EOL combination.
2684            $line =~ s/(\r|\n)+$//;
2685            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2686            if (T(File => 4)) {
2687                my $escapedLine = $line;
2688                $escapedLine =~ s/\n/\\n/g;
2689                $escapedLine =~ s/\r/\\r/g;
2690                $escapedLine =~ s/\t/\\t/g;
2691                Trace("Line read: -->$escapedLine<--");
2692  }  }
2693            # If the line is empty, return a single empty string; otherwise, parse
2694  =head3 ETracing          # it into fields.
2695            if ($line eq "") {
2696  C<< ETracing($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 $emergencyFile;  
2697          } else {          } else {
2698              # Emergency tracing is on. Pull off the destination and              push @retVal, split /\t/,$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 = $cgi->param('Trace') . " Tracer";  
         }  
2699      }      }
2700      # Setup the tracing we've determined from all the stuff above.      } else {
2701      TSetup($tracing, $dest);          # Trace the reason the read failed.
2702      # 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);  
2703      }      }
2704        # Return the result.
2705        return @retVal;
2706  }  }
2707    
2708  =head3 EmergencyFileName  =head3 PutLine
2709    
2710  C<< my $fileName = Tracer::EmergencyFileName($tkey); >>      Tracer::PutLine($handle, \@fields, $eol);
2711    
2712  Return the emergency tracing file name. This is the file that specifies  Write a line of data to a tab-delimited file. The specified field values will be
2713  the tracing information.  output in tab-separated form, with a trailing new-line.
2714    
2715  =over 4  =over 4
2716    
2717  =item tkey  =item handle
2718    
2719  Tracing key for the current program.  Output file handle.
2720    
2721  =item RETURN  =item fields
2722    
2723  Returns the name of the file to contain the emergency tracing information.  List of field values.
2724    
2725    =item eol (optional)
2726    
2727    End-of-line character (default is "\n").
2728    
2729  =back  =back
2730    
2731  =cut  =cut
2732    
2733  sub EmergencyFileName {  sub PutLine {
2734      # Get the parameters.      # Get the parameters.
2735      my ($tkey) = @_;      my ($handle, $fields, $eol) = @_;
2736      # Compute the emergency tracing file name.      # Write the data.
2737      return "$FIG_Config::temp/Emergency$tkey.txt";      print $handle join("\t", @{$fields}) . ($eol || "\n");
2738  }  }
2739    
 =head3 EmergencyFileTarget  
   
 C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>  
2740    
2741  Return the emergency tracing target file name. This is the file that receives  =head3 PrintLine
 the tracing output for file-based tracing.  
2742    
2743  =over 4      Tracer::PrintLine($line);
2744    
2745  =item tkey  Print a line of text with a trailing new-line.
2746    
2747  Tracing key for the current program.  =over 4
2748    
2749  =item RETURN  =item line
2750    
2751  Returns the name of the file to contain the trace output.  Line of text to print.
2752    
2753  =back  =back
2754    
2755  =cut  =cut
2756    
2757  sub EmergencyFileTarget {  sub PrintLine {
2758      # Get the parameters.      # Get the parameters.
2759      my ($tkey) = @_;      my ($line) = @_;
2760      # Compute the emergency tracing file name.      # Print the line.
2761      return "$FIG_Config::temp/trace$tkey.log";      print "$line\n";
2762  }  }
2763    
 =head3 EmergencyTracingDest  
2764    
2765  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>  =head2 Other Useful Methods
2766    
2767  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.  
2768    
2769  =over 4      my $listValue = Tracer::ParseParm($string);
2770    
2771  =item tkey  Convert a parameter into a list reference. If the parameter is undefined,
2772    an undefined value will be returned. Otherwise, it will be parsed as a
2773    comma-separated list of values.
2774    
2775  Tracing key for this environment.  =over 4
2776    
2777  =item myDest  =item string
2778    
2779  Destination from the emergency tracing file.  Incoming string.
2780    
2781  =item RETURN  =item RETURN
2782    
2783  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
2784    was undefined.
2785    
2786  =back  =back
2787    
2788  =cut  =cut
2789    
2790  sub EmergencyTracingDest {  sub ParseParm {
2791      # Get the parameters.      # Get the parameters.
2792      my ($tkey, $myDest) = @_;      my ($string) = @_;
2793      # Declare the return variable.      # Declare the return variable.
2794      my $retVal = $myDest;      my $retVal;
2795      # Process according to the destination value.      # Check for data.
2796      if ($myDest eq 'FILE') {      if (defined $string) {
2797          $retVal = ">" . EmergencyFileTarget($tkey);          # We have some, so split it into a list.
2798      } elsif ($myDest eq 'APPEND') {          $retVal = [ split /\s*,\s*/, $string];
         $retVal = ">>" . EmergencyFileTarget($tkey);  
     } elsif ($myDest eq 'DUAL') {  
         $retVal = "+>" . EmergencyFileTarget($tkey);  
2799      }      }
2800      # Return the result.      # Return the result.
2801      return $retVal;      return $retVal;
2802  }  }
2803    
2804  =head3 Emergency  =head3 Now
   
 C<< Emergency($key, $hours, $dest, $level, @modules); >>  
2805    
2806  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.  
2807    
2808  =over 4  Return a displayable time stamp containing the local time. Whatever format this
2809    method produces must be parseable by L</ParseDate>.
2810    
2811  =item tkey  =cut
2812    
2813  The tracing key. This is used to identify the control file and the trace file.  sub Now {
2814        return DisplayTime(time);
2815    }
2816    
2817  =item hours  =head3 DisplayTime
2818    
2819  Number of hours to keep emergency tracing alive.      my $string = Tracer::DisplayTime($time);
2820    
2821  =item dest  Convert a time value to a displayable time stamp. Whatever format this
2822    method produces must be parseable by L</ParseDate>.
2823    
2824  Tracing destination. If no path information is specified for a file  =over 4
 destination, it is put in the FIG temporary directory.  
2825    
2826  =item level  =item time
2827    
2828  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.
2829    
2830  =item modules  =item RETURN
2831    
2832  A list of the tracing modules to activate.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2833    
2834  =back  =back
2835    
2836  =cut  =cut
2837    
2838  sub Emergency {  sub DisplayTime {
2839      # Get the parameters.      my ($time) = @_;
2840      my ($tkey, $hours, $dest, $level, @modules) = @_;      my $retVal = "(n/a)";
2841      # Create the emergency file.      if (defined $time) {
2842      my $specFile = EmergencyFileName($tkey);          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2843      my $outHandle = Open(undef, ">$specFile");          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2844      print $outHandle join("\n", $hours, $dest, $level, @modules, "");                    _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2845        }
2846        return $retVal;
2847  }  }
2848    
2849  =head3 EmergencyKey  # Pad a number to 2 digits.
2850    sub _p2 {
2851        my ($value) = @_;
2852        $value = "0$value" if ($value < 10);
2853        return $value;
2854    }
2855    
2856  C<< my $tkey = EmergencyKey($parameter); >>  =head3 Escape
2857    
2858  Return the Key to be used for emergency tracing. This could be an IP address,      my $codedString = Tracer::Escape($realString);
2859   a session ID, or a user name, depending on the environment.  
2860    Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2861    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2862    result is to reverse the effect of L</UnEscape>.
2863    
2864  =over 4  =over 4
2865    
2866  =item parameter  =item realString
2867    
2868  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.  
2869    
2870  =item RETURN  =item RETURN
2871    
2872  Returns the key to be used for labels in emergency tracing.  Escaped equivalent of the real string.
2873    
2874  =back  =back
2875    
2876  =cut  =cut
2877    
2878  sub EmergencyKey {  sub Escape {
2879      # Get the parameters.      # Get the parameter.
2880      my ($parameter) = @_;      my ($realString) = @_;
2881      # Declare the return variable.      # Initialize the return variable.
2882      my $retVal;      my $retVal = "";
2883      # Determine the parameter type.      # Loop through the parameter string, looking for sequences to escape.
2884      if (! defined $parameter) {      while (length $realString > 0) {
2885          # Here we're supposed to check the environment.          # Look for the first sequence to escape.
2886          $retVal = $ENV{TRACING};          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2887      } else {              # Here we found it. The text preceding the sequence is in $1. The sequence
2888          my $ptype = ref $parameter;              # itself is in $2. First, move the clear text to the return variable.
2889          if ($ptype eq 'CGI') {              $retVal .= $1;
2890              # Here we were invoked from a web page. Look for a cookie.              # Strip the processed section off the real string.
2891              $retVal = $parameter->cookie('IP');              $realString = substr $realString, (length $2) + (length $1);
2892          } elsif (! $ptype) {              # Get the matched character.
2893              # Here the key was passed in.              my $char = $2;
2894              $retVal = $parameter;              # If we have a CR, we are done.
2895                if ($char ne "\r") {
2896                    # It's not a CR, so encode the escape sequence.
2897                    $char =~ tr/\t\n/tn/;
2898                    $retVal .= "\\" . $char;
2899          }          }
2900            } else {
2901                # Here there are no more escape sequences. The rest of the string is
2902                # transferred unmodified.
2903                $retVal .= $realString;
2904                $realString = "";
2905      }      }
     # If no luck finding a key, use the PID.  
     if (! defined $retVal) {  
         $retVal = $$;  
2906      }      }
2907      # Return the result.      # Return the result.
2908      return $retVal;      return $retVal;
2909  }  }
2910    
2911    =head3 UnEscape
2912    
2913  =head3 TraceParms      my $realString = Tracer::UnEscape($codedString);
   
 C<< Tracer::TraceParms($cgi); >>  
2914    
2915  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2916  at level CGI => 4.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2917    be deleted.
2918    
2919  =over 4  =over 4
2920    
2921  =item cgi  =item codedString
2922    
2923  CGI query object containing the parameters to trace.  String to un-escape.
2924    
2925    =item RETURN
2926    
2927    Returns a copy of the original string with the escape sequences converted to their actual
2928    values.
2929    
2930  =back  =back
2931    
2932  =cut  =cut
2933    
2934  sub TraceParms {  sub UnEscape {
2935      # Get the parameters.      # Get the parameter.
2936      my ($cgi) = @_;      my ($codedString) = @_;
2937      if (T(CGI => 3)) {      # Initialize the return variable.
2938          # Here we want to trace the parameter data.      my $retVal = "";
2939          my @names = $cgi->param;      # Only proceed if the incoming string is nonempty.
2940          for my $parmName (sort @names) {      if (defined $codedString) {
2941              # Note we skip the Trace parameters, which are for our use only.          # Loop through the parameter string, looking for escape sequences. We can't do
2942              if ($parmName ne 'Trace' && $parmName ne 'TF') {          # translating because it causes problems with the escaped slash. ("\\t" becomes
2943                  my @values = $cgi->param($parmName);          # "\<tab>" no matter what we do.)
2944                  Trace("CGI: $parmName = " . join(", ", @values));          while (length $codedString > 0) {
2945              }              # Look for the first escape sequence.
2946                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2947                    # Here we found it. The text preceding the sequence is in $1. The sequence
2948                    # itself is in $2. First, move the clear text to the return variable.
2949                    $retVal .= $1;
2950                    $codedString = substr $codedString, (2 + length $1);
2951                    # Get the escape value.
2952                    my $char = $2;
2953                    # If we have a "\r", we are done.
2954                    if ($char ne 'r') {
2955                        # Here it's not an 'r', so we convert it.
2956                        $char =~ tr/\\tn/\\\t\n/;
2957                        $retVal .= $char;
2958          }          }
2959          # Display the request method.              } else {
2960          my $method = $cgi->request_method();                  # Here there are no more escape sequences. The rest of the string is
2961          Trace("Method: $method");                  # transferred unmodified.
2962                    $retVal .= $codedString;
2963                    $codedString = "";
2964      }      }
     if (T(CGI => 4)) {  
         # Here we want the environment data too.  
         for my $envName (sort keys %ENV) {  
             Trace("ENV: $envName = $ENV{$envName}");  
2965          }          }
2966      }      }
2967        # Return the result.
2968        return $retVal;
2969  }  }
2970    
2971  =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.  
2972    
2973  A typical standard script would loook like the following.      my $percent = Tracer::Percent($number, $base);
2974    
2975      BEGIN {  Returns the percent of the base represented by the given number. If the base
2976          # Print the HTML header.  is zero, returns zero.
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
2977    
2978      my ($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", $varHash);  
2979    
2980  The idea here is that even if the script fails, you'll see trace messages and  =item number
 useful output.  
2981    
2982  =over 4  Percent numerator.
2983    
2984  =item webData  =item base
2985    
2986  A string containing either the full web page to be written to the output or the  Percent base.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
2987    
2988  =item varHash (optional)  =item RETURN
2989    
2990  If specified, then a reference to a hash mapping variable names for a template  Returns the percentage of the base represented by the numerator.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
2991    
2992  =back  =back
2993    
2994  =cut  =cut
2995    
2996  sub ScriptFinish {  sub Percent {
2997      # Get the parameters.      # Get the parameters.
2998      my ($webData, $varHash) = @_;      my ($number, $base) = @_;
2999      # Check for a template file situation.      # Declare the return variable.
3000      my $outputString;      my $retVal = 0;
3001      if (defined $varHash) {      # Compute the percent.
3002          # Here we have a template file. We need to determine the template type.      if ($base != 0) {
3003          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;  
3004      }      }
3005      # Write the output string.      # Return the result.
3006      print $outputString;      return $retVal;
3007  }  }
3008    
3009  =head3 Insure  =head3 Constrain
3010    
3011  C<< Insure($dirName); >>      my $constrained = Constrain($value, $min, $max);
3012    
3013  Insure a directory is present.  Modify a numeric value to bring it to a point in between a maximum and a minimum.
3014    
3015  =over 4  =over 4
3016    
3017  =item dirName  =item value
3018    
3019  Name of the directory to check. If it does not exist, it will be created.  Value to constrain.
3020    
3021    =item min (optional)
3022    
3023    Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3024    
3025    =item max (optional)
3026    
3027    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3028    
3029    =item RETURN
3030    
3031    Returns the incoming value, constrained according to the other parameters.
3032    
3033  =back  =back
3034    
3035  =cut  =cut
3036    
3037  sub Insure {  sub Constrain {
3038      my ($dirName) = @_;      # Get the parameters.
3039      if (! -d $dirName) {      my ($value, $min, $max) = @_;
3040          Trace("Creating $dirName directory.") if T(File => 2);      # Declare the return variable.
3041          eval { mkpath $dirName; };      my $retVal = $value;
3042          if ($@) {      # Apply the minimum constraint.
3043              Confess("Error creating $dirName: $@");      if (defined $min && $retVal < $min) {
3044          }          $retVal = $min;
3045        }
3046        # Apply the maximum constraint.
3047        if (defined $max && $retVal > $max) {
3048            $retVal = $max;
3049      }      }
3050        # Return the result.
3051        return $retVal;
3052  }  }
3053    
3054  =head3 ChDir  =head3 Min
3055    
3056  C<< ChDir($dirName); >>      my $min = Min($value1, $value2, ... $valueN);
3057    
3058  Change to the specified directory.  Return the minimum argument. The arguments are treated as numbers.
3059    
3060  =over 4  =over 4
3061    
3062  =item dirName  =item $value1, $value2, ... $valueN
3063    
3064  Name of the directory to which we want to change.  List of numbers to compare.
3065    
3066    =item RETURN
3067    
3068    Returns the lowest number in the list.
3069    
3070  =back  =back
3071    
3072  =cut  =cut
3073    
3074  sub ChDir {  sub Min {
3075      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
3076      if (! -d $dirName) {      my ($retVal, @values) = @_;
3077          Confess("Cannot change to directory $dirName: no such directory.");      # Loop through the remaining parameters, looking for the lowest.
3078      } else {      for my $value (@values) {
3079          Trace("Changing to directory $dirName.") if T(File => 4);          if ($value < $retVal) {
3080          my $okFlag = chdir $dirName;              $retVal = $value;
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
3081          }          }
3082      }      }
3083        # Return the minimum found.
3084        return $retVal;
3085  }  }
3086    
3087  =head3 SendSMS  =head3 Max
3088    
3089  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>      my $max = Max($value1, $value2, ... $valueN);
3090    
3091  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  Return the maximum argument. The arguments are treated as numbers.
 user name, password, and API ID for the relevant account in the hash reference variable  
 I<$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  
3092    
3093      $phone =  { user => 'BruceTheHumanPet',  =over 4
                 password => 'silly',  
                 api_id => '2561022' };  
3094    
3095  The original purpose of this method was to insure Bruce would be notified immediately when the  =item $value1, $value2, ... $valueN
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3096    
3097  The message ID will be returned if successful, and C<undef> if an error occurs.  List of numbers to compare.
3098    
3099  =over 4  =item RETURN
3100    
3101  =item phoneNumber  Returns the highest number in the list.
3102    
3103  Phone number to receive the message, in international format. A United States phone number  =back
 would be prefixed by "1". A British phone number would be prefixed by "44".  
3104    
3105  =item msg  =cut
3106    
3107  Message to send to the specified phone.  sub Max {
3108        # Get the parameters. Note that we prime the return value with the first parameter.
3109        my ($retVal, @values) = @_;
3110        # Loop through the remaining parameters, looking for the highest.
3111        for my $value (@values) {
3112            if ($value > $retVal) {
3113                $retVal = $value;
3114            }
3115        }
3116        # Return the maximum found.
3117        return $retVal;
3118    }
3119    
3120    
3121    =head3 Strip
3122    
3123        my $string = Tracer::Strip($line);
3124    
3125    Strip all line terminators off a string. This is necessary when dealing with files
3126    that may have been transferred back and forth several times among different
3127    operating environments.
3128    
3129    =over 4
3130    
3131    =item line
3132    
3133    Line of text to be stripped.
3134    
3135  =item RETURN  =item RETURN
3136    
3137  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.
3138    
3139  =back  =back
3140    
3141  =cut  =cut
3142    
3143  sub SendSMS {  sub Strip {
3144      # Get the parameters.      # Get a copy of the parameter string.
3145      my ($phoneNumber, $msg) = @_;      my ($string) = @_;
3146      # Declare the return variable. If we do not change it, C<undef> will be returned.      my $retVal = (defined $string ? $string : "");
3147      my $retVal;      # Strip the line terminator characters.
3148      # 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);  
             }  
         }  
     }  
3149      # Return the result.      # Return the result.
3150      return $retVal;      return $retVal;
3151  }  }
3152    
3153  =head3 CommaFormat  =head3 Pad
3154    
3155  C<< my $formatted = Tracer::CommaFormat($number); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3156    
3157  Insert commas into a number.  Pad a string to a specified length. The pad character will be a
3158    space, and the padding will be on the right side unless specified
3159    in the third parameter.
3160    
3161  =over 4  =over 4
3162    
3163  =item number  =item string
3164    
3165  A sequence of digits.  String to be padded.
3166    
3167    =item len
3168    
3169    Desired length of the padded string.
3170    
3171    =item left (optional)
3172    
3173    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3174    
3175    =item padChar (optional)
3176    
3177    Character to use for padding. The default is a space.
3178    
3179  =item RETURN  =item RETURN
3180    
3181  Returns the same digits with commas strategically inserted.  Returns a copy of the original string with the pad character added to the
3182    specified end so that it achieves the desired length.
3183    
3184  =back  =back
3185    
3186  =cut  =cut
3187    
3188  sub CommaFormat {  sub Pad {
3189      # Get the parameters.      # Get the parameters.
3190      my ($number) = @_;      my ($string, $len, $left, $padChar) = @_;
3191      # Pad the length up to a multiple of three.      # Compute the padding character.
3192      my $padded = "$number";      if (! defined $padChar) {
3193      $padded = " " . $padded while length($padded) % 3 != 0;          $padChar = " ";
3194      # This is a fancy PERL trick. The parentheses in the SPLIT pattern      }
3195      # cause the delimiters to be included in the output stream. The      # Compute the number of spaces needed.
3196      # GREP removes the empty strings in between the delimiters.      my $needed = $len - length $string;
3197      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));      # Copy the string into the return variable.
3198      # Clean out the spaces.      my $retVal = $string;
3199      $retVal =~ s/ //g;      # Only proceed if padding is needed.
3200        if ($needed > 0) {
3201            # Create the pad string.
3202            my $pad = $padChar x $needed;
3203            # Affix it to the return value.
3204            if ($left) {
3205                $retVal = $pad . $retVal;
3206            } else {
3207                $retVal .= $pad;
3208            }
3209        }
3210      # Return the result.      # Return the result.
3211      return $retVal;      return $retVal;
3212  }  }
 =head3 SetPermissions  
3213    
3214  C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  =head3 EOF
3215    
3216    This is a constant that is lexically greater than any useful string.
3217    
3218  Set the permissions for a directory and all the files and folders inside it.  =cut
 In addition, the group ownership will be changed to the specified value.  
3219    
3220  This method is more vulnerable than most to permission and compatability  sub EOF {
3221  problems, so it does internal error recovery.      return "\xFF\xFF\xFF\xFF\xFF";
3222    }
3223    
3224    =head3 TICK
3225    
3226        my @results = TICK($commandString);
3227    
3228    Perform a back-tick operation on a command. If this is a Windows environment, any leading
3229    dot-slash (C<./> will be removed. So, for example, if you were doing
3230    
3231        `./protein.cgi`
3232    
3233    from inside a CGI script, it would work fine in Unix, but would issue an error message
3234    in Windows complaining that C<'.'> is not a valid command. If instead you code
3235    
3236        TICK("./protein.cgi")
3237    
3238    it will work correctly in both environments.
3239    
3240  =over 4  =over 4
3241    
3242  =item dirName  =item commandString
3243    
3244  Name of the directory to process.  The command string to pass to the system.
3245    
3246  =item group  =item RETURN
3247    
3248    Returns the standard output from the specified command, as a list.
3249    
3250    =back
3251    
3252    =cut
3253    #: Return Type @;
3254    sub TICK {
3255        # Get the parameters.
3256        my ($commandString) = @_;
3257        # Chop off the dot-slash if this is Windows.
3258        if ($FIG_Config::win_mode) {
3259            $commandString =~ s!^\./!!;
3260        }
3261        # Activate the command and return the result.
3262        return `$commandString`;
3263    }
3264    
 Name of the group to be assigned.  
3265    
3266  =item mask  =head3 CommaFormat
3267    
3268  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.  
3269    
3270  =item otherMasks  Insert commas into a number.
3271    
3272  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>.  
3273    
3274      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  =item number
3275    
3276  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>.  
3277    
3278      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  =item RETURN
                                                    '^tmp' => 0666);  
3279    
3280  Note that the pattern matches are all case-insensitive, and only directory  Returns the same digits with commas strategically inserted.
 names are matched, not file names.  
3281    
3282  =back  =back
3283    
3284  =cut  =cut
3285    
3286  sub SetPermissions {  sub CommaFormat {
3287      # Get the parameters.      # Get the parameters.
3288      my ($dirName, $group, $mask, @otherMasks) = @_;      my ($number) = @_;
3289      # Set up for error recovery.      # Pad the length up to a multiple of three.
3290      eval {      my $padded = "$number";
3291          # Switch to the specified directory.      $padded = " " . $padded while length($padded) % 3 != 0;
3292          ChDir($dirName);      # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3293          # Get the group ID.      # cause the delimiters to be included in the output stream. The
3294          my $gid = getgrnam($group);      # GREP removes the empty strings in between the delimiters.
3295          # Get the mask for tracing.      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3296          my $traceMask = sprintf("%04o", $mask) . "($mask)";      # Clean out the spaces.
3297          Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);      $retVal =~ s/ //g;
3298          my $fixCount = 0;      # Return the result.
3299          my $lookCount = 0;      return $retVal;
         # @dirs will be a stack of directories to be processed.  
         my @dirs = (getcwd());  
         while (scalar(@dirs) > 0) {  
             # Get the current directory.  
             my $dir = pop @dirs;  
             # Check for a match to one of the specified directory names. To do  
             # that, we need to pull the individual part of the name off of the  
             # whole path.  
             my $simpleName = $dir;  
             if ($dir =~ m!/([^/]+)$!) {  
                 $simpleName = $1;  
             }  
             Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);  
             # Search for a match.  
             my $match = 0;  
             my $i;  
             for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {  
                 my $pattern = $otherMasks[$i];  
                 if ($simpleName =~ /$pattern/i) {  
                     $match = 1;  
                 }  
             }  
             # Check for a match. Note we use $i-1 because the loop added 2  
             # before terminating due to the match.  
             if ($match && $otherMasks[$i-1] != $mask) {  
                 # This directory matches one of the incoming patterns, and it's  
                 # a different mask, so we process it recursively with that mask.  
                 SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);  
             } else {  
                 # Here we can process normally. Get all of the non-hidden members.  
                 my @submems = OpenDir($dir, 1);  
                 for my $submem (@submems) {  
                     # Get the full name.  
                     my $thisMem = "$dir/$submem";  
                     Trace("Checking member $thisMem.") if T(4);  
                     $lookCount++;  
                     if ($lookCount % 1000 == 0) {  
                         Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);  
                     }  
                     # Fix the group.  
                     chown -1, $gid, $thisMem;  
                     # Insure this member is not a symlink.  
                     if (! -l $thisMem) {  
                         # Get its info.  
                         my $fileInfo = stat $thisMem;  
                         # Only proceed if we got the info. Otherwise, it's a hard link  
                         # and we want to skip it anyway.  
                         if ($fileInfo) {  
                             my $fileMode = $fileInfo->mode;  
                             if (($fileMode & $mask) != $mask) {  
                                 # Fix this member.  
                                 $fileMode |= $mask;  
                                 chmod $fileMode, $thisMem;  
                                 $fixCount++;  
                             }  
                             # If it's a subdirectory, stack it.  
                             if (-d $thisMem) {  
                                 push @dirs, $thisMem;  
                             }  
                         }  
                     }  
                 }  
             }  
         }  
         Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);  
     };  
     # Check for an error.  
     if ($@) {  
         Confess("SetPermissions error: $@");  
     }  
3300  }  }
3301    
3302    
3303  =head3 CompareLists  =head3 CompareLists
3304    
3305  C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3306    
3307  Compare two lists of tuples, and return a hash analyzing the differences. The lists  Compare two lists of tuples, and return a hash analyzing the differences. The lists
3308  are presumed to be sorted alphabetically by the value in the $keyIndex column.  are presumed to be sorted alphabetically by the value in the $keyIndex column.
# Line 2950  Line 3367 
3367      return ($inserted, $deleted);      return ($inserted, $deleted);
3368  }  }
3369    
 =head3 GetLine  
   
 C<< my @data = Tracer::GetLine($handle); >>  
   
 Read a line of data from a tab-delimited file.  
   
 =over 4  
   
 =item handle  
   
 Open file handle from which to read.  
   
 =item RETURN  
   
 Returns a list of the fields in the record read. The fields are presumed to be  
 tab-delimited. If we are at the end of the file, then an empty list will be  
 returned. If an empty line is read, a single list item consisting of a null  
 string will be returned.  
   
 =back  
   
 =cut  
   
 sub GetLine {  
     # Get the parameters.  
     my ($handle) = @_;  
     # Declare the return variable.  
     my @retVal = ();  
     Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);  
     # Read from the file.  
     my $line = <$handle>;  
     # Only proceed if we found something.  
     if (defined $line) {  
         # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an  
         # upload control and have a nonstandard EOL combination.  
         $line =~ s/(\r|\n)+$//;  
         # Here we do some fancy tracing to help in debugging complicated EOL marks.  
         if (T(File => 4)) {  
             my $escapedLine = $line;  
             $escapedLine =~ s/\n/\\n/g;  
             $escapedLine =~ s/\r/\\r/g;  
             $escapedLine =~ s/\t/\\t/g;