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revision 1.79, Thu Nov 9 21:12:46 2006 UTC revision 1.116, Thu Feb 5 06:40:13 2009 UTC
# Line 1  Line 1 
1  #  # -*- perl -*-
2    ########################################################################
3  # Copyright (c) 2003-2006 University of Chicago and Fellowship  # Copyright (c) 2003-2006 University of Chicago and Fellowship
4  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
5  #  #
# Line 13  Line 14 
14  # at info@ci.uchicago.edu or the Fellowship for Interpretation of  # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15  # Genomes at veronika@thefig.info or download a copy from  # Genomes at veronika@thefig.info or download a copy from
16  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
17  #  ########################################################################
18    
19  package Tracer;  package Tracer;
20    
     require Exporter;  
     @ISA = ('Exporter');  
     @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);  
     @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);  
21      use strict;      use strict;
22      use Carp qw(longmess croak);      use base qw(Exporter);
23        use vars qw(@EXPORT @EXPORT_OK);
24        @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn TraceDump IDHASH);
25        @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
26        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        use Fcntl qw(:DEFAULT :flock);
42        use Data::Dumper;
43    
44    
45  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
46    
# Line 159  Line 165 
165    
166  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
167  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
168  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
169  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
170  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
171  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
172  the tracing in your environment without stepping on other users.  the tracing in your environment without stepping on other users.
# Line 183  Line 189 
189    
190  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
191  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
192  using the L</StandardScript> or L</StandardSetup> methods, emergency tracing  using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
193  will be configured automatically.  will be configured automatically.
194    
 =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.  
   
195  =cut  =cut
196    
197  # Declare the configuration variables.  # Declare the configuration variables.
198    
199  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
200  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
201                              # standard output                              # standard output
202  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
203                              # hash of active category names                              # hash of active category names
204    my @LevelNames = qw(error warn notice info detail);
205  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
206                              # messages                              # messages
207  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
208  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
209    my $LastLevel = 0;          # level of the last test call
210  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
211  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
212    my $SavedCGI;               # CGI object passed to ETracing
213    my $CommandLine;            # Command line passed to StandardSetup
214    umask 2;                    # Fix the damn umask so everything is group-writable.
215    
216  =head2 Public Methods  =head2 Tracing Methods
217    
218    =head3 Setups
219    
220        my $count = Tracer::Setups();
221    
222    Return the number of times L</TSetup> has been called.
223    
224    This method allows for the creation of conditional tracing setups where, for example, we
225    may want to set up tracing if nobody else has done it before us.
226    
227    =cut
228    
229    sub Setups {
230        return $SetupCount;
231    }
232    
233  =head3 TSetup  =head3 TSetup
234    
235  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
236    
237  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
238  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 347  Line 282 
282          }          }
283      }      }
284      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
285      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
286      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
287        # the standard output (tee mode).
288      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
289          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
290              $TeeFlag = 1;              $TeeFlag = 1;
291              $target = substr($target, 1);              $target = substr($target, 1);
292          }          }
293          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
294                # We need to initialize the file (which clears it).
295              open TRACEFILE, $target;              open TRACEFILE, $target;
296              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
297              close TRACEFILE;              close TRACEFILE;
298                # Set to append mode now that the file has been cleared.
299              $Destination = ">$target";              $Destination = ">$target";
300          } else {          } else {
301              $Destination = $target;              $Destination = $target;
# Line 369  Line 307 
307      $SetupCount++;      $SetupCount++;
308  }  }
309    
310  =head3 StandardSetup  =head3 SetLevel
   
 C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>  
   
 This method performs standard command-line parsing and tracing setup. The return  
 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.  
   
 This is a complex method that does a lot of grunt work. The parameters can  
 be more easily understood, however, once they are examined individually.  
   
 The I<categories> parameter is the most obtuse. It is a reference to a list of  
 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  
311    
312      ["Sprout", "SproutLoad", "ERDB"]      Tracer::SetLevel($newLevel);
313    
314  This would cause trace messages in the specified three packages to appear in  Modify the trace level. A higher trace level will cause more messages to appear.
 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.  
315    
316  =over 4  =over 4
317    
318  =item SQL  =item newLevel
   
 Traces SQL commands and activity.  
   
 =item Tracer  
319    
320  Traces error messages and call stacks.  Proposed new trace level.
321    
322  =back  =back
323    
324  C<SQL> is only turned on if the C<-sql> option is specified in the command line.  =cut
 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.  
325    
326      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  sub SetLevel {
327        $TraceLevel = $_[0];
328    }
329    
330  Standard tracing is output to the standard output and echoed to the file  =head3 ParseDate
 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  
331    
332  The default trace level is 2. To get all messages, specify a trace level of 4.      my $time = Tracer::ParseDate($dateString);
 For a genome-by-genome update, use 3.  
333    
334      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  Convert a date into a PERL time number. This method expects a date-like string
335    and parses it into a number. The string must be vaguely date-like or it will
336    return an undefined value. Our requirement is that a month and day be
337    present and that three pieces of the date string (time of day, month and day,
338    year) be separated by likely delimiters, such as spaces, commas, and such-like.
339    
340  would send the trace output to C<traceBruce.log> in the temporary directory.  If a time of day is present, it must be in military time with two digits for
341    everything but the hour.
342    
343  The I<options> parameter is a reference to a hash containing the command-line  The year must be exactly four digits.
 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.  
344    
345  You can specify a different default trace level by setting C<$options->{trace}>  Additional stuff can be in the string. We presume it's time zones or weekdays or something
346  prior to calling this method.  equally innocuous. This means, however, that a sufficiently long sentence with date-like
347    parts in it may be interpreted as a date. Hopefully this will not be a problem.
348    
349  An example at this point would help. Consider, for example, the command-line utility  It should be guaranteed that this method will parse the output of the L</Now> function.
 C<TransactFeatures>. It accepts a list of positional parameters plus the options  
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
350    
351      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  The parameters are as follows.
                         { 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);  
352    
353    =over 4
354    
355  The call to C<ParseCommand> specifies the default values for the options and  =item dateString
 stores the actual options in a hash that is returned as C<$options>. The  
 positional parameters are returned in C<@parameters>.  
356    
357  The following is a sample command line for C<TransactFeatures>.  The date string to convert.
358    
359      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  =item RETURN
360    
361  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
362  parameters, and would find themselves in I<@parameters> after executing the  the date string is invalid. A valid date string must contain a month and day.
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
363    
364      { trace => 2, sql => 0, safe => 0,  =back
       noAlias => 1, start => ' ', tblFiles => 0 }  
365    
366  Use of C<StandardSetup> in this way provides a simple way of performing  =cut
 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.  
367    
368  If the C<background> option is specified on the command line, then the  # Universal month conversion table.
369  standard and error outputs will be directed to files in the temporary  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
370  directory, using the same suffix as the trace file. So, if the command                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
371  line specified                              Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
372                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
373                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
374                                Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
375                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
376                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
377                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
378                                Oct =>  9, October  =>   9, '10' =>  9,
379                                Nov => 10, November =>  10, '11' => 10,
380                                Dec => 11, December =>  11, '12' => 11
381                            };
382    
383      -user=Bruce -background  sub ParseDate {
384        # Get the parameters.
385        my ($dateString) = @_;
386        # Declare the return variable.
387        my $retVal;
388        # Find the month and day of month. There are two ways that can happen. We check for the
389        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
390        # won't be fooled into thinking the month is Sunday.
391        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
392            my ($mon, $mday) = (MONTHS->{$1}, $2);
393            # Insist that the month and day are valid.
394            if (defined($mon) && $2 >= 1 && $2 <= 31) {
395                # Find the time.
396                my ($hour, $min, $sec) = (0, 0, 0);
397                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
398                    ($hour, $min, $sec) = ($1, $2, $3);
399                }
400                # Find the year.
401                my $year;
402                if ($dateString =~ /\b(\d{4})\b/) {
403                    $year = $1;
404                } else {
405                    # Get the default year, which is this one. Note we must convert it to
406                    # the four-digit value expected by "timelocal".
407                    (undef, undef, undef, undef, undef, $year) = localtime();
408                    $year += 1900;
409                }
410                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
411            }
412        }
413        # Return the result.
414        return $retVal;
415    }
416    
417  then the trace output would go to C<traceBruce.log>, the standard output to  =head3 LogErrors
 C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to  
 simplify starting a command in the background.  
418    
419  The user name is also used as the tracing key for L</Emergency Tracing>.      Tracer::LogErrors($fileName);
 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.  
420    
421  Finally, if the special option C<-h> is specified, the option names will  Route the standard error output to a log file.
 be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
422    
423      TransactFeatures -h  =over 4
424    
425  he would see the following output.  =item fileName
426    
427      TransactFeatures [options] command transactionDirectory IDfile  Name of the file to receive the error output.
         -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  
428    
429  The caller has the option of modifying the tracing scheme by placing a value  =back
 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,  
430    
431      { trace => [0, "tracing level (default 0)"],  =cut
        ...  
432    
433  would set the default trace level to 0 instead of E, while  sub LogErrors {
434        # Get the file name.
435        my ($fileName) = @_;
436        # Open the file as the standard error output.
437        open STDERR, '>', $fileName;
438    }
439    
440      { trace => ["2-", "tracing level (default 2)"],  =head3 Trace
        ...  
441    
442  would set the default to 2, but trace only to the log file, not to the      Trace($message);
 standard output.  
443    
444  The parameters to this method are as follows.  Write a trace message to the target location specified in L</TSetup>. If there has not been
445    any prior call to B<TSetup>.
446    
447  =over 4  =over 4
448    
449  =item categories  =item message
450    
451  Reference to a list of tracing category names. These should be names of  Message to write.
 packages whose internal workings will need to be debugged to get the  
 command working.  
452    
453  =item options  =back
454    
455  Reference to a hash containing the legal options for the current command mapped  =cut
 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).  
456    
457  =item parmHelp  sub Trace {
458        # Get the parameters.
459        my ($message) = @_;
460        # Strip off any line terminators at the end of the message. We will add
461        # new-line stuff ourselves.
462        my $stripped = Strip($message);
463        # Compute the caller information.
464        my ($callPackage, $callFile, $callLine) = caller();
465        my $callFileTitle = basename($callFile);
466        # Check the caller.
467        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
468        # Get the timestamp.
469        my $timeStamp = Now();
470        # Build the prefix.
471        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
472        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
473        # Format the message.
474        my $formatted = "$prefix $stripped";
475        # Process according to the destination.
476        if ($Destination eq "TEXT") {
477            # Write the message to the standard output.
478            print "$formatted\n";
479        } elsif ($Destination eq "ERROR") {
480            # Write the message to the error output. Here, we want our prefix fields.
481            print STDERR "$formatted\n";
482        } elsif ($Destination eq "WARN") {
483            # Emit the message to the standard error output. It is presumed that the
484            # error logger will add its own prefix fields, the notable exception being
485            # the caller info.
486            print STDERR "$callerInfo$stripped\n";
487        } elsif ($Destination eq "QUEUE") {
488            # Push the message into the queue.
489            push @Queue, "$formatted";
490        } elsif ($Destination eq "HTML") {
491            # Convert the message to HTML.
492            my $escapedMessage = CGI::escapeHTML($stripped);
493            # The stuff after the first line feed should be pre-formatted.
494            my @lines = split /\s*\n/, $escapedMessage;
495            # Get the normal portion.
496            my $line1 = shift @lines;
497            print "<p>$timeStamp $LastCategory $LastLevel: $line1</p>\n";
498            if (@lines) {
499                print "<pre>" . join("\n", @lines, "<pre>");
500            }
501        } elsif ($Destination =~ m/^>>/) {
502            # Write the trace message to an output file.
503            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
504            # Lock the file.
505            flock TRACING, LOCK_EX;
506            print TRACING "$formatted\n";
507            close TRACING;
508            # If the Tee flag is on, echo it to the standard output.
509            if ($TeeFlag) {
510                print "$formatted\n";
511            }
512        }
513    }
514    
515  A string that vaguely describes the positional parameters. This is used  =head3 TraceDump
 if the user specifies the C<-h> option.  
516    
517  =item argv      TraceDump($title, $object);
518    
519  List of command line parameters, including the option switches, which must  Dump an object to the trace log. This method simply calls the C<Dumper>
520  precede the positional parameters and be prefixed by a hyphen.  function, but routes the output to the trace log instead of returning it
521    as a string. The output is arranged so that it comes out monospaced when
522    it appears in an HTML trace dump.
523    
524  =item RETURN  =over 4
525    
526  Returns a list. The first element of the list is the reference to a hash that  =item title
527  maps the command-line option switches to their values. These will either be the  
528  default values or overrides specified on the command line. The remaining  Title to give to the object being dumped.
529  elements of the list are the position parameters, in order.  
530    =item object
531    
532    Reference to a list, hash, or object to dump.
533    
534  =back  =back
535    
536  =cut  =cut
537    
538  sub StandardSetup {  sub TraceDump {
539        # Get the parameters.
540        my ($title, $object) = @_;
541        # Trace the object.
542        Trace("Object dump for $title:\n" . Dumper($object));
543    }
544    
545    =head3 T
546    
547        my $switch = T($category, $traceLevel);
548    
549        or
550    
551        my $switch = T($traceLevel);
552    
553    Return TRUE if the trace level is at or above a specified value and the specified category
554    is active, else FALSE. If no category is specified, the caller's package name is used.
555    
556    =over 4
557    
558    =item category
559    
560    Category to which the message belongs. If not specified, the caller's package name is
561    used.
562    
563    =item traceLevel
564    
565    Relevant tracing level.
566    
567    =item RETURN
568    
569    TRUE if a message at the specified trace level would appear in the trace, else FALSE.
570    
571    =back
572    
573    =cut
574    
575    sub T {
576        # Declare the return variable.
577        my $retVal = 0;
578        # Only proceed if tracing is turned on.
579        if ($Destination ne "NONE") {
580            # Get the parameters.
581            my ($category, $traceLevel) = @_;
582            if (!defined $traceLevel) {
583                # Here we have no category, so we need to get the calling package.
584                # The calling package is normally the first parameter. If it is
585                # omitted, the first parameter will be the tracelevel. So, the
586                # first thing we do is shift the so-called category into the
587                # $traceLevel variable where it belongs.
588                $traceLevel = $category;
589                my ($package, $fileName, $line) = caller;
590                # If there is no calling package, we default to "main".
591                if (!$package) {
592                    $category = "main";
593                } else {
594                    my @cats = split /::/, $package;
595                    $category = $cats[$#cats];
596                }
597            }
598            # Save the category name and level.
599            $LastCategory = $category;
600            $LastLevel = $traceLevel;
601            # Convert it to lower case before we hash it.
602            $category = lc $category;
603            # Validate the trace level.
604            if (ref $traceLevel) {
605                Confess("Bad trace level.");
606            } elsif (ref $TraceLevel) {
607                Confess("Bad trace config.");
608            }
609            # Make the check. Note that level 0 shows even if the category is turned off.
610            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
611        }
612        # Return the computed result.
613        return $retVal;
614    }
615    
616    =head3 QTrace
617    
618        my $data = QTrace($format);
619    
620    Return the queued trace data in the specified format.
621    
622    =over 4
623    
624    =item format
625    
626    C<html> to format the data as an HTML list, C<text> to format it as straight text.
627    
628    =back
629    
630    =cut
631    
632    sub QTrace {
633        # Get the parameter.
634        my ($format) = @_;
635        # Create the return variable.
636        my $retVal = "";
637        # Only proceed if there is an actual queue.
638        if (@Queue) {
639            # Process according to the format.
640            if ($format =~ m/^HTML$/i) {
641                # Convert the queue into an HTML list.
642                $retVal = "<ul>\n";
643                for my $line (@Queue) {
644                    my $escapedLine = CGI::escapeHTML($line);
645                    $retVal .= "<li>$escapedLine</li>\n";
646                }
647                $retVal .= "</ul>\n";
648            } elsif ($format =~ m/^TEXT$/i) {
649                # Convert the queue into a list of text lines.
650                $retVal = join("\n", @Queue) . "\n";
651            }
652            # Clear the queue.
653            @Queue = ();
654        }
655        # Return the formatted list.
656        return $retVal;
657    }
658    
659    =head3 Confess
660    
661        Confess($message);
662    
663    Trace the call stack and abort the program with the specified message. When used with
664    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
665    So, for example
666    
667        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
668    
669    Will abort the program with a stack trace if the value of C<$recNum> is negative.
670    
671    =over 4
672    
673    =item message
674    
675    Message to include in the trace.
676    
677    =back
678    
679    =cut
680    
681    sub Confess {
682        # Get the parameters.
683        my ($message) = @_;
684        # Set up the category and level.
685        $LastCategory = "(confess)";
686        $LastLevel = 0;
687        # Trace the call stack.
688        Cluck($message);
689        # Abort the program.
690        croak(">>> $message");
691    }
692    
693    =head3 SaveCGI
694    
695        Tracer::SaveCGI($cgi);
696    
697    This method saves the CGI object but does not activate emergency tracing.
698    It is used to allow L</Warn> to work in situations where emergency
699    tracing is contra-indicated (e.g. the wiki).
700    
701    =over 4
702    
703    =item cgi
704    
705    Active CGI query object.
706    
707    =back
708    
709    =cut
710    
711    sub SaveCGI {
712        $SavedCGI = $_[0];
713    }
714    
715    =head3 Warn
716    
717        Warn($message, @options);
718    
719    This method traces an important message. If an RSS feed is configured
720    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
721    then the message will be echoed to the feed. In general, a tracing
722    destination of C<WARN> indicates that the caller is running as a web
723    service in a production environment; however, this is not a requirement.
724    
725    To force warnings into the RSS feed even when the tracing destination
726    is not C<WARN>, simply specify the C<Feed> tracing module. This can be
727    configured automatically when L</StandardSetup> is used.
728    
729    The L</Cluck> method calls this one for its final message. Since
730    L</Confess> calls L</Cluck>, this means that any error which is caught
731    and confessed will put something in the feed. This insures that someone
732    will be alerted relatively quickly when a failure occurs.
733    
734    =over 4
735    
736    =item message
737    
738    Message to be traced.
739    
740    =item options
741    
742    A list containing zero or more options.
743    
744    =back
745    
746    The permissible options are as follows.
747    
748    =over 4
749    
750    =item noStack
751    
752    If specified, then the stack trace is not included in the output.
753    
754    =back
755    
756    =cut
757    
758    sub Warn {
759        # Get the parameters.
760        my $message = shift @_;
761        my %options = map { $_ => 1 } @_;
762        # Save $@;
763        my $savedError = $@;
764        # Trace the message.
765        Trace($message);
766        # This will contain the lock handle. If it's defined, it means we need to unlock.
767        my $lock;
768        # Check for feed forcing.
769        my $forceFeed = exists $Categories{feed};
770        # An error here would be disastrous. Note that if debug mode is specified,
771        # we do this stuff even in a test environment.
772        eval {
773            # Do we need to put this in the RSS feed?
774            if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
775                # Probably. We need to check first, however, to see if it's from an
776                # ignored IP. For non-CGI situations, we default the IP to the self-referent.
777                my $key = "127.0.0.1";
778                if (defined $SavedCGI) {
779                    # Get the IP address.
780                    $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
781                }
782                # Is the IP address in the ignore list?
783                my $found = scalar(grep { $_ eq $key } @FIG_Config::error_ignore_ips);
784                if (! $found) {
785                    # No. We're good. We now need to compute the date, the link, and the title.
786                    # First, the date, in a very specific format.
787                    my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
788                        (tz_local_offset() / 30);
789                    # Environment data goes in here. We start with the date.
790                    my $environment = "$date.  ";
791                    # If we need to recap the message (because it's too long to be a title), we'll
792                    # put it in here.
793                    my $recap;
794                    # Copy the message and remove excess space.
795                    my $title = $message;
796                    $title =~ s/\s+/ /gs;
797                    # If it's too long, we have to split it up.
798                    if (length $title > 60) {
799                        # Put the full message in the environment string.
800                        $recap = $title;
801                        # Excerpt it as the title.
802                        $title = substr($title, 0, 50) . "...";
803                    }
804                    # If we have a CGI object, then this is a web error. Otherwise, it's
805                    # command-line.
806                    if (defined $SavedCGI) {
807                        # We're in a web service. The environment is the user's IP, and the link
808                        # is the URL that got us here.
809                        $environment .= "Event Reported at IP address $key process $$.";
810                        my $url = $SavedCGI->self_url();
811                        # We need the user agent string and (if available) the referrer.
812                        # The referrer will be the link.
813                        $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
814                        if ($ENV{HTTP_REFERER}) {
815                            my $link = $ENV{HTTP_REFERER};
816                            $environment .= " referred from <a href=\"$link\">$link</a>.";
817                        } else {
818                            $environment .= " referrer unknown.";
819                        }
820                        # Close off the sentence with the original link.
821                        $environment .= " URL of event is <a href=\"$url\">$url</a>.";
822                    } else {
823                        # No CGI object, so we're a command-line tool. Use the tracing
824                        # key and the PID as the user identifier, and add the command.
825                        my $key = EmergencyKey();
826                        $environment .= "Event Reported by $key process $$.";
827                        if ($CommandLine) {
828                            # We're in a StandardSetup script, so we have the real command line.
829                            $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
830                        } elsif ($ENV{_}) {
831                            # We're in a BASH script, so the command has been stored in the _ variable.
832                            $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
833                        }
834                    }
835                    # Build a GUID. We use the current time, the title, and the process ID,
836                    # then digest the result.
837                    my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
838                    # Finally, the description. This is a stack trace plus various environmental stuff.
839                    # The trace is optional.
840                    my $stackTrace;
841                    if ($options{noStack}) {
842                        $stackTrace = "";
843                    } else {
844                        my @trace = LongMess();
845                        # Only proceed if we got something back.
846                        if (scalar(@trace) > 0) {
847                            $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
848                            $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
849                        }
850                    }
851                    # We got the stack trace. Now it's time to put it all together.
852                    # We have a goofy thing here in that we need to HTML-escape some sections of the description
853                    # twice. They will be escaped once here, and then once when written by XML::Simple. They are
854                    # unescaped once when processed by the RSS reader, and stuff in the description is treated as
855                    # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
856                    # our <br>s and <pre>s are used to format the description.
857                    $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
858                    my $description = "$recap$environment  $stackTrace";
859                    # Okay, we have all the pieces. Create a hash of the new event.
860                    my $newItem = { title => $title,
861                                    description => $description,
862                                    category => $LastCategory,
863                                    pubDate => $date,
864                                    guid => $guid,
865                                  };
866                    # We need XML capability for this.
867                    require XML::Simple;
868                    # The RSS document goes in here.
869                    my $rss;
870                    # Get the name of the RSS file. It's in the FIG temporary directory.
871                    my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
872                    # Open the config file and lock it.
873                    $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
874                    flock $lock, LOCK_EX;
875                    # Does it exist?
876                    if (-s $fileName) {
877                        # Slurp it in.
878                        $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
879                    } else {
880                        my $size = -s $fileName;
881                        # Create an empty channel.
882                        $rss = {
883                            channel => {
884                                title => 'NMPDR Warning Feed',
885                                link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
886                                description => "Important messages regarding the status of the NMPDR.",
887                                generator => "NMPDR Trace Facility",
888                                docs => "http://blogs.law.harvard.edu/tech/rss",
889                                item => []
890                            },
891                        };
892                    }
893                    # Get the channel object.
894                    my $channel = $rss->{channel};
895                    # Update the last-build date.
896                    $channel->{lastBuildDate} = $date;
897                    # Get the item array.
898                    my $items = $channel->{item};
899                    # Insure it has only 100 entries.
900                    while (scalar @{$items} > 100) {
901                        pop @{$items};
902                    }
903                    # Add our new item at the front.
904                    unshift @{$items}, $newItem;
905                    # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
906                    # the requirements for those.
907                    my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
908                    # Here we put in the root and declaration. The problem is that the root has to have the version attribute
909                    # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
910                    $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
911                    # We don't use Open here because we can't afford an error.
912                    if (open XMLOUT, ">$fileName") {
913                        print XMLOUT $xml;
914                        close XMLOUT;
915                    }
916                }
917            }
918        };
919        if ($@) {
920            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
921            # (which is a good thing).
922            my $error = $@;
923            Trace("Feed Error: $error") if T(Feed => 0);
924        }
925        # Be sure to unlock.
926        if ($lock) {
927            flock $lock, LOCK_UN;
928            undef $lock;
929        }
930        # Restore the error message.
931        $@ = $savedError;
932    }
933    
934    
935    
936    
937    =head3 Assert
938    
939        Assert($condition1, $condition2, ... $conditionN);
940    
941    Return TRUE if all the conditions are true. This method can be used in conjunction with
942    the OR operator and the L</Confess> method as a debugging assert.
943    So, for example
944    
945        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
946    
947    Will abort the program with a stack trace if the value of C<$recNum> is negative.
948    
949    =cut
950    sub Assert {
951        my $retVal = 1;
952        LOOP: for my $condition (@_) {
953            if (! $condition) {
954                $retVal = 0;
955                last LOOP;
956            }
957        }
958        return $retVal;
959    }
960    
961    =head3 Cluck
962    
963        Cluck($message);
964    
965    Trace the call stack. Note that for best results, you should qualify the call with a
966    trace condition. For example,
967    
968        Cluck("Starting record parse.") if T(3);
969    
970    will only trace the stack if the trace level for the package is 3 or more.
971    
972    =over 4
973    
974    =item message
975    
976    Message to include in the trace.
977    
978    =back
979    
980    =cut
981    
982    sub Cluck {
983        # Get the parameters.
984        my ($message) = @_;
985        # Trace what's happening.
986        Trace("Stack trace for event: $message");
987        # Get the stack trace.
988        my @trace = LongMess();
989        # Convert the trace to a series of messages.
990        for my $line (@trace) {
991            # Replace the tab at the beginning with spaces.
992            $line =~ s/^\t/    /;
993            # Trace the line.
994            Trace($line);
995        }
996        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
997        Warn($message);
998    }
999    
1000    =head3 LongMess
1001    
1002        my @lines = Tracer::LongMess();
1003    
1004    Return a stack trace with all tracing methods removed. The return will be in the form of a list
1005    of message strings.
1006    
1007    =cut
1008    
1009    sub LongMess {
1010        # Declare the return variable.
1011        my @retVal = ();
1012        my $confession = longmess("");
1013        for my $line (split /\s*\n/, $confession) {
1014            unless ($line =~ /Tracer\.pm/) {
1015                # Here we have a line worth keeping. Push it onto the result list.
1016                push @retVal, $line;
1017            }
1018        }
1019        # Return the result.
1020        return @retVal;
1021    }
1022    
1023    =head3 ETracing
1024    
1025        ETracing($parameter);
1026    
1027    Set up emergency tracing. Emergency tracing is tracing that is turned
1028    on automatically for any program that calls this method. The emergency
1029    tracing parameters are stored in a a file identified by a tracing key.
1030    If this method is called with a CGI object, then the tracing key is
1031    taken from a cookie. If it is called with no parameters, then the tracing
1032    key is taken from an environment variable. If it is called with a string,
1033    the tracing key is that string.
1034    
1035    =over 4
1036    
1037    =item parameter
1038    
1039    A parameter from which the tracing key is computed. If it is a scalar,
1040    that scalar is used as the tracing key. If it is a CGI object, the
1041    tracing key is taken from the C<IP> cookie. If it is omitted, the
1042    tracing key is taken from the C<TRACING> environment variable. If it
1043    is a CGI object and emergency tracing is not on, the C<Trace> and
1044    C<TF> parameters will be used to determine the type of tracing.
1045    
1046    =back
1047    
1048    =cut
1049    
1050    sub ETracing {
1051        # Get the parameter.
1052        my ($parameter) = @_;
1053        # Check for CGI mode.
1054        if (defined $parameter && ref $parameter eq 'CGI') {
1055            $SavedCGI = $parameter;
1056        } else {
1057            $SavedCGI = undef;
1058        }
1059        # Default to no tracing except errors.
1060        my ($tracing, $dest) = ("0", "WARN");
1061        # Check for emergency tracing.
1062        my $tkey = EmergencyKey($parameter);
1063        my $emergencyFile = EmergencyFileName($tkey);
1064        if (-e $emergencyFile) {
1065            # We have the file. Read in the data.
1066            my @tracing = GetFile($emergencyFile);
1067            # Pull off the time limit.
1068            my $expire = shift @tracing;
1069            # Convert it to seconds.
1070            $expire *= 3600;
1071            # Check the file data.
1072            my $stat = stat($emergencyFile);
1073            my ($now) = gettimeofday;
1074            if ($now - $stat->mtime > $expire) {
1075                # Delete the expired file.
1076                unlink $emergencyFile;
1077            } else {
1078                # Emergency tracing is on. Pull off the destination and
1079                # the trace level;
1080                $dest = shift @tracing;
1081                my $level = shift @tracing;
1082                # Convert the destination to a real tracing destination.
1083                # temp directory.
1084                $dest = EmergencyTracingDest($tkey, $dest);
1085                # Insure Tracer is specified.
1086                my %moduleHash = map { $_ => 1 } @tracing;
1087                $moduleHash{Tracer} = 1;
1088                # Set the trace parameter.
1089                $tracing = join(" ", $level, sort keys %moduleHash);
1090            }
1091        } elsif (defined $SavedCGI) {
1092            # There's no emergency tracing, but we have a CGI object, so check
1093            # for tracing from the form parameters.
1094            if ($SavedCGI->param('Trace')) {
1095                # Here the user has requested tracing via a form.
1096                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1097                $tracing = $SavedCGI->param('Trace') . " Tracer";
1098            }
1099        }
1100        # Setup the tracing we've determined from all the stuff above.
1101        TSetup($tracing, $dest);
1102        # Check to see if we're a web script.
1103        if (defined $SavedCGI) {
1104            # Yes we are. Trace the form and environment data.
1105            TraceParms($SavedCGI);
1106            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1107            # emitted by the script in its raw form.
1108            if (T(Raw => 3)) {
1109                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1110            }
1111        }
1112    }
1113    
1114    =head3 EmergencyFileName
1115    
1116        my $fileName = Tracer::EmergencyFileName($tkey);
1117    
1118    Return the emergency tracing file name. This is the file that specifies
1119    the tracing information.
1120    
1121    =over 4
1122    
1123    =item tkey
1124    
1125    Tracing key for the current program.
1126    
1127    =item RETURN
1128    
1129    Returns the name of the file to contain the emergency tracing information.
1130    
1131    =back
1132    
1133    =cut
1134    
1135    sub EmergencyFileName {
1136        # Get the parameters.
1137        my ($tkey) = @_;
1138        # Compute the emergency tracing file name.
1139        return "$FIG_Config::temp/Emergency$tkey.txt";
1140    }
1141    
1142    =head3 EmergencyFileTarget
1143    
1144        my $fileName = Tracer::EmergencyFileTarget($tkey);
1145    
1146    Return the emergency tracing target file name. This is the file that receives
1147    the tracing output for file-based tracing.
1148    
1149    =over 4
1150    
1151    =item tkey
1152    
1153    Tracing key for the current program.
1154    
1155    =item RETURN
1156    
1157    Returns the name of the file to contain the trace output.
1158    
1159    =back
1160    
1161    =cut
1162    
1163    sub EmergencyFileTarget {
1164        # Get the parameters.
1165        my ($tkey) = @_;
1166        # Compute the emergency tracing file name.
1167        return "$FIG_Config::temp/trace$tkey.log";
1168    }
1169    
1170    =head3 EmergencyTracingDest
1171    
1172        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1173    
1174    This method converts an emergency tracing destination to a real
1175    tracing destination. The main difference is that if the
1176    destination is C<FILE> or C<APPEND>, we convert it to file
1177    output. If the destination is C<DUAL>, we convert it to file
1178    and standard output.
1179    
1180    =over 4
1181    
1182    =item tkey
1183    
1184    Tracing key for this environment.
1185    
1186    =item myDest
1187    
1188    Destination from the emergency tracing file.
1189    
1190    =item RETURN
1191    
1192    Returns a destination that can be passed into L</TSetup>.
1193    
1194    =back
1195    
1196    =cut
1197    
1198    sub EmergencyTracingDest {
1199        # Get the parameters.
1200        my ($tkey, $myDest) = @_;
1201        # Declare the return variable.
1202        my $retVal = $myDest;
1203        # Process according to the destination value.
1204        if ($myDest eq 'FILE') {
1205            $retVal = ">" . EmergencyFileTarget($tkey);
1206        } elsif ($myDest eq 'APPEND') {
1207            $retVal = ">>" . EmergencyFileTarget($tkey);
1208        } elsif ($myDest eq 'DUAL') {
1209            $retVal = "+>" . EmergencyFileTarget($tkey);
1210        } elsif ($myDest eq 'WARN') {
1211            $retVal = "WARN";
1212        }
1213        # Return the result.
1214        return $retVal;
1215    }
1216    
1217    =head3 Emergency
1218    
1219        Emergency($key, $hours, $dest, $level, @modules);
1220    
1221    Turn on emergency tracing. This method is normally invoked over the web from
1222    a debugging console, but it can also be called by the C<trace.pl> script.
1223    The caller specifies the duration of the emergency in hours, the desired tracing
1224    destination, the trace level, and a list of the trace modules to activate.
1225    For the length of the duration, when a program in an environment with the
1226    specified tracing key active invokes a Sprout CGI script, tracing will be
1227    turned on automatically. See L</TSetup> for more about tracing setup and
1228    L</ETracing> for more about emergency tracing.
1229    
1230    =over 4
1231    
1232    =item tkey
1233    
1234    The tracing key. This is used to identify the control file and the trace file.
1235    
1236    =item hours
1237    
1238    Number of hours to keep emergency tracing alive.
1239    
1240    =item dest
1241    
1242    Tracing destination. If no path information is specified for a file
1243    destination, it is put in the FIG temporary directory.
1244    
1245    =item level
1246    
1247    Tracing level. A higher level means more trace messages.
1248    
1249    =item modules
1250    
1251    A list of the tracing modules to activate.
1252    
1253    =back
1254    
1255    =cut
1256    
1257    sub Emergency {
1258        # Get the parameters.
1259        my ($tkey, $hours, $dest, $level, @modules) = @_;
1260        # Create the emergency file.
1261        my $specFile = EmergencyFileName($tkey);
1262        my $outHandle = Open(undef, ">$specFile");
1263        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1264    }
1265    
1266    =head3 EmergencyKey
1267    
1268        my $tkey = EmergencyKey($parameter);
1269    
1270    Return the Key to be used for emergency tracing. This could be an IP address,
1271     a session ID, or a user name, depending on the environment.
1272    
1273    =over 4
1274    
1275    =item parameter
1276    
1277    Parameter defining the method for finding the tracing key. If it is a scalar,
1278    then it is presumed to be the tracing key itself. If it is a CGI object, then
1279    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1280    taken from the C<TRACING> environment variable.
1281    
1282    =item RETURN
1283    
1284    Returns the key to be used for labels in emergency tracing.
1285    
1286    =back
1287    
1288    =cut
1289    
1290    sub EmergencyKey {
1291        # Get the parameters.
1292        my ($parameter) = @_;
1293        # Declare the return variable.
1294        my $retVal;
1295        # Determine the parameter type.
1296        if (! defined $parameter || defined($ENV{TRACING})) {
1297            # Here we're supposed to check the environment. If that fails, we
1298            # get the effective login ID.
1299            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1300        } else {
1301            my $ptype = ref $parameter;
1302            if ($ptype eq 'CGI') {
1303                # Here we were invoked from a web page. Look for a cookie.
1304                $retVal = $parameter->cookie('IP');
1305            } elsif (! $ptype) {
1306                # Here the key was passed in.
1307                $retVal = $parameter;
1308            }
1309        }
1310        # If no luck finding a key, use the PID.
1311        if (! defined $retVal) {
1312            $retVal = $$;
1313        }
1314        # Return the result.
1315        return $retVal;
1316    }
1317    
1318    
1319    =head3 TraceParms
1320    
1321        Tracer::TraceParms($cgi);
1322    
1323    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1324    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1325    
1326    =over 4
1327    
1328    =item cgi
1329    
1330    CGI query object containing the parameters to trace.
1331    
1332    =back
1333    
1334    =cut
1335    
1336    sub TraceParms {
1337        # Get the parameters.
1338        my ($cgi) = @_;
1339        if (T(CGI => 2)) {
1340            # Here we trace the GET-style URL for the script, but only if it's
1341            # relatively small.
1342            my $url = $cgi->url(-relative => 1, -query => 1);
1343            my $len = length($url);
1344            if ($len < 500) {
1345                Trace("[URL] $url");
1346            } elsif ($len > 2048) {
1347                Trace("[URL] URL is too long to use with GET ($len characters).");
1348            } else {
1349                Trace("[URL] URL length is $len characters.");
1350            }
1351        }
1352        if (T(CGI => 3)) {
1353            # Here we want to trace the parameter data.
1354            my @names = $cgi->param;
1355            for my $parmName (sort @names) {
1356                # Note we skip the Trace parameters, which are for our use only.
1357                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1358                    my @values = $cgi->param($parmName);
1359                    Trace("[CGI] $parmName = " . join(", ", @values));
1360                }
1361            }
1362            # Display the request method.
1363            my $method = $cgi->request_method();
1364            Trace("Method: $method");
1365        }
1366        if (T(CGI => 4)) {
1367            # Here we want the environment data too.
1368            for my $envName (sort keys %ENV) {
1369                Trace("[ENV] $envName = $ENV{$envName}");
1370            }
1371        }
1372    }
1373    
1374    =head3 TraceImages
1375    
1376        Tracer::TraceImages($htmlString);
1377    
1378    Trace information about all of an html document's images. The tracing
1379    will be for type "IMG" at level 3. The image's source string
1380    will be displayed. This is generally either the URL of the image or
1381    raw data for the image itself. If the source is too long, only the first 300
1382    characters will be shown at trace level 3. The entire source will be shown,
1383    however, at trace level 4. This method is not very smart, and might catch
1384    Javascript code, but it is still useful when debugging the arcane
1385    behavior of images in multiple browser environments.
1386    
1387    =over 4
1388    
1389    =item htmlString
1390    
1391    HTML text for an outgoing web page.
1392    
1393    =back
1394    
1395    =cut
1396    
1397    sub TraceImages {
1398        # Only proceed if we're at the proper trace level.
1399        if (T(IMG => 3)) {
1400            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1401            # into a variable called "$htmlString". This is because we expect html strings to be
1402            # long, and don't want to copy them any more than we have to.
1403            Trace(length($_[0]) . " characters in web page.");
1404            # Loop through the HTML, culling image tags.
1405            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1406                # Extract the source string and determine whether or not it's too long.
1407                my $srcString = $1;
1408                my $pos = pos($_[0]) - length($srcString);
1409                my $excess = length($srcString) - 300;
1410                # We'll put the display string in here.
1411                my $srcDisplay = $srcString;
1412                # If it's a data string, split it at the comma.
1413                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1414                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1415                # a long string, however, we only show the first 300 characters.
1416                if ($excess > 0 && ! T(IMG => 4)) {
1417                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1418                }
1419                # Output the trace message.
1420                Trace("Image tag at position $pos:\n$srcDisplay");
1421            }
1422        }
1423    }
1424    
1425    =head2 Command-Line Utility Methods
1426    
1427    =head3 SendSMS
1428    
1429        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1430    
1431    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1432    user name, password, and API ID for the relevant account in the hash reference variable
1433    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1434    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1435    is C<2561022>, then the FIG_Config file must contain
1436    
1437        $phone =  { user => 'BruceTheHumanPet',
1438                    password => 'silly',
1439                    api_id => '2561022' };
1440    
1441    The original purpose of this method was to insure Bruce would be notified immediately when the
1442    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1443    when you call this method.
1444    
1445    The message ID will be returned if successful, and C<undef> if an error occurs.
1446    
1447    =over 4
1448    
1449    =item phoneNumber
1450    
1451    Phone number to receive the message, in international format. A United States phone number
1452    would be prefixed by "1". A British phone number would be prefixed by "44".
1453    
1454    =item msg
1455    
1456    Message to send to the specified phone.
1457    
1458    =item RETURN
1459    
1460    Returns the message ID if successful, and C<undef> if the message could not be sent.
1461    
1462    =back
1463    
1464    =cut
1465    
1466    sub SendSMS {
1467        # Get the parameters.
1468        my ($phoneNumber, $msg) = @_;
1469        # Declare the return variable. If we do not change it, C<undef> will be returned.
1470        my $retVal;
1471        # Only proceed if we have phone support.
1472        if (! defined $FIG_Config::phone) {
1473            Trace("Phone support not present in FIG_Config.") if T(1);
1474        } else {
1475            # Get the phone data.
1476            my $parms = $FIG_Config::phone;
1477            # Get the Clickatell URL.
1478            my $url = "http://api.clickatell.com/http/";
1479            # Create the user agent.
1480            my $ua = LWP::UserAgent->new;
1481            # Request a Clickatell session.
1482            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1483                                         password => $parms->{password},
1484                                         api_id => $parms->{api_id},
1485                                         to => $phoneNumber,
1486                                         text => $msg});
1487            # Check for an error.
1488            if (! $resp->is_success) {
1489                Trace("Alert failed.") if T(1);
1490            } else {
1491                # Get the message ID.
1492                my $rstring = $resp->content;
1493                if ($rstring =~ /^ID:\s+(.*)$/) {
1494                    $retVal = $1;
1495                } else {
1496                    Trace("Phone attempt failed with $rstring") if T(1);
1497                }
1498            }
1499        }
1500        # Return the result.
1501        return $retVal;
1502    }
1503    
1504    =head3 StandardSetup
1505    
1506        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1507    
1508    This method performs standard command-line parsing and tracing setup. The return
1509    values are a hash of the command-line options and a list of the positional
1510    parameters. Tracing is automatically set up and the command-line options are
1511    validated.
1512    
1513    This is a complex method that does a lot of grunt work. The parameters can
1514    be more easily understood, however, once they are examined individually.
1515    
1516    The I<categories> parameter is the most obtuse. It is a reference to a list of
1517    special-purpose tracing categories. Most tracing categories are PERL package
1518    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1519    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1520    
1521        ["Sprout", "SproutLoad", "ERDB"]
1522    
1523    This would cause trace messages in the specified three packages to appear in
1524    the output. There are two special tracing categories that are automatically
1525    handled by this method. In other words, if you used L</TSetup> you would need
1526    to include these categories manually, but if you use this method they are turned
1527    on automatically.
1528    
1529    =over 4
1530    
1531    =item SQL
1532    
1533    Traces SQL commands and activity.
1534    
1535    =item Tracer
1536    
1537    Traces error messages and call stacks.
1538    
1539    =back
1540    
1541    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1542    The trace level is specified using the C<-trace> command-line option. For example,
1543    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1544    all tracing at level 3.
1545    
1546        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1547    
1548    Standard tracing is output to the standard output and echoed to the file
1549    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1550    process ID. You can also specify the C<user> parameter to put a user ID
1551    instead of a process ID in the trace file name. So, for example
1552    
1553    The default trace level is 2. To get all messages, specify a trace level of 4.
1554    For a genome-by-genome update, use 3.
1555    
1556        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1557    
1558    would send the trace output to C<traceBruce.log> in the temporary directory.
1559    
1560    The I<options> parameter is a reference to a hash containing the command-line
1561    options, their default values, and an explanation of what they mean. Command-line
1562    options may be in the form of switches or keywords. In the case of a switch, the
1563    option value is 1 if it is specified and 0 if it is not specified. In the case
1564    of a keyword, the value is separated from the option name by an equal sign. You
1565    can see this last in the command-line example above.
1566    
1567    You can specify a different default trace level by setting C<$options->{trace}>
1568    prior to calling this method.
1569    
1570    An example at this point would help. Consider, for example, the command-line utility
1571    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1572    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1573    the following code.
1574    
1575        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1576                            { safe => [0, "use database transactions"],
1577                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1578                              start => [' ', "start with this genome"],
1579                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1580                            "<command> <transactionDirectory> <IDfile>",
1581                          @ARGV);
1582    
1583    
1584    The call to C<ParseCommand> specifies the default values for the options and
1585    stores the actual options in a hash that is returned as C<$options>. The
1586    positional parameters are returned in C<@parameters>.
1587    
1588    The following is a sample command line for C<TransactFeatures>.
1589    
1590        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1591    
1592    Single and double hyphens are equivalent. So, you could also code the
1593    above command as
1594    
1595        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1596    
1597    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1598    parameters, and would find themselves in I<@parameters> after executing the
1599    above code fragment. The tracing would be set to level 2, and the categories
1600    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1601    and C<DocUtils> was included because it came in within the first parameter
1602    to this method. The I<$options> hash would be
1603    
1604        { trace => 2, sql => 0, safe => 0,
1605          noAlias => 1, start => ' ', tblFiles => 0 }
1606    
1607    Use of C<StandardSetup> in this way provides a simple way of performing
1608    standard tracing setup and command-line parsing. Note that the caller is
1609    not even aware of the command-line switches C<-trace> and C<-sql>, which
1610    are used by this method to control the tracing. If additional tracing features
1611    need to be added in the future, they can be processed by this method without
1612    upsetting the command-line utilities.
1613    
1614    If the C<background> option is specified on the command line, then the
1615    standard and error outputs will be directed to files in the temporary
1616    directory, using the same suffix as the trace file. So, if the command
1617    line specified
1618    
1619        -user=Bruce -background
1620    
1621    then the trace output would go to C<traceBruce.log>, the standard output to
1622    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1623    simplify starting a command in the background.
1624    
1625    The user name is also used as the tracing key for L</Emergency Tracing>.
1626    Specifying a value of C<E> for the trace level causes emergency tracing to
1627    be used instead of custom tracing. If the user name is not specified,
1628    the tracing key is taken from the C<Tracing> environment variable. If there
1629    is no value for that variable, the tracing key will be computed from the active
1630    login ID.
1631    
1632    Since the default situation in StandardSetup is to trace to the standard
1633    output, errors that occur in command-line scripts will not generate
1634    RSS events. To force the events, use the C<warn> option.
1635    
1636        TransactFeatures -background -warn register ../xacts IDs.tbl
1637    
1638    Finally, if the special option C<-help> is specified, the option
1639    names will be traced at level 0 and the program will exit without processing.
1640    This provides a limited help capability. For example, if the user enters
1641    
1642        TransactFeatures -help
1643    
1644    he would see the following output.
1645    
1646        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1647            -trace    tracing level (default E)
1648            -sql      trace SQL commands
1649            -safe     use database transactions
1650            -noAlias  do not expect aliases in CHANGE transactions
1651            -start    start with this genome
1652            -tblFiles output TBL files containing the corrected IDs
1653            -forked   do not erase the trace file before tracing
1654    
1655    The caller has the option of modifying the tracing scheme by placing a value
1656    for C<trace> in the incoming options hash. The default value can be overridden,
1657    or the tracing to the standard output can be turned off by suffixing a minus
1658    sign to the trace level. So, for example,
1659    
1660        { trace => [0, "tracing level (default 0)"],
1661           ...
1662    
1663    would set the default trace level to 0 instead of E, while
1664    
1665        { trace => ["2-", "tracing level (default 2)"],
1666           ...
1667    
1668    would set the default to 2, but trace only to the log file, not to the
1669    standard output.
1670    
1671    The parameters to this method are as follows.
1672    
1673    =over 4
1674    
1675    =item categories
1676    
1677    Reference to a list of tracing category names. These should be names of
1678    packages whose internal workings will need to be debugged to get the
1679    command working.
1680    
1681    =item options
1682    
1683    Reference to a hash containing the legal options for the current command mapped
1684    to their default values and descriptions. The user can override the defaults
1685    by specifying the options as command-line switches prefixed by a hyphen.
1686    Tracing-related options may be added to this hash. If the C<-h> option is
1687    specified on the command line, the option descriptions will be used to
1688    explain the options. To turn off tracing to the standard output, add a
1689    minus sign to the value for C<trace> (see above).
1690    
1691    =item parmHelp
1692    
1693    A string that vaguely describes the positional parameters. This is used
1694    if the user specifies the C<-h> option.
1695    
1696    =item argv
1697    
1698    List of command line parameters, including the option switches, which must
1699    precede the positional parameters and be prefixed by a hyphen.
1700    
1701    =item RETURN
1702    
1703    Returns a list. The first element of the list is the reference to a hash that
1704    maps the command-line option switches to their values. These will either be the
1705    default values or overrides specified on the command line. The remaining
1706    elements of the list are the position parameters, in order.
1707    
1708    =back
1709    
1710    =cut
1711    
1712    sub StandardSetup {
1713      # Get the parameters.      # Get the parameters.
1714      my ($categories, $options, $parmHelp, @argv) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
1715      # Get the default tracing key.      # Get the default tracing key.
1716      my $tkey = EmergencyKey();      my $tkey = EmergencyKey();
1717        # Save the command line.
1718        $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1719      # Add the tracing options.      # Add the tracing options.
1720      if (! exists $options->{trace}) {      if (! exists $options->{trace}) {
1721          $options->{trace} = ['E', "tracing level (E for emergency tracing)"];          $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1722        }
1723        if (! exists $options->{forked}) {
1724            $options->{forked} = [0, "keep old trace file"];
1725      }      }
1726      $options->{sql} = [0, "turn on SQL tracing"];      $options->{sql} = [0, "turn on SQL tracing"];
1727      $options->{h} = [0, "display command-line options"];      $options->{help} = [0, "display command-line options"];
1728      $options->{user} = [$tkey, "tracing key"];      $options->{user} = [$tkey, "tracing key"];
1729      $options->{background} = [0, "spool standard and error output"];      $options->{background} = [0, "spool standard and error output"];
1730        $options->{warn} = [0, "send errors to RSS feed"];
1731        $options->{moreTracing} = ["", "comma-delimited list of additional trace modules for debugging"];
1732      # Create a parsing hash from the options hash. The parsing hash      # Create a parsing hash from the options hash. The parsing hash
1733      # contains the default values rather than the default value      # contains the default values rather than the default value
1734      # and the description. While we're at it, we'll memorize the      # and the description. While we're at it, we'll memorize the
# Line 593  Line 1745 
1745      my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);      my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1746      # Get the logfile suffix.      # Get the logfile suffix.
1747      my $suffix = $retOptions->{user};      my $suffix = $retOptions->{user};
1748      # Check for background mode.      # We'll put the trace file name in here. We need it later if background
1749      if ($retOptions->{background}) {      # mode is on.
1750          my $outFileName = "$FIG_Config::temp/out$suffix.log";      my $traceFileName;
         my $errFileName = "$FIG_Config::temp/err$suffix.log";  
         open STDOUT, ">$outFileName";  
         open STDERR, ">$errFileName";  
     }  
1751      # Now we want to set up tracing. First, we need to know if the user      # Now we want to set up tracing. First, we need to know if the user
1752      # wants emergency tracing.      # wants emergency tracing.
1753      if ($retOptions->{trace} eq 'E') {      if ($retOptions->{trace} eq 'E') {
# Line 610  Line 1758 
1758          if ($retOptions->{sql}) {          if ($retOptions->{sql}) {
1759              push @cats, "SQL";              push @cats, "SQL";
1760          }          }
1761            if ($retOptions->{warn}) {
1762                push @cats, "Feed";
1763            }
1764          # Add the default categories.          # Add the default categories.
1765          push @cats, "Tracer";          push @cats, "Tracer";
1766            # Check for more tracing groups.
1767            if ($retOptions->{moreTracing}) {
1768                push @cats, split /,/, $retOptions->{moreTracing};
1769            }
1770          # Next, we create the category string by joining the categories.          # Next, we create the category string by joining the categories.
1771          my $cats = join(" ", @cats);          my $cats = join(" ", @cats);
1772          # Check to determine whether or not the caller wants to turn off tracing          # Check to determine whether or not the caller wants to turn off tracing
# Line 626  Line 1781 
1781          my $traceMode;          my $traceMode;
1782          # Verify that we can open a file in the FIG temporary directory.          # Verify that we can open a file in the FIG temporary directory.
1783          my $traceFileName = "$FIG_Config::temp/trace$suffix.log";          my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1784          if (open TESTTRACE, ">$traceFileName") {          my $traceFileSpec = ($retOptions->{forked} ? ">>$traceFileName" : ">$traceFileName");
1785            if (open TESTTRACE, "$traceFileSpec") {
1786              # Here we can trace to a file.              # Here we can trace to a file.
1787              $traceMode = ">$traceFileName";              $traceMode = ">>$traceFileName";
1788              if ($textOKFlag) {              if ($textOKFlag) {
1789                  # Echo to standard output if the text-OK flag is set.                  # Echo to standard output if the text-OK flag is set.
1790                  $traceMode = "+$traceMode";                  $traceMode = "+$traceMode";
1791              }              }
1792              # Close the test file.              # Close the test file.
1793              close TESTTRACE;              close TESTTRACE;
         } else {  
             # Here we can't trace to a file. We trace to the standard output if it's  
             # okay, and the error log otherwise.  
             if ($textOKFlag) {  
                 $traceMode = "TEXT";  
             } else {  
                 $traceMode = "WARN";  
             }  
         }  
         # Now set up the tracing.  
         TSetup("$traceLevel $cats", $traceMode);  
     }  
     # Check for the "h" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($retOptions->{h}) {  
         $0 =~ m#[/\\](\w+)(\.pl)?$#i;  
         print "$1 [options] $parmHelp\n";  
         for my $key (sort keys %{$options}) {  
             my $name = Pad($key, $longestName, 0, ' ');  
             my $desc = $options->{$key}->[1];  
             if ($options->{$key}->[0]) {  
                 $desc .= " (default " . $options->{$key}->[0] . ")";  
             }  
             print "  $name $desc\n";  
         }  
         exit(0);  
     }  
     # Return the parsed parameters.  
     return ($retOptions, @retParameters);  
 }  
   
 =head3 Setups  
   
 C<< my $count = Tracer::Setups(); >>  
   
 Return the number of times L</TSetup> has been called.  
   
 This method allows for the creation of conditional tracing setups where, for example, we  
 may want to set up tracing if nobody else has done it before us.  
   
 =cut  
   
 sub Setups {  
     return $SetupCount;  
 }  
   
 =head3 Open  
   
 C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  
   
 Open a file.  
   
 The I<$fileSpec> is essentially the second argument of the PERL C<open>  
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
   
     Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  
   
 would open for output appended to the specified file, and  
   
     Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  
   
 would open a pipe that sorts the records written and removes duplicates. Note  
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
   
     my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  
   
 The I<$message> parameter is used if the open fails. If it is set to C<0>, then  
 the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a  
 failed open will throw an exception and the third parameter will be used to construct  
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
   
     Could not open "/usr/spool/news/twitlog"  
   
 Note that the mode characters are automatically cleaned from the file name.  
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
   
     Could not open "/usr/spool/news/twitlog": file not found.  
   
 In some versions of PERL the only error message we get is a number, which  
 corresponds to the C++ C<errno> value.  
   
     Could not open "/usr/spool/news/twitlog": 6.  
   
 =over 4  
   
 =item fileHandle  
   
 File handle. If this parameter is C<undef>, a file handle will be generated  
 and returned as the value of this method.  
   
 =item fileSpec  
   
 File name and mode, as per the PERL C<open> function.  
   
 =item message (optional)  
   
 Error message to use if the open fails. If omitted, a standard error message  
 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>.  
   
 =item RETURN  
   
 Returns the name of the file handle assigned to the file, or C<undef> if the  
 open failed.  
   
 =back  
   
 =cut  
   
 sub Open {  
     # Get the parameters.  
     my ($fileHandle, $fileSpec, $message) = @_;  
     # Attempt to open the file.  
     my $rv = open $fileHandle, $fileSpec;  
     # If the open failed, generate an error message.  
     if (! $rv) {  
         # Save the system error message.  
         my $sysMessage = $!;  
         # See if we need a default message.  
         if (!$message) {  
             # Clean any obvious mode characters and leading spaces from the  
             # filename.  
             my ($fileName) = FindNamePart($fileSpec);  
             $message = "Could not open \"$fileName\"";  
         }  
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
     }  
     # Return the file handle.  
     return $fileHandle;  
 }  
   
 =head3 FindNamePart  
   
 C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>  
   
 Extract the portion of a file specification that contains the file name.  
   
 A file specification is the string passed to an C<open> call. It specifies the file  
 mode and name. In a truly complex situation, it can specify a pipe sequence. This  
 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>.  
   
     >>/usr/fig/myfile.txt  
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
   
 If the method cannot find a file name using its normal methods, it will return the  
 whole incoming string.  
   
 =over 4  
   
 =item fileSpec  
   
 File specification string from which the file name is to be extracted.  
   
 =item RETURN  
   
 Returns a three-element list. The first element contains the file name portion of  
 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.  
   
 =back  
   
 =cut  
 #: Return Type $;  
 sub FindNamePart {  
     # Get the parameters.  
     my ($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);  
 }  
   
 =head3 OpenDir  
   
 C<< my @files = OpenDir($dirName, $filtered, $flag); >>  
   
 Open a directory and return all the file names. This function essentially performs  
 the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  
 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  
 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be  
 filtered out of the return list. If the directory does not open and I<$flag> is not  
 set, an exception is thrown. So, for example,  
   
     my @files = OpenDir("/Volumes/fig/contigs", 1);  
   
 is effectively the same as  
   
     opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
   
 Similarly, the following code  
   
     my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  
   
 Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  
 automatically returns an empty list if the directory fails to open.  
   
 =over 4  
   
 =item dirName  
   
 Name of the directory to open.  
   
 =item filtered  
   
 TRUE if files whose names begin with a period (C<.>) should be automatically removed  
 from the list, else FALSE.  
   
 =item flag  
   
 TRUE if a failure to open is okay, else FALSE  
   
 =back  
   
 =cut  
 #: Return Type @;  
 sub OpenDir {  
     # Get the parameters.  
     my ($dirName, $filtered, $flag) = @_;  
     # Declare the return variable.  
     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;  
1794          } else {          } else {
1795              @retVal = readdir $dirHandle;              # Here we can't trace to a file. Complain about this.
1796                warn "Could not open trace file $traceFileName: $!\n";
1797                # We trace to the standard output if it's
1798                # okay, and the error log otherwise.
1799                if ($textOKFlag) {
1800                    $traceMode = "TEXT";
1801                } else {
1802                    $traceMode = "WARN";
1803          }          }
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
1804      }      }
1805      # Return the result.          # Now set up the tracing.
1806      return @retVal;          TSetup("$traceLevel $cats", $traceMode);
1807  }  }
1808        # Check for background mode.
1809  =head3 SetLevel      if ($retOptions->{background}) {
1810            my $outFileName = "$FIG_Config::temp/out$suffix$$.log";
1811  C<< Tracer::SetLevel($newLevel); >>          my $errFileName = "$FIG_Config::temp/err$suffix$$.log";
1812            # Spool the output.
1813  Modify the trace level. A higher trace level will cause more messages to appear.          open STDOUT, ">$outFileName";
1814            # If we have a trace file, trace the errors to the log. Otherwise,
1815  =over 4          # spool the errors.
1816            if (defined $traceFileName) {
1817  =item newLevel              open STDERR, "| Tracer $traceFileName";
1818            } else {
1819  Proposed new trace level.              open STDERR, ">$errFileName";
   
 =back  
   
 =cut  
   
 sub SetLevel {  
     $TraceLevel = $_[0];  
1820  }  }
1821            # Check for phone support. If we have phone support and a phone number,
1822  =head3 Now          # we want to turn it on.
1823            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1824  C<< my $string = Tracer::Now(); >>              $retOptions->{phone} = $ENV{PHONE};
   
 Return a displayable time stamp containing the local time.  
   
 =cut  
   
 sub Now {  
     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;  
1825  }  }
   
 # Pad a number to 2 digits.  
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
1826  }  }
1827        # Check for the "help" option. If it is specified, dump the command-line
1828  =head3 ParseTraceDate      # options and exit the program.
1829        if ($retOptions->{help}) {
1830  C<< my $time = Tracer::ParseTraceDate($dateString); >>          $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1831            print "$1 [options] $parmHelp\n";
1832  Convert a date from the trace file into a PERL timestamp.          for my $key (sort keys %{$options}) {
1833                my $name = Pad($key, $longestName, 0, ' ');
1834  =over 4              my $desc = $options->{$key}->[1];
1835                if ($options->{$key}->[0]) {
1836  =item dateString                  $desc .= " (default " . $options->{$key}->[0] . ")";
   
 The date string from the trace file. The format of the string is determined by the  
 L</Now> method.  
   
 =item RETURN  
   
 Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if  
 the time string is invalid.  
   
 =back  
   
 =cut  
   
 sub ParseTraceDate {  
     # Get the parameters.  
     my ($dateString) = @_;  
     # Declare the return variable.  
     my $retVal;  
     # Parse the date.  
     if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {  
         # Create a time object. Note we need to convert the day, month,  
         # 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);  
1837      }      }
1838      # Return the result.              print "  $name $desc\n";
     return $retVal;  
1839  }  }
1840            exit(0);
1841  =head3 LogErrors      }
1842        # Trace the options, if applicable.
1843  C<< Tracer::LogErrors($fileName); >>      if (T(3)) {
1844            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1845  Route the standard error output to a log file.          Trace("Selected options: " . join(", ", sort @parms) . ".");
1846        }
1847  =over 4      # Return the parsed parameters.
1848        return ($retOptions, @retParameters);
 =item fileName  
   
 Name of the file to receive the error output.  
   
 =back  
   
 =cut  
   
 sub LogErrors {  
     # Get the file name.  
     my ($fileName) = @_;  
     # Open the file as the standard error output.  
     open STDERR, '>', $fileName;  
1849  }  }
1850    
1851  =head3 ReadOptions  =head3 ReadOptions
1852    
1853  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1854    
1855  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
1856  format  format
# Line 1056  Line 1911 
1911    
1912  =head3 GetOptions  =head3 GetOptions
1913    
1914  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1915    
1916  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
1917  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 1065  Line 1920 
1920    
1921  Consider the following example.  Consider the following example.
1922    
1923  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1924    
1925  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1926  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 1073  Line 1928 
1928  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1929  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1930    
1931  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1932    
1933  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1934    
# Line 1117  Line 1972 
1972    
1973  =head3 MergeOptions  =head3 MergeOptions
1974    
1975  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
1976    
1977  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
1978  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 1149  Line 2004 
2004      }      }
2005  }  }
2006    
2007  =head3 Trace  =head3 UnparseOptions
   
 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); >>  
2008    
2009      or      my $optionString = Tracer::UnparseOptions(\%options);
   
 C<< my $switch = T($traceLevel); >>  
2010    
2011  Return TRUE if the trace level is at or above a specified value and the specified category  Convert an option hash into a command-line string. This will not
2012  is active, else FALSE. If no category is specified, the caller's package name is used.  necessarily be the same text that came in, but it will nonetheless
2013    produce the same ultimate result when parsed by L</StandardSetup>.
2014    
2015  =over 4  =over 4
2016    
2017  =item category  =item options
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
2018    
2019  Relevant tracing level.  Reference to a hash of options to convert into an option string.
2020    
2021  =item RETURN  =item RETURN
2022    
2023  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  Returns a string that will parse to the same set of options when
2024    parsed by L</StandardSetup>.
2025    
2026  =back  =back
2027    
2028  =cut  =cut
2029    
2030  sub T {  sub UnparseOptions {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
2031          # Get the parameters.          # Get the parameters.
2032          my ($category, $traceLevel) = @_;      my ($options) = @_;
2033          if (!defined $traceLevel) {      # The option segments will be put in here.
2034              # Here we have no category, so we need to get the calling package.      my @retVal = ();
2035              # The calling package is normally the first parameter. If it is      # Loop through the options.
2036              # omitted, the first parameter will be the tracelevel. So, the      for my $key (keys %$options) {
2037              # first thing we do is shift the so-called category into the          # Get the option value.
2038              # $traceLevel variable where it belongs.          my $value = $options->{$key};
2039              $traceLevel = $category;          # Only use it if it's nonempty.
2040              my ($package, $fileName, $line) = caller;          if (defined $value && $value ne "") {
2041              # If there is no calling package, we default to "main".              my $segment = "--$key=$value";
2042              if (!$package) {              # Quote it if necessary.
2043                  $category = "main";              if ($segment =~ /[ |<>*]/) {
2044              } else {                  $segment = '"' . $segment . '"';
                 $category = $package;  
             }  
2045          }          }
2046          # Save the category name.              # Add it to the return list.
2047          $LastCategory = $category;              push @retVal, $segment;
         # 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.");  
2048          }          }
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
2049      }      }
2050      # Return the computed result.      # Return the result.
2051      return $retVal;      return join(" ", @retVal);
2052  }  }
2053    
2054  =head3 ParseCommand  =head3 ParseCommand
2055    
2056  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2057    
2058  Parse a command line consisting of a list of parameters. The initial parameters may be option  Parse a command line consisting of a list of parameters. The initial parameters may be option
2059  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2060  off and merged into a table of default options. The remainder of the command line is  off and merged into a table of default options. The remainder of the command line is
2061  returned as a list of positional arguments. For example, consider the following invocation.  returned as a list of positional arguments. For example, consider the following invocation.
2062    
2063  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2064    
2065  In this case, the list @words will be treated as a command line. There are two options available,  In this case, the list @words will be treated as a command line and there are two options available,
2066  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
2067    
2068  C<< -logFile=error.log apple orange rutabaga >>      -logFile=error.log apple orange rutabaga
2069    
2070  then at the end of the invocation, C<$options> will be  then at the end of the invocation, C<$options> will be
2071    
2072  C<< { errors => 0, logFile => 'error.log' } >>      { errors => 0, logFile => 'error.log' }
2073    
2074  and C<@arguments> will contain  and C<@arguments> will contain
2075    
2076  C<< apple orange rutabaga >>      apple orange rutabaga
2077    
2078  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2079  support for quote characters.  support for quote characters. Options can be specified with single or double hyphens.
2080    
2081  =over 4  =over 4
2082    
# Line 1320  Line 2101 
2101      my ($optionTable, @inputList) = @_;      my ($optionTable, @inputList) = @_;
2102      # Process any options in the input list.      # Process any options in the input list.
2103      my %overrides = ();      my %overrides = ();
2104      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2105          # Get the current option.          # Get the current option.
2106          my $arg = shift @inputList;          my $arg = shift @inputList;
2107          # Pull out the option name.          # Pull out the option name.
2108          $arg =~ /^-([^=]*)/g;          $arg =~ /^--?([^=]*)/g;
2109          my $name = $1;          my $name = $1;
2110          # Check for an option value.          # Check for an option value.
2111          if ($arg =~ /\G=(.*)$/g) {          if ($arg =~ /\G=(.*)$/g) {
# Line 1346  Line 2127 
2127      return ($optionTable, @retVal);      return ($optionTable, @retVal);
2128  }  }
2129    
 =head3 Escape  
2130    
2131  C<< my $codedString = Tracer::Escape($realString); >>  =head2 File Utility Methods
2132    
2133  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  =head3 GetFile
2134  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
2135  result is to reverse the effect of L</UnEscape>.      my @fileContents = Tracer::GetFile($fileName);
2136    
2137        or
2138    
2139        my $fileContents = Tracer::GetFile($fileName);
2140    
2141    Return the entire contents of a file. In list context, line-ends are removed and
2142    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2143    
2144  =over 4  =over 4
2145    
2146  =item realString  =item fileName
2147    
2148  String to escape.  Name of the file to read.
2149    
2150  =item RETURN  =item RETURN
2151    
2152  Escaped equivalent of the real string.  In a list context, returns the entire file as a list with the line terminators removed.
2153    In a scalar context, returns the entire file as a string. If an error occurs opening
2154    the file, an empty list will be returned.
2155    
2156  =back  =back
2157    
2158  =cut  =cut
2159    
2160  sub Escape {  sub GetFile {
2161      # Get the parameter.      # Get the parameters.
2162      my ($realString) = @_;      my ($fileName) = @_;
2163      # Initialize the return variable.      # Declare the return variable.
2164      my $retVal = "";      my @retVal = ();
2165      # Loop through the parameter string, looking for sequences to escape.      # Open the file for input.
2166      while (length $realString > 0) {      my $handle = Open(undef, "<$fileName");
2167          # Look for the first sequence to escape.      # Read the whole file into the return variable, stripping off any terminator
2168          if ($realString =~ /^(.*?)([\n\t\r\\])/) {      # characters.
2169              # Here we found it. The text preceding the sequence is in $1. The sequence      my $lineCount = 0;
2170              # itself is in $2. First, move the clear text to the return variable.      while (my $line = <$handle>) {
2171              $retVal .= $1;          $lineCount++;
2172              # Strip the processed section off the real string.          $line = Strip($line);
2173              $realString = substr $realString, (length $2) + (length $1);          push @retVal, $line;
             # 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 = "";  
2174          }          }
2175        # Close it.
2176        close $handle;
2177        my $actualLines = @retVal;
2178        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2179        # Return the file's contents in the desired format.
2180        if (wantarray) {
2181            return @retVal;
2182        } else {
2183            return join "\n", @retVal;
2184      }      }
     # Return the result.  
     return $retVal;  
2185  }  }
2186    
2187  =head3 UnEscape  =head3 PutFile
2188    
2189  C<< my $realString = Tracer::UnEscape($codedString); >>      Tracer::PutFile($fileName, \@lines);
2190    
2191  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Write out a file from a list of lines of text.
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
2192    
2193  =over 4  =over 4
2194    
2195  =item codedString  =item fileName
2196    
2197  String to un-escape.  Name of the output file.
2198    
2199  =item RETURN  =item lines
2200    
2201  Returns a copy of the original string with the escape sequences converted to their actual  Reference to a list of text lines. The lines will be written to the file in order, with trailing
2202  values.  new-line characters. Alternatively, may be a string, in which case the string will be written without
2203    modification.
2204    
2205  =back  =back
2206    
2207  =cut  =cut
2208    
2209  sub UnEscape {  sub PutFile {
2210      # Get the parameter.      # Get the parameters.
2211      my ($codedString) = @_;      my ($fileName, $lines) = @_;
2212      # Initialize the return variable.      # Open the output file.
2213      my $retVal = "";      my $handle = Open(undef, ">$fileName");
2214      # Only proceed if the incoming string is nonempty.      # Count the lines written.
2215      if (defined $codedString) {      if (ref $lines ne 'ARRAY') {
2216          # Loop through the parameter string, looking for escape sequences. We can't do          # Here we have a scalar, so we write it raw.
2217          # translating because it causes problems with the escaped slash. ("\\t" becomes          print $handle $lines;
2218          # "\<tab>" no matter what we do.)          Trace("Scalar put to file $fileName.") if T(File => 3);
         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;  
                 }  
2219              } else {              } else {
2220                  # Here there are no more escape sequences. The rest of the string is          # Write the lines one at a time.
2221                  # transferred unmodified.          my $count = 0;
2222                  $retVal .= $codedString;          for my $line (@{$lines}) {
2223                  $codedString = "";              print $handle "$line\n";
2224              }              $count++;
2225          }          }
2226            Trace("$count lines put to file $fileName.") if T(File => 3);
2227      }      }
2228      # Return the result.      # Close the output file.
2229      return $retVal;      close $handle;
2230  }  }
2231    
2232  =head3 ParseRecord  =head3 ParseRecord
2233    
2234  C<< my @fields = Tracer::ParseRecord($line); >>      my @fields = Tracer::ParseRecord($line);
2235    
2236  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2237  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
# Line 1508  Line 2276 
2276    
2277  =head3 Merge  =head3 Merge
2278    
2279  C<< my @mergedList = Tracer::Merge(@inputList); >>      my @mergedList = Tracer::Merge(@inputList);
2280    
2281  Sort a list of strings and remove duplicates.  Sort a list of strings and remove duplicates.
2282    
# Line 1554  Line 2322 
2322      return @inputList;      return @inputList;
2323  }  }
2324    
2325  =head3 Percent  =head3 Open
2326    
2327  C<< my $percent = Tracer::Percent($number, $base); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2328    
2329  Returns the percent of the base represented by the given number. If the base  Open a file.
2330  is zero, returns zero.  
2331    The I<$fileSpec> is essentially the second argument of the PERL C<open>
2332    function. The mode is specified using Unix-like shell information. So, for
2333    example,
2334    
2335        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2336    
2337    would open for output appended to the specified file, and
2338    
2339        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2340    
2341    would open a pipe that sorts the records written and removes duplicates. Note
2342    the use of file handle syntax in the Open call. To use anonymous file handles,
2343    code as follows.
2344    
2345        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2346    
2347    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2348    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2349    failed open will throw an exception and the third parameter will be used to construct
2350    an error message. If the parameter is omitted, a standard message is constructed
2351    using the file spec.
2352    
2353        Could not open "/usr/spool/news/twitlog"
2354    
2355    Note that the mode characters are automatically cleaned from the file name.
2356    The actual error message from the file system will be captured and appended to the
2357    message in any case.
2358    
2359        Could not open "/usr/spool/news/twitlog": file not found.
2360    
2361    In some versions of PERL the only error message we get is a number, which
2362    corresponds to the C++ C<errno> value.
2363    
2364        Could not open "/usr/spool/news/twitlog": 6.
2365    
2366  =over 4  =over 4
2367    
2368  =item number  =item fileHandle
2369    
2370  Percent numerator.  File handle. If this parameter is C<undef>, a file handle will be generated
2371    and returned as the value of this method.
2372    
2373  =item base  =item fileSpec
2374    
2375  Percent base.  File name and mode, as per the PERL C<open> function.
2376    
2377    =item message (optional)
2378    
2379    Error message to use if the open fails. If omitted, a standard error message
2380    will be generated. In either case, the error information from the file system
2381    is appended to the message. To specify a conditional open that does not throw
2382    an error if it fails, use C<0>.
2383    
2384  =item RETURN  =item RETURN
2385    
2386  Returns the percentage of the base represented by the numerator.  Returns the name of the file handle assigned to the file, or C<undef> if the
2387    open failed.
2388    
2389    =back
2390    
2391    =cut
2392    
2393    sub Open {
2394        # Get the parameters.
2395        my ($fileHandle, $fileSpec, $message) = @_;
2396        # Attempt to open the file.
2397        my $rv = open $fileHandle, $fileSpec;
2398        # If the open failed, generate an error message.
2399        if (! $rv) {
2400            # Save the system error message.
2401            my $sysMessage = $!;
2402            # See if we need a default message.
2403            if (!$message) {
2404                # Clean any obvious mode characters and leading spaces from the
2405                # filename.
2406                my ($fileName) = FindNamePart($fileSpec);
2407                $message = "Could not open \"$fileName\"";
2408            }
2409            # Terminate with an error using the supplied message and the
2410            # error message from the file system.
2411            Confess("$message: $!");
2412        }
2413        # Return the file handle.
2414        return $fileHandle;
2415    }
2416    
2417    =head3 FindNamePart
2418    
2419        my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2420    
2421    Extract the portion of a file specification that contains the file name.
2422    
2423    A file specification is the string passed to an C<open> call. It specifies the file
2424    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2425    method assumes that the file name is whatever follows the first angle bracket
2426    sequence.  So, for example, in the following strings the file name is
2427    C</usr/fig/myfile.txt>.
2428    
2429        >>/usr/fig/myfile.txt
2430        </usr/fig/myfile.txt
2431        | sort -u > /usr/fig/myfile.txt
2432    
2433    If the method cannot find a file name using its normal methods, it will return the
2434    whole incoming string.
2435    
2436    =over 4
2437    
2438    =item fileSpec
2439    
2440    File specification string from which the file name is to be extracted.
2441    
2442    =item RETURN
2443    
2444    Returns a three-element list. The first element contains the file name portion of
2445    the specified string, or the whole string if a file name cannot be found via normal
2446    methods. The second element contains the start position of the file name portion and
2447    the third element contains the length.
2448    
2449    =back
2450    
2451    =cut
2452    #: Return Type $;
2453    sub FindNamePart {
2454        # Get the parameters.
2455        my ($fileSpec) = @_;
2456        # Default to the whole input string.
2457        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2458        # Parse out the file name if we can.
2459        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2460            $retVal = $2;
2461            $len = length $retVal;
2462            $pos = (length $fileSpec) - (length $3) - $len;
2463        }
2464        # Return the result.
2465        return ($retVal, $pos, $len);
2466    }
2467    
2468    =head3 OpenDir
2469    
2470        my @files = OpenDir($dirName, $filtered, $flag);
2471    
2472    Open a directory and return all the file names. This function essentially performs
2473    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2474    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2475    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2476    filtered out of the return list. If the directory does not open and I<$flag> is not
2477    set, an exception is thrown. So, for example,
2478    
2479        my @files = OpenDir("/Volumes/fig/contigs", 1);
2480    
2481    is effectively the same as
2482    
2483        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2484        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2485    
2486    Similarly, the following code
2487    
2488        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2489    
2490    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2491    automatically returns an empty list if the directory fails to open.
2492    
2493    =over 4
2494    
2495    =item dirName
2496    
2497    Name of the directory to open.
2498    
2499    =item filtered
2500    
2501    TRUE if files whose names begin with a period (C<.>) should be automatically removed
2502    from the list, else FALSE.
2503    
2504    =item flag
2505    
2506    TRUE if a failure to open is okay, else FALSE
2507    
2508  =back  =back
2509    
2510  =cut  =cut
2511    #: Return Type @;
2512  sub Percent {  sub OpenDir {
2513      # Get the parameters.      # Get the parameters.
2514      my ($number, $base) = @_;      my ($dirName, $filtered, $flag) = @_;
2515      # Declare the return variable.      # Declare the return variable.
2516      my $retVal = 0;      my @retVal = ();
2517      # Compute the percent.      # Open the directory.
2518      if ($base != 0) {      if (opendir(my $dirHandle, $dirName)) {
2519          $retVal = $number * 100 / $base;          # The directory opened successfully. Get the appropriate list according to the
2520            # strictures of the filter parameter.
2521            if ($filtered) {
2522                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2523            } else {
2524                @retVal = readdir $dirHandle;
2525            }
2526        } elsif (! $flag) {
2527            # Here the directory would not open and it's considered an error.
2528            Confess("Could not open directory $dirName.");
2529      }      }
2530      # Return the result.      # Return the result.
2531      return $retVal;      return @retVal;
2532  }  }
2533    
 =head3 GetFile  
   
 C<< my @fileContents = Tracer::GetFile($fileName); >>  
2534    
2535      or  =head3 Insure
2536    
2537  C<< my $fileContents = Tracer::GetFile($fileName); >>      Insure($dirName, $chmod);
2538    
2539  Return the entire contents of a file. In list context, line-ends are removed and  Insure a directory is present.
 each line is a list element. In scalar context, line-ends are replaced by C<\n>.  
2540    
2541  =over 4  =over 4
2542    
2543  =item fileName  =item dirName
2544    
2545  Name of the file to read.  Name of the directory to check. If it does not exist, it will be created.
2546    
2547  =item RETURN  =item chmod (optional)
2548    
2549  In a list context, returns the entire file as a list with the line terminators removed.  Security privileges to be given to the directory if it is created.
 In a scalar context, returns the entire file as a string. If an error occurs opening  
 the file, an empty list will be returned.  
2550    
2551  =back  =back
2552    
2553  =cut  =cut
2554    
2555  sub GetFile {  sub Insure {
2556      # Get the parameters.      my ($dirName, $chmod) = @_;
2557      my ($fileName) = @_;      if (! -d $dirName) {
2558      # Declare the return variable.          Trace("Creating $dirName directory.") if T(2);
2559      my @retVal = ();          eval {
2560      # Open the file for input.              mkpath $dirName;
2561      my $handle = Open(undef, "<$fileName");              # If we have permissions specified, set them here.
2562      # Read the whole file into the return variable, stripping off any terminator              if (defined($chmod)) {
2563      # characters.                  chmod $chmod, $dirName;
2564      my $lineCount = 0;              }
2565      while (my $line = <$handle>) {          };
2566          $lineCount++;          if ($@) {
2567          $line = Strip($line);              Confess("Error creating $dirName: $@");
         push @retVal, $line;  
2568      }      }
     # Close it.  
     close $handle;  
     my $actualLines = @retVal;  
     Trace("$actualLines lines read from file $fileName.") if T(File => 2);  
     # Return the file's contents in the desired format.  
     if (wantarray) {  
         return @retVal;  
     } else {  
         return join "\n", @retVal;  
2569      }      }
2570  }  }
2571    
2572  =head3 PutFile  =head3 ChDir
2573    
2574  C<< Tracer::PutFile($fileName, \@lines); >>      ChDir($dirName);
2575    
2576  Write out a file from a list of lines of text.  Change to the specified directory.
2577    
2578  =over 4  =over 4
2579    
2580  =item fileName  =item dirName
   
 Name of the output file.  
   
 =item lines  
2581    
2582  Reference to a list of text lines. The lines will be written to the file in order, with trailing  Name of the directory to which we want to change.
 new-line characters. Alternatively, may be a string, in which case the string will be written without  
 modification.  
2583    
2584  =back  =back
2585    
2586  =cut  =cut
2587    
2588  sub PutFile {  sub ChDir {
2589      # Get the parameters.      my ($dirName) = @_;
2590      my ($fileName, $lines) = @_;      if (! -d $dirName) {
2591      # Open the output file.          Confess("Cannot change to directory $dirName: no such directory.");
     my $handle = Open(undef, ">$fileName");  
     # Count the lines written.  
     if (ref $lines ne 'ARRAY') {  
         # Here we have a scalar, so we write it raw.  
         print $handle $lines;  
         Trace("Scalar put to file $fileName.") if T(File => 3);  
2592      } else {      } else {
2593          # Write the lines one at a time.          Trace("Changing to directory $dirName.") if T(File => 4);
2594          my $count = 0;          my $okFlag = chdir $dirName;
2595          for my $line (@{$lines}) {          if (! $okFlag) {
2596              print $handle "$line\n";              Confess("Error switching to directory $dirName.");
             $count++;  
2597          }          }
         Trace("$count lines put to file $fileName.") if T(File => 3);  
2598      }      }
     # Close the output file.  
     close $handle;  
2599  }  }
2600    
2601  =head3 QTrace  =head3 SetPermissions
2602    
2603  C<< my $data = QTrace($format); >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2604    
2605  Return the queued trace data in the specified format.  Set the permissions for a directory and all the files and folders inside it.
2606    In addition, the group ownership will be changed to the specified value.
2607    
2608    This method is more vulnerable than most to permission and compatability
2609    problems, so it does internal error recovery.
2610    
2611  =over 4  =over 4
2612    
2613  =item format  =item dirName
2614    
2615  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Name of the directory to process.
2616    
2617    =item group
2618    
2619    Name of the group to be assigned.
2620    
2621    =item mask
2622    
2623    Permission mask. Bits that are C<1> in this mask will be ORed into the
2624    permission bits of any file or directory that does not already have them
2625    set to 1.
2626    
2627    =item otherMasks
2628    
2629    Map of search patterns to permission masks. If a directory name matches
2630    one of the patterns, that directory and all its members and subdirectories
2631    will be assigned the new pattern. For example, the following would
2632    assign 0664 to most files, but would use 0777 for directories named C<tmp>.
2633    
2634        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2635    
2636    The list is ordered, so the following would use 0777 for C<tmp1> and
2637    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2638    
2639        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2640                                                       '^tmp' => 0666);
2641    
2642    Note that the pattern matches are all case-insensitive, and only directory
2643    names are matched, not file names.
2644    
2645  =back  =back
2646    
2647  =cut  =cut
2648    
2649  sub QTrace {  sub SetPermissions {
2650      # Get the parameter.      # Get the parameters.
2651      my ($format) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2652      # Create the return variable.      # Set up for error recovery.
2653      my $retVal = "";      eval {
2654      # Only proceed if there is an actual queue.          # Switch to the specified directory.
2655      if (@Queue) {          ChDir($dirName);
2656          # Process according to the format.          # Get the group ID.
2657          if ($format =~ m/^HTML$/i) {          my $gid = getgrnam($group);
2658              # Convert the queue into an HTML list.          # Get the mask for tracing.
2659              $retVal = "<ul>\n";          my $traceMask = sprintf("%04o", $mask) . "($mask)";
2660              for my $line (@Queue) {          Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2661                  my $escapedLine = CGI::escapeHTML($line);          my $fixCount = 0;
2662                  $retVal .= "<li>$escapedLine</li>\n";          my $lookCount = 0;
2663            # @dirs will be a stack of directories to be processed.
2664            my @dirs = (getcwd());
2665            while (scalar(@dirs) > 0) {
2666                # Get the current directory.
2667                my $dir = pop @dirs;
2668                # Check for a match to one of the specified directory names. To do
2669                # that, we need to pull the individual part of the name off of the
2670                # whole path.
2671                my $simpleName = $dir;
2672                if ($dir =~ m!/([^/]+)$!) {
2673                    $simpleName = $1;
2674              }              }
2675              $retVal .= "</ul>\n";              Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2676          } elsif ($format =~ m/^TEXT$/i) {              # Search for a match.
2677              # Convert the queue into a list of text lines.              my $match = 0;
2678              $retVal = join("\n", @Queue) . "\n";              my $i;
2679                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2680                    my $pattern = $otherMasks[$i];
2681                    if ($simpleName =~ /$pattern/i) {
2682                        $match = 1;
2683          }          }
         # Clear the queue.  
         @Queue = ();  
2684      }      }
2685      # Return the formatted list.              # Find out if we have a match. Note we use $i-1 because the loop added 2
2686      return $retVal;              # before terminating due to the match.
2687                if ($match && $otherMasks[$i-1] != $mask) {
2688                    # This directory matches one of the incoming patterns, and it's
2689                    # a different mask, so we process it recursively with that mask.
2690                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2691                } else {
2692                    # Here we can process normally. Get all of the non-hidden members.
2693                    my @submems = OpenDir($dir, 1);
2694                    for my $submem (@submems) {
2695                        # Get the full name.
2696                        my $thisMem = "$dir/$submem";
2697                        Trace("Checking member $thisMem.") if T(4);
2698                        $lookCount++;
2699                        if ($lookCount % 1000 == 0) {
2700                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2701                        }
2702                        # Fix the group.
2703                        chown -1, $gid, $thisMem;
2704                        # Insure this member is not a symlink.
2705                        if (! -l $thisMem) {
2706                            # Get its info.
2707                            my $fileInfo = stat $thisMem;
2708                            # Only proceed if we got the info. Otherwise, it's a hard link
2709                            # and we want to skip it anyway.
2710                            if ($fileInfo) {
2711                                my $fileMode = $fileInfo->mode;
2712                                if (($fileMode & $mask) != $mask) {
2713                                    # Fix this member.
2714                                    $fileMode |= $mask;
2715                                    chmod $fileMode, $thisMem;
2716                                    $fixCount++;
2717                                }
2718                                # If it's a subdirectory, stack it.
2719                                if (-d $thisMem) {
2720                                    push @dirs, $thisMem;
2721                                }
2722                            }
2723                        }
2724                    }
2725                }
2726            }
2727            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2728        };
2729        # Check for an error.
2730        if ($@) {
2731            Confess("SetPermissions error: $@");
2732        }
2733  }  }
2734    
2735  =head3 Confess  =head3 GetLine
   
 C<< Confess($message); >>  
   
 Trace the call stack and abort the program with the specified message. When used with  
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
2736    
2737  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my @data = Tracer::GetLine($handle);
2738    
2739  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Read a line of data from a tab-delimited file.
2740    
2741  =over 4  =over 4
2742    
2743  =item message  =item handle
2744    
2745  Message to include in the trace.  Open file handle from which to read.
2746    
2747    =item RETURN
2748    
2749    Returns a list of the fields in the record read. The fields are presumed to be
2750    tab-delimited. If we are at the end of the file, then an empty list will be
2751    returned. If an empty line is read, a single list item consisting of a null
2752    string will be returned.
2753    
2754  =back  =back
2755    
2756  =cut  =cut
2757    
2758  sub Confess {  sub GetLine {
2759      # Get the parameters.      # Get the parameters.
2760      my ($message) = @_;      my ($handle) = @_;
2761      # Trace the call stack.      # Declare the return variable.
2762      Cluck($message);      my @retVal = ();
2763      # Abort the program.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2764      croak(">>> $message");      # Read from the file.
2765        my $line = <$handle>;
2766        # Only proceed if we found something.
2767        if (defined $line) {
2768            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2769            # upload control and have a nonstandard EOL combination.
2770            $line =~ s/(\r|\n)+$//;
2771            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2772            if (T(File => 4)) {
2773                my $escapedLine = $line;
2774                $escapedLine =~ s/\n/\\n/g;
2775                $escapedLine =~ s/\r/\\r/g;
2776                $escapedLine =~ s/\t/\\t/g;
2777                Trace("Line read: -->$escapedLine<--");
2778  }  }
2779            # If the line is empty, return a single empty string; otherwise, parse
2780  =head3 Assert          # it into fields.
2781            if ($line eq "") {
2782  C<< Assert($condition1, $condition2, ... $conditionN); >>              push @retVal, "";
2783            } else {
2784  Return TRUE if all the conditions are true. This method can be used in conjunction with              push @retVal, split /\t/,$line;
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
   
 C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  
   
 Will abort the program with a stack trace if the value of C<$recNum> is negative.  
   
 =cut  
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
2785          }          }
2786        } else {
2787            # Trace the reason the read failed.
2788            Trace("End of file: $!") if T(File => 3);
2789      }      }
2790      return $retVal;      # Return the result.
2791        return @retVal;
2792  }  }
2793    
2794  =head3 Cluck  =head3 PutLine
2795    
2796  C<< Cluck($message); >>      Tracer::PutLine($handle, \@fields, $eol);
2797    
2798  Trace the call stack. Note that for best results, you should qualify the call with a  Write a line of data to a tab-delimited file. The specified field values will be
2799  trace condition. For example,  output in tab-separated form, with a trailing new-line.
2800    
2801  C<< Cluck("Starting record parse.") if T(3); >>  =over 4
2802    
2803  will only trace the stack if the trace level for the package is 3 or more.  =item handle
2804    
2805  =over 4  Output file handle.
2806    
2807  =item message  =item fields
2808    
2809  Message to include in the trace.  List of field values.
2810    
2811    =item eol (optional)
2812    
2813    End-of-line character (default is "\n").
2814    
2815  =back  =back
2816    
2817  =cut  =cut
2818    
2819  sub Cluck {  sub PutLine {
2820      # Get the parameters.      # Get the parameters.
2821      my ($message) = @_;      my ($handle, $fields, $eol) = @_;
2822      # Trace what's happening.      # Write the data.
2823      Trace("Stack trace for event: $message");      print $handle join("\t", @{$fields}) . ($eol || "\n");
     my $confession = longmess($message);  
     # Convert the confession to a series of trace messages. Note we skip any  
     # messages relating to calls into Tracer.  
     for my $line (split /\s*\n/, $confession) {  
         Trace($line) if ($line !~ /Tracer\.pm/);  
     }  
2824  }  }
2825    
 =head3 Min  
   
 C<< my $min = Min($value1, $value2, ... $valueN); >>  
2826    
2827  Return the minimum argument. The arguments are treated as numbers.  =head3 PrintLine
2828    
2829  =over 4      Tracer::PrintLine($line);
2830    
2831  =item $value1, $value2, ... $valueN  Print a line of text with a trailing new-line.
2832    
2833  List of numbers to compare.  =over 4
2834    
2835  =item RETURN  =item line
2836    
2837  Returns the lowest number in the list.  Line of text to print.
2838    
2839  =back  =back
2840    
2841  =cut  =cut
2842    
2843  sub Min {  sub PrintLine {
2844      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2845      my ($retVal, @values) = @_;      my ($line) = @_;
2846      # Loop through the remaining parameters, looking for the lowest.      # Print the line.
2847      for my $value (@values) {      print "$line\n";
         if ($value < $retVal) {  
             $retVal = $value;  
         }  
     }  
     # Return the minimum found.  
     return $retVal;  
2848  }  }
2849    
 =head3 Max  
   
 C<< my $max = Max($value1, $value2, ... $valueN); >>  
2850    
2851  Return the maximum argument. The arguments are treated as numbers.  =head2 Other Useful Methods
   
 =over 4  
   
 =item $value1, $value2, ... $valueN  
   
 List of numbers to compare.  
2852    
2853  =item RETURN  =head3 IDHASH
2854    
2855  Returns the highest number in the list.      my $hash = SHTargetSearch::IDHASH(@keys);
2856    
2857  =back  This is a dinky little method that converts a list of values to a reference
2858    to hash of values to labels. The values and labels are the same.
2859    
2860  =cut  =cut
2861    
2862  sub Max {  sub IDHASH {
2863      # Get the parameters. Note that we prime the return value with the first parameter.      my %retVal = map { $_ => $_ } @_;
2864      my ($retVal, @values) = @_;      return \%retVal;
     # Loop through the remaining parameters, looking for the highest.  
     for my $value (@values) {  
         if ($value > $retVal) {  
             $retVal = $value;  
         }  
     }  
     # Return the maximum found.  
     return $retVal;  
2865  }  }
2866    
2867  =head3 AddToListMap  =head3 Pluralize
2868    
2869  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>      my $plural = Tracer::Pluralize($word);
2870    
2871  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  This is a very simple pluralization utility. It adds an C<s> at the end
2872  is created for the key. Otherwise, the new value is pushed onto the list.  of the input word unless it already ends in an C<s>, in which case it
2873    adds C<es>.
2874    
2875  =over 4  =over 4
2876    
2877  =item hash  =item word
   
 Reference to the target hash.  
   
 =item key  
2878    
2879  Key for which the value is to be added.  Singular word to pluralize.
2880    
2881  =item value1, value2, ... valueN  =item RETURN
2882    
2883  List of values to add to the key's value list.  Returns the probable plural form of the word.
2884    
2885  =back  =back
2886    
2887  =cut  =cut
2888    
2889  sub AddToListMap {  sub Pluralize {
2890      # Get the parameters.      # Get the parameters.
2891      my ($hash, $key, @values) = @_;      my ($word) = @_;
     # Process according to whether or not the key already has a value.  
     if (! exists $hash->{$key}) {  
         $hash->{$key} = [@values];  
     } else {  
         push @{$hash->{$key}}, @values;  
     }  
 }  
   
 =head3 DebugMode  
   
 C<< if (Tracer::DebugMode) { ...code... } >>  
   
 Return TRUE if debug mode has been turned on, else abort.  
   
 Certain CGI scripts are too dangerous to exist in the production  
 environment. This method provides a simple way to prevent them  
 from working unless they are explicitly turned on by creating a password  
 cookie via the B<SetPassword> script.  If debugging mode  
 is not turned on, an error will occur.  
   
 =cut  
   
 sub DebugMode {  
2892      # Declare the return variable.      # Declare the return variable.
2893      my $retVal = 0;      my $retVal;
2894      # Check the debug configuration.      if ($word =~ /s$/) {
2895      my $password = CGI::cookie("DebugMode");          $retVal = $word . 'es';
     my $encrypted = Digest::MD5::md5_hex($password);  
     if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {  
         $retVal = 1;  
2896      } else {      } else {
2897          # Here debug mode is off, so we generate an error.          $retVal = $word . 's';
         Confess("Cannot use this facility without logging in.");  
2898      }      }
2899      # Return the determination indicator.      # Return the result.
2900      return $retVal;      return $retVal;
2901  }  }
2902    
2903  =head3 Strip  =head3 Numeric
2904    
2905  C<< my $string = Tracer::Strip($line); >>      my $okFlag = Tracer::Numeric($string);
2906    
2907  Strip all line terminators off a string. This is necessary when dealing with files  Return the value of the specified string if it is numeric, or an undefined value
2908  that may have been transferred back and forth several times among different  if it is not numeric.
 operating environments.  
2909    
2910  =over 4  =over 4
2911    
2912  =item line  =item string
2913    
2914  Line of text to be stripped.  String to check.
2915    
2916  =item RETURN  =item RETURN
2917    
2918  The same line of text with all the line-ending characters chopped from the end.  Returns the numeric value of the string if successful, or C<undef> if the string
2919    is not numeric.
2920    
2921  =back  =back
2922    
2923  =cut  =cut
2924    
2925  sub Strip {  sub Numeric {
2926      # Get a copy of the parameter string.      # Get the parameters.
2927      my ($string) = @_;      my ($string) = @_;
2928      my $retVal = (defined $string ? $string : "");      # We'll put the value in here if we succeed.
2929      # Strip the line terminator characters.      my $retVal;
2930      $retVal =~ s/(\r|\n)+$//g;      # Get a working copy of the string.
2931        my $copy = $string;
2932        # Trim leading and trailing spaces.
2933        $copy =~ s/^\s+//;
2934        $copy =~ s/\s+$//;
2935        # Check the result.
2936        if ($copy =~ /^[+-]?\d+$/) {
2937            $retVal = $copy;
2938        } elsif ($copy =~ /^([+-]\d+|\d*)[eE][+-]?\d+$/) {
2939            $retVal = $copy;
2940        } elsif ($copy =~ /^([+-]\d+|\d*)\.\d*([eE][+-]?\d+)?$/) {
2941            $retVal = $copy;
2942        }
2943      # Return the result.      # Return the result.
2944      return $retVal;      return $retVal;
2945  }  }
2946    
 =head3 Pad  
2947    
2948  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>  =head3 ParseParm
2949    
2950  Pad a string to a specified length. The pad character will be a      my $listValue = Tracer::ParseParm($string);
2951  space, and the padding will be on the right side unless specified  
2952  in the third parameter.  Convert a parameter into a list reference. If the parameter is undefined,
2953    an undefined value will be returned. Otherwise, it will be parsed as a
2954    comma-separated list of values.
2955    
2956  =over 4  =over 4
2957    
2958  =item string  =item string
2959    
2960  String to be padded.  Incoming string.
   
 =item len  
   
 Desired length of the padded string.  
   
 =item left (optional)  
   
 TRUE if the string is to be left-padded; otherwise it will be padded on the right.  
   
 =item padChar (optional)  
   
 Character to use for padding. The default is a space.  
2961    
2962  =item RETURN  =item RETURN
2963    
2964  Returns a copy of the original string with the pad character added to the  Returns a reference to a list of values, or C<undef> if the incoming value
2965  specified end so that it achieves the desired length.  was undefined.
2966    
2967  =back  =back
2968    
2969  =cut  =cut
2970    
2971  sub Pad {  sub ParseParm {
2972      # Get the parameters.      # Get the parameters.
2973      my ($string, $len, $left, $padChar) = @_;      my ($string) = @_;
2974      # Compute the padding character.      # Declare the return variable.
2975      if (! defined $padChar) {      my $retVal;
2976          $padChar = " ";      # Check for data.
2977      }      if (defined $string) {
2978      # Compute the number of spaces needed.          # We have some, so split it into a list.
2979      my $needed = $len - length $string;          $retVal = [ split /\s*,\s*/, $string];
     # Copy the string into the return variable.  
     my $retVal = $string;  
     # Only proceed if padding is needed.  
     if ($needed > 0) {  
         # Create the pad string.  
         my $pad = $padChar x $needed;  
         # Affix it to the return value.  
         if ($left) {  
             $retVal = $pad . $retVal;  
         } else {  
             $retVal .= $pad;  
         }  
2980      }      }
2981      # Return the result.      # Return the result.
2982      return $retVal;      return $retVal;
2983  }  }
2984    
2985  =head3 EOF  =head3 Now
2986    
2987  This is a constant that is lexically greater than any useful string.      my $string = Tracer::Now();
2988    
2989    Return a displayable time stamp containing the local time. Whatever format this
2990    method produces must be parseable by L</ParseDate>.
2991    
2992  =cut  =cut
2993    
2994  sub EOF {  sub Now {
2995      return "\xFF\xFF\xFF\xFF\xFF";      return DisplayTime(time);
2996  }  }
2997    
2998  =head3 TICK  =head3 DisplayTime
   
 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  
2999    
3000      TICK("./protein.cgi")      my $string = Tracer::DisplayTime($time);
3001    
3002  it will work correctly in both environments.  Convert a time value to a displayable time stamp. Whatever format this
3003    method produces must be parseable by L</ParseDate>.
3004    
3005  =over 4  =over 4
3006    
3007  =item commandString  =item time
3008    
3009  The command string to pass to the system.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
3010    
3011  =item RETURN  =item RETURN
3012    
3013  Returns the standard output from the specified command, as a list.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
3014    
3015  =back  =back
3016    
3017  =cut  =cut
3018  #: Return Type @;  
3019  sub TICK {  sub DisplayTime {
3020      # Get the parameters.      my ($time) = @_;
3021      my ($commandString) = @_;      my $retVal = "(n/a)";
3022      # Chop off the dot-slash if this is Windows.      if (defined $time) {
3023      if ($FIG_Config::win_mode) {          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
3024          $commandString =~ s!^\./!!;          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
3025                      _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
3026      }      }
3027      # Activate the command and return the result.      return $retVal;
     return `$commandString`;  
3028  }  }
3029    
3030  =head3 ScriptSetup  # Pad a number to 2 digits.
3031    sub _p2 {
3032  C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>      my ($value) = @_;
3033        $value = "0$value" if ($value < 10);
3034  Perform standard tracing and debugging setup for scripts. The value returned is      return $value;
3035  the CGI object followed by a pre-built variable hash.  }
3036    
3037  The C<Trace> form parameter is used to determine whether or not tracing is active and  =head3 Escape
 which trace modules (other than C<Tracer> itself) should be turned on. Specifying  
 the C<CGI> trace module will trace parameter and environment information. Parameters are  
 traced at level 3 and environment variables at level 4. To trace to a file instead of to  
 the web page, set C<TF> to 1. At the end of the script, the client should call  
 L</ScriptFinish> to output the web page.  
3038    
3039  In some situations, it is not practical to invoke tracing via form parameters. For this      my $codedString = Tracer::Escape($realString);
3040  situation, you can turn on emergency tracing from the debugging control panel.  
3041  Tracing will then be turned on automatically for all programs that use the L</ETracing>  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
3042  method, which includes every program that uses this method or L</StandardSetup>.  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
3043    result is to reverse the effect of L</UnEscape>.
3044    
3045  =over 4  =over 4
3046    
3047  =item noTrace (optional)  =item realString
3048    
3049  If specified, tracing will be suppressed. This is useful if the script wants to set up  String to escape.
 tracing manually.  
3050    
3051  =item RETURN  =item RETURN
3052    
3053  Returns a two-element list consisting of a CGI query object and a variable hash for  Escaped equivalent of the real string.
 the output page.  
3054    
3055  =back  =back
3056    
3057  =cut  =cut
3058    
3059  sub ScriptSetup {  sub Escape {
3060      # Get the parameters.      # Get the parameter.
3061      my ($noTrace) = @_;      my ($realString) = @_;
3062      # Get the CGI query object.      # Initialize the return variable.
3063      my $cgi = CGI->new();      my $retVal = "";
3064      # Set up tracing if it's not suppressed.      # Loop through the parameter string, looking for sequences to escape.
3065      ETracing($cgi) unless $noTrace;      while (length $realString > 0) {
3066      # Create the variable hash.          # Look for the first sequence to escape.
3067      my $varHash = { results => '' };          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
3068      # Return the query object and variable hash.              # Here we found it. The text preceding the sequence is in $1. The sequence
3069      return ($cgi, $varHash);              # itself is in $2. First, move the clear text to the return variable.
3070                $retVal .= $1;
3071                # Strip the processed section off the real string.
3072                $realString = substr $realString, (length $2) + (length $1);
3073                # Get the matched character.
3074                my $char = $2;
3075                # If we have a CR, we are done.
3076                if ($char ne "\r") {
3077                    # It's not a CR, so encode the escape sequence.
3078                    $char =~ tr/\t\n/tn/;
3079                    $retVal .= "\\" . $char;
3080                }
3081            } else {
3082                # Here there are no more escape sequences. The rest of the string is
3083                # transferred unmodified.
3084                $retVal .= $realString;
3085                $realString = "";
3086            }
3087        }
3088        # Return the result.
3089        return $retVal;
3090  }  }
3091    
3092  =head3 ETracing  =head3 UnEscape
3093    
3094  C<< ETracing($parameter); >>      my $realString = Tracer::UnEscape($codedString);
3095    
3096  Set up emergency tracing. Emergency tracing is tracing that is turned  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
3097  on automatically for any program that calls this method. The emergency  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
3098  tracing parameters are stored in a a file identified by a tracing key.  be deleted.
 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.  
3099    
3100  =over 4  =over 4
3101    
3102  =item parameter  =item codedString
3103    
3104  A parameter from which the tracing key is computed. If it is a scalar,  String to un-escape.
3105  that scalar is used as the tracing key. If it is a CGI object, the  
3106  tracing key is taken from the C<IP> cookie. If it is omitted, the  =item RETURN
3107  tracing key is taken from the C<TRACING> environment variable. If it  
3108  is a CGI object and emergency tracing is not on, the C<Trace> and  Returns a copy of the original string with the escape sequences converted to their actual
3109  C<TF> parameters will be used to determine the type of tracing.  values.
3110    
3111  =back  =back
3112    
3113  =cut  =cut
3114    
3115  sub ETracing {  sub UnEscape {
3116      # Get the parameter.      # Get the parameter.
3117      my ($parameter) = @_;      my ($codedString) = @_;
3118      # Check for CGI mode.      # Initialize the return variable.
3119      my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);      my $retVal = "";
3120      # Default to no tracing except errors.      # Only proceed if the incoming string is nonempty.
3121      my ($tracing, $dest) = ("0", "WARN");      if (defined $codedString) {
3122      # Check for emergency tracing.          # Loop through the parameter string, looking for escape sequences. We can't do
3123      my $tkey = EmergencyKey($parameter);          # translating because it causes problems with the escaped slash. ("\\t" becomes
3124      my $emergencyFile = EmergencyFileName($tkey);          # "\<tab>" no matter what we do.)
3125      if (-e $emergencyFile) {          while (length $codedString > 0) {
3126          # We have the file. Read in the data.              # Look for the first escape sequence.
3127          my @tracing = GetFile($emergencyFile);              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
3128          # Pull off the time limit.                  # Here we found it. The text preceding the sequence is in $1. The sequence
3129          my $expire = shift @tracing;                  # itself is in $2. First, move the clear text to the return variable.
3130          # Convert it to seconds.                  $retVal .= $1;
3131          $expire *= 3600;                  $codedString = substr $codedString, (2 + length $1);
3132          # Check the file data.                  # Get the escape value.
3133          my $stat = stat($emergencyFile);                  my $char = $2;
3134          my ($now) = gettimeofday;                  # If we have a "\r", we are done.
3135          if ($now - $stat->mtime > $expire) {                  if ($char ne 'r') {
3136              # Delete the expired file.                      # Here it's not an 'r', so we convert it.
3137              unlink $emergencyFile;                      $char =~ tr/\\tn/\\\t\n/;
3138          } else {                      $retVal .= $char;
             # Emergency tracing is on. Pull off the destination and  
             # the trace level;  
             $dest = shift @tracing;  
             my $level = shift @tracing;  
             # Convert the destination to a real tracing destination.  
             # temp directory.  
             $dest = EmergencyTracingDest($tkey, $dest);  
             # Insure Tracer is specified.  
             my %moduleHash = map { $_ => 1 } @tracing;  
             $moduleHash{Tracer} = 1;  
             # Set the trace parameter.  
             $tracing = join(" ", $level, sort keys %moduleHash);  
3139          }          }
3140      } elsif (defined $cgi) {              } else {
3141          # There's no emergency tracing, but we have a CGI object, so check                  # Here there are no more escape sequences. The rest of the string is
3142          # for tracing from the form parameters.                  # transferred unmodified.
3143          if ($cgi->param('Trace')) {                  $retVal .= $codedString;
3144              # Here the user has requested tracing via a form.                  $codedString = "";
             $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");  
             $tracing = $cgi->param('Trace') . " Tracer";  
3145          }          }
3146      }      }
     # Setup the tracing we've determined from all the stuff above.  
     TSetup($tracing, $dest);  
     # If we're a web script, trace the parameter and environment data.  
     if (defined $cgi) {  
         TraceParms($cgi);  
3147      }      }
3148        # Return the result.
3149        return $retVal;
3150  }  }
3151    
3152  =head3 EmergencyFileName  =head3 Percent
3153    
3154  C<< my $fileName = Tracer::EmergencyFileName($tkey); >>      my $percent = Tracer::Percent($number, $base);
3155    
3156  Return the emergency tracing file name. This is the file that specifies  Returns the percent of the base represented by the given number. If the base
3157  the tracing information.  is zero, returns zero.
3158    
3159  =over 4  =over 4
3160    
3161  =item tkey  =item number
3162    
3163  Tracing key for the current program.  Percent numerator.
3164    
3165    =item base
3166    
3167    Percent base.
3168    
3169  =item RETURN  =item RETURN
3170    
3171  Returns the name of the file to contain the emergency tracing information.  Returns the percentage of the base represented by the numerator.
3172    
3173  =back  =back
3174    
3175  =cut  =cut
3176    
3177  sub EmergencyFileName {  sub Percent {
3178      # Get the parameters.      # Get the parameters.
3179      my ($tkey) = @_;      my ($number, $base) = @_;
3180      # Compute the emergency tracing file name.      # Declare the return variable.
3181      return "$FIG_Config::temp/Emergency$tkey.txt";      my $retVal = 0;
3182        # Compute the percent.
3183        if ($base != 0) {
3184            $retVal = $number * 100 / $base;
3185        }
3186        # Return the result.
3187        return $retVal;
3188  }  }
3189    
3190  =head3 EmergencyFileTarget  =head3 In
   
 C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>  
   
 Return the emergency tracing target file name. This is the file that receives  
 the tracing output for file-based tracing.  
   
 =over 4  
   
 =item tkey  
   
 Tracing key for the current program.  
   
 =item RETURN  
3191    
3192  Returns the name of the file to contain the trace output.      my $flag = Tracer::In($value, $min, $max);
3193    
3194  =back  Return TRUE if the value is between the minimum and the maximum, else FALSE.
3195    
3196  =cut  =cut
3197    
3198  sub EmergencyFileTarget {  sub In {
3199      # Get the parameters.      return ($_[0] <= $_[2] && $_[0] >= $_[1]);
     my ($tkey) = @_;  
     # Compute the emergency tracing file name.  
     return "$FIG_Config::temp/trace$tkey.log";  
3200  }  }
3201    
 =head3 EmergencyTracingDest  
3202    
3203  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>  =head3 Constrain
3204    
3205  This method converts an emergency tracing destination to a real      my $constrained = Constrain($value, $min, $max);
3206  tracing destination. The main difference is that if the  
3207  destination is C<FILE> or C<APPEND>, we convert it to file  Modify a numeric value to bring it to a point in between a maximum and a minimum.
 output.  
3208    
3209  =over 4  =over 4
3210    
3211  =item tkey  =item value
3212    
3213  Tracing key for this environment.  Value to constrain.
3214    
3215  =item myDest  =item min (optional)
3216    
3217  Destination from the emergency tracing file.  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3218    
3219    =item max (optional)
3220    
3221    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3222    
3223  =item RETURN  =item RETURN
3224    
3225  Returns a destination that can be passed into L</TSetup>.  Returns the incoming value, constrained according to the other parameters.
3226    
3227  =back  =back
3228    
3229  =cut  =cut
3230    
3231  sub EmergencyTracingDest {  sub Constrain {
3232      # Get the parameters.      # Get the parameters.
3233      my ($tkey, $myDest) = @_;      my ($value, $min, $max) = @_;
3234      # Declare the return variable.      # Declare the return variable.
3235      my $retVal;      my $retVal = $value;
3236      # Process according to the destination value.      # Apply the minimum constraint.
3237      if ($myDest eq 'FILE') {      if (defined $min && $retVal < $min) {
3238          $retVal = ">" . EmergencyFileTarget($tkey);          $retVal = $min;
3239      } elsif ($myDest eq 'APPEND') {      }
3240          $retVal = ">>" . EmergencyFileTarget($tkey);      # Apply the maximum constraint.
3241      } else {      if (defined $max && $retVal > $max) {
3242          $retVal = $myDest;          $retVal = $max;
3243      }      }
3244      # Return the result.      # Return the result.
3245      return $retVal;      return $retVal;
3246  }  }
3247    
3248  =head3 Emergency  =head3 Min
3249    
3250  C<< Emergency($key, $hours, $dest, $level, @modules); >>      my $min = Min($value1, $value2, ... $valueN);
3251    
3252  Turn on emergency tracing. This method can only be invoked over the web and is  Return the minimum argument. The arguments are treated as numbers.
 should not be called if debug mode is off. The caller specifies the duration of the  
 emergency in hours, the desired tracing destination, the trace level,  
 and a list of the trace modules to activate. For the length of the duration, when a  
 program in an environment with the specified tracing key active invokes a Sprout  
 CGI script, tracing will be turned on automatically. See L</TSetup> for more  
 about tracing setup and L</ETracing> for more about emergency tracing.  
3253    
3254  =over 4  =over 4
3255    
3256  =item tkey  =item $value1, $value2, ... $valueN
   
 The tracing key. This is used to identify the control file and the trace file.  
   
 =item hours  
   
 Number of hours to keep emergency tracing alive.  
   
 =item dest  
   
 Tracing destination. If no path information is specified for a file  
 destination, it is put in the FIG temporary directory.  
   
 =item level  
3257    
3258  Tracing level. A higher level means more trace messages.  List of numbers to compare.
3259    
3260  =item modules  =item RETURN
3261    
3262  A list of the tracing modules to activate.  Returns the lowest number in the list.
3263    
3264  =back  =back
3265    
3266  =cut  =cut
3267    
3268  sub Emergency {  sub Min {
3269      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3270      my ($tkey, $hours, $dest, $level, @modules) = @_;      my ($retVal, @values) = @_;
3271      # Create the emergency file.      # Loop through the remaining parameters, looking for the lowest.
3272      my $specFile = EmergencyFileName($tkey);      for my $value (@values) {
3273      my $outHandle = Open(undef, ">$specFile");          if ($value < $retVal) {
3274      print $outHandle join("\n", $hours, $dest, $level, @modules, "");              $retVal = $value;
3275            }
3276        }
3277        # Return the minimum found.
3278        return $retVal;
3279  }  }
3280    
3281  =head3 EmergencyKey  =head3 Max
3282    
3283  C<< my $tkey = EmergencyKey($parameter); >>      my $max = Max($value1, $value2, ... $valueN);
3284    
3285  Return the Key to be used for emergency tracing. This could be an IP address,  Return the maximum argument. The arguments are treated as numbers.
  a session ID, or a user name, depending on the environment.  
3286    
3287  =over 4  =over 4
3288    
3289  =item parameter  =item $value1, $value2, ... $valueN
3290    
3291  Parameter defining the method for finding the tracing key. If it is a scalar,  List of numbers to compare.
 then it is presumed to be the tracing key itself. If it is a CGI object, then  
 the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is  
 taken from the C<TRACING> environment variable.  
3292    
3293  =item RETURN  =item RETURN
3294    
3295  Returns the key to be used for labels in emergency tracing.  Returns the highest number in the list.
3296    
3297  =back  =back
3298    
3299  =cut  =cut
3300    
3301  sub EmergencyKey {  sub Max {
3302      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3303      my ($parameter) = @_;      my ($retVal, @values) = @_;
3304      # Declare the return variable.      # Loop through the remaining parameters, looking for the highest.
3305      my $retVal;      for my $value (@values) {
3306      # Determine the parameter type.          if ($value > $retVal) {
3307      if (! defined $parameter) {              $retVal = $value;
         # Here we're supposed to check the environment.  
         $retVal = $ENV{TRACING};  
     } else {  
         my $ptype = ref $parameter;  
         if ($ptype eq 'CGI') {  
             # Here we were invoked from a web page. Look for a cookie.  
             $retVal = $parameter->cookie('IP');  
         } elsif (! $ptype) {  
             # Here the key was passed in.  
             $retVal = $parameter;  
         }  
3308      }      }
     # If no luck finding a key, use the PID.  
     if (! defined $retVal) {  
         $retVal = $$;  
3309      }      }
3310      # Return the result.      # Return the maximum found.
3311      return $retVal;      return $retVal;
3312  }  }
3313    
3314    =head3 Strip
3315    
3316  =head3 TraceParms      my $string = Tracer::Strip($line);
   
 C<< Tracer::TraceParms($cgi); >>  
3317    
3318  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Strip all line terminators off a string. This is necessary when dealing with files
3319  at level CGI => 4.  that may have been transferred back and forth several times among different
3320    operating environments.
3321    
3322  =over 4  =over 4
3323    
3324  =item cgi  =item line
3325    
3326  CGI query object containing the parameters to trace.  Line of text to be stripped.
3327    
3328    =item RETURN
3329    
3330    The same line of text with all the line-ending characters chopped from the end.
3331    
3332  =back  =back
3333    
3334  =cut  =cut
3335    
3336  sub TraceParms {  sub Strip {
3337      # Get the parameters.      # Get a copy of the parameter string.
3338      my ($cgi) = @_;      my ($string) = @_;
3339      if (T(CGI => 3)) {      my $retVal = (defined $string ? $string : "");
3340          # Here we want to trace the parameter data.      # Strip the line terminator characters.
3341          my @names = $cgi->param;      $retVal =~ s/(\r|\n)+$//g;
3342          for my $parmName (sort @names) {      # Return the result.
3343              # Note we skip the Trace parameters, which are for our use only.      return $retVal;
             if ($parmName ne 'Trace' && $parmName ne 'TF') {  
                 my @values = $cgi->param($parmName);  
                 Trace("CGI: $parmName = " . join(", ", @values));  
             }  
         }  
         # Display the request method.  
         my $method = $cgi->request_method();  
         Trace("Method: $method");  
     }  
     if (T(CGI => 4)) {  
         # Here we want the environment data too.  
         for my $envName (sort keys %ENV) {  
             Trace("ENV: $envName = $ENV{$envName}");  
         }  
     }  
3344  }  }
3345    
3346  =head3 ScriptFinish  =head3 Trim
   
 C<< ScriptFinish($webData, $varHash); >>  
   
 Output a web page at the end of a script. Either the string to be output or the  
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
   
 A typical standard script would loook like the following.  
   
     BEGIN {  
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
3347    
3348      my ($cgi, $varHash) = ScriptSetup();      my $string = Tracer::Trim($line);
     eval {  
         # ... get data from $cgi, put it in $varHash ...  
     };  
     if ($@) {  
         Trace("Script Error: $@") if T(0);  
     }  
     ScriptFinish("Html/MyTemplate.html", $varHash);  
3349    
3350  The idea here is that even if the script fails, you'll see trace messages and  Trim all spaces from the beginning and ending of a string.
 useful output.  
3351    
3352  =over 4  =over 4
3353    
3354  =item webData  =item line
3355    
3356  A string containing either the full web page to be written to the output or the  Line of text to be trimmed.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3357    
3358  =item varHash (optional)  =item RETURN
3359    
3360  If specified, then a reference to a hash mapping variable names for a template  The same line of text with all whitespace chopped off either end.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3361    
3362  =back  =back
3363    
3364  =cut  =cut
3365    
3366  sub ScriptFinish {  sub Trim {
3367      # Get the parameters.      # Get a copy of the parameter string.
3368      my ($webData, $varHash) = @_;      my ($string) = @_;
3369      # Check for a template file situation.      my $retVal = (defined $string ? $string : "");
3370      my $outputString;      # Strip the front spaces.
3371      if (defined $varHash) {      $retVal =~ s/^\s+//;
3372          # Here we have a template file. We need to determine the template type.      # Strip the back spaces.
3373          my $template;      $retVal =~ s/\s+$//;
3374          if ($FIG_Config::template_url && $webData =~ /\.php$/) {      # Return the result.
3375              $template = "$FIG_Config::template_url/$webData";      return $retVal;
         } 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;  
     }  
     # Write the output string.  
     print $outputString;  
3376  }  }
3377    
3378  =head3 Insure  =head3 Pad
3379    
3380  C<< Insure($dirName); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3381    
3382  Insure a directory is present.  Pad a string to a specified length. The pad character will be a
3383    space, and the padding will be on the right side unless specified
3384    in the third parameter.
3385    
3386  =over 4  =over 4
3387    
3388  =item dirName  =item string
   
 Name of the directory to check. If it does not exist, it will be created.  
3389    
3390  =back  String to be padded.
3391    
3392  =cut  =item len
3393    
3394  sub Insure {  Desired length of the padded string.
     my ($dirName) = @_;  
     if (! -d $dirName) {  
         Trace("Creating $dirName directory.") if T(File => 2);  
         eval { mkpath $dirName; };  
         if ($@) {  
             Confess("Error creating $dirName: $@");  
         }  
     }  
 }  
3395    
3396  =head3 ChDir  =item left (optional)
3397    
3398  C<< ChDir($dirName); >>  TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3399    
3400  Change to the specified directory.  =item padChar (optional)
3401    
3402  =over 4  Character to use for padding. The default is a space.
3403    
3404  =item dirName  =item RETURN
3405    
3406  Name of the directory to which we want to change.  Returns a copy of the original string with the pad character added to the
3407    specified end so that it achieves the desired length.
3408    
3409  =back  =back
3410    
3411  =cut  =cut
3412    
3413  sub ChDir {  sub Pad {
3414      my ($dirName) = @_;      # Get the parameters.
3415      if (! -d $dirName) {      my ($string, $len, $left, $padChar) = @_;
3416          Confess("Cannot change to directory $dirName: no such directory.");      # Compute the padding character.
3417        if (! defined $padChar) {
3418            $padChar = " ";
3419        }
3420        # Compute the number of spaces needed.
3421        my $needed = $len - length $string;
3422        # Copy the string into the return variable.
3423        my $retVal = $string;
3424        # Only proceed if padding is needed.
3425        if ($needed > 0) {
3426            # Create the pad string.
3427            my $pad = $padChar x $needed;
3428            # Affix it to the return value.
3429            if ($left) {
3430                $retVal = $pad . $retVal;
3431      } else {      } else {
3432          Trace("Changing to directory $dirName.") if T(File => 4);              $retVal .= $pad;
         my $okFlag = chdir $dirName;  
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
3433          }          }
3434      }      }
3435        # Return the result.
3436        return $retVal;
3437  }  }
3438    
3439  =head3 SendSMS  =head3 EOF
3440    
3441    This is a constant that is lexically greater than any useful string.
3442    
3443    =cut
3444    
3445    sub EOF {
3446        return "\xFF\xFF\xFF\xFF\xFF";
3447    }
3448    
3449  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>  =head3 TICK
3450    
3451  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the      my @results = TICK($commandString);
 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  
3452    
3453      $phone =  { user => 'BruceTheHumanPet',  Perform a back-tick operation on a command. If this is a Windows environment, any leading
3454                  password => 'silly',  dot-slash (C<./> will be removed. So, for example, if you were doing
                 api_id => '2561022' };  
3455    
3456  The original purpose of this method was to insure Bruce would be notified immediately when the      `./protein.cgi`
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3457    
3458  The message ID will be returned if successful, and C<undef> if an error occurs.  from inside a CGI script, it would work fine in Unix, but would issue an error message
3459    in Windows complaining that C<'.'> is not a valid command. If instead you code
3460    
3461  =over 4      TICK("./protein.cgi")
3462    
3463  =item phoneNumber  it will work correctly in both environments.
3464    
3465  Phone number to receive the message, in international format. A United States phone number  =over 4
 would be prefixed by "1". A British phone number would be prefixed by "44".  
3466    
3467  =item msg