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revision 1.73, Tue Oct 3 12:04:50 2006 UTC revision 1.100, Thu May 8 14:38:44 2008 UTC
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1  #  # -*- perl -*-
2    ########################################################################
3  # Copyright (c) 2003-2006 University of Chicago and Fellowship  # Copyright (c) 2003-2006 University of Chicago and Fellowship
4  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
5  #  #
# Line 13  Line 14 
14  # at info@ci.uchicago.edu or the Fellowship for Interpretation of  # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15  # Genomes at veronika@thefig.info or download a copy from  # Genomes at veronika@thefig.info or download a copy from
16  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
17  #  ########################################################################
18    
19  package Tracer;  package Tracer;
20    
21      require Exporter;      require Exporter;
22      @ISA = ('Exporter');      @ISA = ('Exporter');
23      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn);
24      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
25      use strict;      use strict;
26      use Carp qw(longmess croak);      use Carp qw(longmess croak carp);
27      use CGI;      use CGI;
28      use Cwd;      use Cwd;
29      use FIG_Config;      use FIG_Config;
# Line 34  Line 35 
35      use LWP::UserAgent;      use LWP::UserAgent;
36      use Time::HiRes 'gettimeofday';      use Time::HiRes 'gettimeofday';
37      use URI::Escape;      use URI::Escape;
38        use Time::Local;
39        use POSIX qw(strftime);
40        use Time::Zone;
41    
42    
43  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
44    
# Line 158  Line 163 
163    
164  Sometimes, you need a way for tracing to happen automatically without putting parameters  Sometimes, you need a way for tracing to happen automatically without putting parameters
165  in a form or on the command line. Emergency tracing does this. You invoke emergency tracing  in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
166  from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.  from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
167  Emergency tracing requires you specify a tracing key. For command-line tools, the key is  that you specify a tracing key. For command-line tools, the key is
168  taken from the C<TRACING> environment variable. For web services, the key is taken from  taken from the C<TRACING> environment variable. For web services, the key is taken from
169  a cookie. Either way, the key tells the tracing facility who you are, so that you control  a cookie. Either way, the key tells the tracing facility who you are, so that you control
170  the tracing in your environment without stepping on other users.  the tracing in your environment without stepping on other users.
# Line 182  Line 187 
187    
188  The web script will look for the tracing key in the cookies, and the command-line  The web script will look for the tracing key in the cookies, and the command-line
189  script will look for it in the C<TRACING> environment variable. If you are  script will look for it in the C<TRACING> environment variable. If you are
190  using the L</StandardScript> or L</StandardSetup> methods, emergency tracing  using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
191  will be configured automatically.  will be configured automatically.
192    
 =head3 Debugging Control Panel  
   
 The debugging control panel provides several tools to assist in development of  
 SEED and Sprout software. You access the debugging control panel from the URL  
 C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,  
 for example, the panel access point for the development NMPDR system is  
 C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to  
 find out what the password is. From this page, you can also specify a tracing  
 key. If you don't specify a key, one will be generated for you.  
   
 =head4 Emergency Tracing Form  
   
 At the bottom of the debugging control panel is a form that allows you to  
 specify a trace level and tracing categories. Special and common categories  
 are listed with check boxes. You can hold your mouse over a check box to see  
 what its category does. In general, however, a category name is the same as  
 the name of the package in which the trace message occurs.  
   
 Additional categories can be entered in an input box, delimited by spaces or commas.  
   
 The B<Activate> button turns on Emergency tracing at the level you specify with the  
 specified categories active. The B<Terminate> button turns tracing off. The  
 B<Show File> button displays the current contents of the trace file. The tracing  
 form at the bottom of the control panel is designed for emergency tracing, so it  
 will only affect programs that call L</ETracing>, L</StandardScript>,  
 or L</StandardSetup>.  
   
 =head4 Script Form  
   
 The top form of the debugging control panel allows you to enter a tiny script and  
 have the output generated in a formatted table. Certain object variables are  
 predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),  
 and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.  
   
 The last line of the script must be a scalar, but it can be a reference to a hash,  
 a list, a list of lists, and various other combinations. If you select the appropriate  
 data type in the dropdown box, the output will be formatted accordingly. The form  
 also has controls for specifying tracing. These controls override any emergency  
 tracing in effect.  
   
 =head4 Database Query Forms  
   
 The forms between the script form and the emergency tracing form allow you to  
 make queries against the database. The FIG query form allows simple queries against  
 a single FIG table. The Sprout query form uses the B<GetAll> method to do a  
 multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>  
 package, and it takes five parameters.  
   
     GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);  
   
 Each of the five parameters corresponds to a text box on the query form:  
   
 =over 4  
   
 =item Objects  
   
 Comma-separated list containing the names of the entity and relationship objects to be retrieved.  
   
 =item Filter  
   
 WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  
 be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form  
 B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a  
 field, I<objectName> is the name of the entity or relationship object containing the field, and  
 I<number> is the 1-based position of the object in the object list. Any parameters  
 specified in the filter clause should be specified in the B<Params> field.  
 The fields in a filter clause can come from primary entity relations,  
 relationship relations, or secondary entity relations; however, all of the  
 entities and relationships involved must be included in the list of object names.  
   
 =item Params  
   
 List of the parameters to be substituted in for the parameters marks in the filter clause. This  
 is a comma-separated list without any quoting or escaping.  
   
 =item fields  
   
 Comma-separated list of the fields to be returned in each element of the list returned. Fields  
 are specified in the same manner as in the filter clause.  
   
 =item count  
   
 Maximum number of records to return. If omitted or 0, all available records will be returned.  
   
 =back  
   
 B<GetAll> automatically joins together the entities and relationships listed in the object  
 names. This simplifies the coding of the filter clause, but it means that some queries are  
 not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation  
 that has yet to be addressed.  
   
193  =cut  =cut
194    
195  # Declare the configuration variables.  # Declare the configuration variables.
196    
197  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
198  my $TeeFlag = 0;            # TRUE if output is going to a file and to the  my $TeeFlag = 0;            # TRUE if output is going to a file and to the
199                              # standard output                              # standard output
200  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
201                              # hash of active category names                              # hash of active category names
202    my @LevelNames = qw(error warn notice info detail);
203  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
204                              # messages                              # messages
205  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
206  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
207    my $LastLevel = 0;          # level of the last test call
208  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
209  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
210    my $SavedCGI;               # CGI object passed to ETracing
211    umask 2;                    # Fix the damn umask so everything is group-writable.
212    
213  =head2 Public Methods  =head2 Tracing Methods
214    
215    =head3 Setups
216    
217        my $count = Tracer::Setups();
218    
219    Return the number of times L</TSetup> has been called.
220    
221    This method allows for the creation of conditional tracing setups where, for example, we
222    may want to set up tracing if nobody else has done it before us.
223    
224    =cut
225    
226    sub Setups {
227        return $SetupCount;
228    }
229    
230  =head3 TSetup  =head3 TSetup
231    
232  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
233    
234  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
235  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 346  Line 279 
279          }          }
280      }      }
281      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
282      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
283      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
284        # the standard output (tee mode).
285      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
286          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
287              $TeeFlag = 1;              $TeeFlag = 1;
288              $target = substr($target, 1);              $target = substr($target, 1);
289          }          }
290          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
291                # We need to initialize the file (which clears it).
292              open TRACEFILE, $target;              open TRACEFILE, $target;
293              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
294              close TRACEFILE;              close TRACEFILE;
295                # Set to append mode now that the file has been cleared.
296              $Destination = ">$target";              $Destination = ">$target";
297          } else {          } else {
298              $Destination = $target;              $Destination = $target;
# Line 368  Line 304 
304      $SetupCount++;      $SetupCount++;
305  }  }
306    
307  =head3 StandardSetup  =head3 SetLevel
308    
309  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
310    
311  This method performs standard command-line parsing and tracing setup. The return  Modify the trace level. A higher trace level will cause more messages to appear.
 values are a hash of the command-line options and a list of the positional  
 parameters. Tracing is automatically set up and the command-line options are  
 validated.  
312    
313  This is a complex method that does a lot of grunt work. The parameters can  =over 4
 be more easily understood, however, once they are examined individually.  
314    
315  The I<categories> parameter is the most obtuse. It is a reference to a list of  =item newLevel
 special-purpose tracing categories. Most tracing categories are PERL package  
 names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,  
 B<ERDB>, and B<SproutLoad> packages, you would specify the categories  
316    
317      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
318    
319  This would cause trace messages in the specified three packages to appear in  =back
 the output. There are two special tracing categories that are automatically  
 handled by this method. In other words, if you used L</TSetup> you would need  
 to include these categories manually, but if you use this method they are turned  
 on automatically.  
320    
321  =over 4  =cut
322    
323  =item SQL  sub SetLevel {
324        $TraceLevel = $_[0];
325    }
326    
327  Traces SQL commands and activity.  =head3 ParseDate
328    
329  =item Tracer      my $time = Tracer::ParseDate($dateString);
330    
331  Traces error messages and call stacks.  Convert a date into a PERL time number. This method expects a date-like string
332    and parses it into a number. The string must be vaguely date-like or it will
333    return an undefined value. Our requirement is that a month and day be
334    present and that three pieces of the date string (time of day, month and day,
335    year) be separated by likely delimiters, such as spaces, commas, and such-like.
336    
337  =back  If a time of day is present, it must be in military time with two digits for
338    everything but the hour.
339    
340  C<SQL> is only turned on if the C<-sql> option is specified in the command line.  The year must be exactly four digits.
 The trace level is specified using the C<-trace> command-line option. For example,  
 the following command line for C<TransactFeatures> turns on SQL tracing and runs  
 all tracing at level 3.  
341    
342      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  Additional stuff can be in the string. We presume it's time zones or weekdays or something
343    equally innocuous. This means, however, that a sufficiently long sentence with date-like
344    parts in it may be interpreted as a date. Hopefully this will not be a problem.
345    
346  Standard tracing is output to the standard output and echoed to the file  It should be guaranteed that this method will parse the output of the L</Now> function.
 C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the  
 process ID. You can also specify the C<user> parameter to put a user ID  
 instead of a process ID in the trace file name. So, for example  
347    
348  The default trace level is 2. To get all messages, specify a trace level of 4.  The parameters are as follows.
 For a genome-by-genome update, use 3.  
349    
350      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  =over 4
351    
352  would send the trace output to C<traceBruce.log> in the temporary directory.  =item dateString
353    
354  The I<options> parameter is a reference to a hash containing the command-line  The date string to convert.
 options, their default values, and an explanation of what they mean. Command-line  
 options may be in the form of switches or keywords. In the case of a switch, the  
 option value is 1 if it is specified and 0 if it is not specified. In the case  
 of a keyword, the value is separated from the option name by an equal sign. You  
 can see this last in the command-line example above.  
355    
356  You can specify a different default trace level by setting C<$options->{trace}>  =item RETURN
 prior to calling this method.  
357    
358  An example at this point would help. Consider, for example, the command-line utility  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
359  C<TransactFeatures>. It accepts a list of positional parameters plus the options  the date string is invalid. A valid date string must contain a month and day.
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
360    
361      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  =back
                         { safe => [0, "use database transactions"],  
                           noAlias => [0, "do not expect aliases in CHANGE transactions"],  
                           start => [' ', "start with this genome"],  
                           tblFiles => [0, "output TBL files containing the corrected IDs"] },  
                         "command transactionDirectory IDfile",  
                       @ARGV);  
362    
363    =cut
364    
365  The call to C<ParseCommand> specifies the default values for the options and  # Universal month conversion table.
366  stores the actual options in a hash that is returned as C<$options>. The  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
367  positional parameters are returned in C<@parameters>.                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
368                                Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
369                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
370                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
371                                Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
372                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
373                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
374                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
375                                Oct =>  9, October  =>   9, '10' =>  9,
376                                Nov => 10, November =>  10, '11' => 10,
377                                Dec => 11, December =>  11, '12' => 11
378                            };
379    
380  The following is a sample command line for C<TransactFeatures>.  sub ParseDate {
381        # Get the parameters.
382        my ($dateString) = @_;
383        # Declare the return variable.
384        my $retVal;
385        # Find the month and day of month. There are two ways that can happen. We check for the
386        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
387        # won't be fooled into thinking the month is Sunday.
388        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
389            my ($mon, $mday) = (MONTHS->{$1}, $2);
390            # Insist that the month and day are valid.
391            if (defined($mon) && $2 >= 1 && $2 <= 31) {
392                # Find the time.
393                my ($hour, $min, $sec) = (0, 0, 0);
394                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
395                    ($hour, $min, $sec) = ($1, $2, $3);
396                }
397                # Find the year.
398                my $year;
399                if ($dateString =~ /\b(\d{4})\b/) {
400                    $year = $1;
401                } else {
402                    # Get the default year, which is this one. Note we must convert it to
403                    # the four-digit value expected by "timelocal".
404                    (undef, undef, undef, undef, undef, $year) = localtime();
405                    $year += 1900;
406                }
407                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
408            }
409        }
410        # Return the result.
411        return $retVal;
412    }
413    
414      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  =head3 LogErrors
415    
416  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional      Tracer::LogErrors($fileName);
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
417    
418      { trace => 2, sql => 0, safe => 0,  Route the standard error output to a log file.
       noAlias => 1, start => ' ', tblFiles => 0 }  
419    
420  Use of C<StandardSetup> in this way provides a simple way of performing  =over 4
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
421    
422  If the C<background> option is specified on the command line, then the  =item fileName
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
423    
424      -user=Bruce -background  Name of the file to receive the error output.
425    
426  then the trace output would go to C<traceBruce.log>, the standard output to  =back
 C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to  
 simplify starting a command in the background.  
427    
428  The user name is also used as the tracing key for L</Emergency Tracing>.  =cut
 Specifying a value of C<E> for the trace level causes emergency tracing to  
 be used instead of custom tracing. If the user name is not specified,  
 the tracing key is taken from the C<Tracing> environment variable. If there  
 is no value for that variable, the tracing key will be computed from the PID.  
429    
430  Finally, if the special option C<-h> is specified, the option names will  sub LogErrors {
431  be traced at level 0 and the program will exit without processing.      # Get the file name.
432  This provides a limited help capability. For example, if the user enters      my ($fileName) = @_;
433        # Open the file as the standard error output.
434        open STDERR, '>', $fileName;
435    }
436    
437      TransactFeatures -h  =head3 Trace
438    
439  he would see the following output.      Trace($message);
440    
441      TransactFeatures [options] command transactionDirectory IDfile  Write a trace message to the target location specified in L</TSetup>. If there has not been
442          -trace    tracing level (default E)  any prior call to B<TSetup>.
         -sql      trace SQL commands  
         -safe     use database transactions  
         -noAlias  do not expect aliases in CHANGE transactions  
         -start    start with this genome  
         -tblFiles output TBL files containing the corrected IDs  
443    
444  The caller has the option of modifying the tracing scheme by placing a value  =over 4
 for C<trace> in the incoming options hash. The default value can be overridden,  
 or the tracing to the standard output can be turned off by suffixing a minus  
 sign to the trace level. So, for example,  
445    
446      { trace => [0, "tracing level (default 0)"],  =item message
        ...  
447    
448  would set the default trace level to 0 instead of E, while  Message to write.
449    
450      { trace => ["2-", "tracing level (default 2)"],  =back
        ...  
451    
452  would set the default to 2, but trace only to the log file, not to the  =cut
 standard output.  
453    
454  The parameters to this method are as follows.  sub Trace {
455        # Get the parameters.
456        my ($message) = @_;
457        # Strip off any line terminators at the end of the message. We will add
458        # new-line stuff ourselves.
459        my $stripped = Strip($message);
460        # Compute the caller information.
461        my ($callPackage, $callFile, $callLine) = caller();
462        my $callFileTitle = basename($callFile);
463        # Check the caller.
464        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
465        # Get the timestamp.
466        my $timeStamp = Now();
467        # Build the prefix.
468        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
469        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
470        # Format the message.
471        my $formatted = "$prefix $stripped";
472        # Process according to the destination.
473        if ($Destination eq "TEXT") {
474            # Write the message to the standard output.
475            print "$formatted\n";
476        } elsif ($Destination eq "ERROR") {
477            # Write the message to the error output. Here, we want our prefix fields.
478            print STDERR "$formatted\n";
479        } elsif ($Destination eq "WARN") {
480            # Emit the message to the standard error output. It is presumed that the
481            # error logger will add its own prefix fields, the notable exception being
482            # the caller info.
483            print STDERR "$callerInfo$stripped\n";
484        } elsif ($Destination eq "QUEUE") {
485            # Push the message into the queue.
486            push @Queue, "$formatted";
487        } elsif ($Destination eq "HTML") {
488            # Convert the message to HTML and write it to the standard output.
489            my $escapedMessage = CGI::escapeHTML($stripped);
490            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
491        } elsif ($Destination =~ m/^>>/) {
492            # Write the trace message to an output file.
493            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
494            print TRACING "$formatted\n";
495            close TRACING;
496            # If the Tee flag is on, echo it to the standard output.
497            if ($TeeFlag) {
498                print "$formatted\n";
499            }
500        }
501    }
502    
503  =over 4  =head3 T
504    
505  =item categories      my $switch = T($category, $traceLevel);
506    
507  Reference to a list of tracing category names. These should be names of      or
 packages whose internal workings will need to be debugged to get the  
 command working.  
508    
509  =item options      my $switch = T($traceLevel);
510    
511  Reference to a hash containing the legal options for the current command mapped  Return TRUE if the trace level is at or above a specified value and the specified category
512  to their default values and descriptions. The user can override the defaults  is active, else FALSE. If no category is specified, the caller's package name is used.
 by specifying the options as command-line switches prefixed by a hyphen.  
 Tracing-related options may be added to this hash. If the C<-h> option is  
 specified on the command line, the option descriptions will be used to  
 explain the options. To turn off tracing to the standard output, add a  
 minus sign to the value for C<trace> (see above).  
513    
514  =item parmHelp  =over 4
515    
516  A string that vaguely describes the positional parameters. This is used  =item category
 if the user specifies the C<-h> option.  
517    
518  =item argv  Category to which the message belongs. If not specified, the caller's package name is
519    used.
520    
521  List of command line parameters, including the option switches, which must  =item traceLevel
522  precede the positional parameters and be prefixed by a hyphen.  
523    Relevant tracing level.
524    
525  =item RETURN  =item RETURN
526    
527  Returns a list. The first element of the list is the reference to a hash that  TRUE if a message at the specified trace level would appear in the trace, else FALSE.
 maps the command-line option switches to their values. These will either be the  
 default values or overrides specified on the command line. The remaining  
 elements of the list are the position parameters, in order.  
528    
529  =back  =back
530    
531  =cut  =cut
532    
533  sub StandardSetup {  sub T {
534        # Declare the return variable.
535        my $retVal = 0;
536        # Only proceed if tracing is turned on.
537        if ($Destination ne "NONE") {
538      # Get the parameters.      # Get the parameters.
539      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
540      # Get the default tracing key.          if (!defined $traceLevel) {
541      my $tkey = EmergencyKey();              # Here we have no category, so we need to get the calling package.
542      # Add the tracing options.              # The calling package is normally the first parameter. If it is
543      if (! exists $options->{trace}) {              # omitted, the first parameter will be the tracelevel. So, the
544          $options->{trace} = ['E', "tracing level (E for emergency tracing)"];              # first thing we do is shift the so-called category into the
545      }              # $traceLevel variable where it belongs.
546      $options->{sql} = [0, "turn on SQL tracing"];              $traceLevel = $category;
547      $options->{h} = [0, "display command-line options"];              my ($package, $fileName, $line) = caller;
548      $options->{user} = [$tkey, "tracing key"];              # If there is no calling package, we default to "main".
549      $options->{background} = [0, "spool standard and error output"];              if (!$package) {
550      # Create a parsing hash from the options hash. The parsing hash                  $category = "main";
     # contains the default values rather than the default value  
     # and the description. While we're at it, we'll memorize the  
     # length of the longest option name.  
     my $longestName = 0;  
     my %parseOptions = ();  
     for my $key (keys %{$options}) {  
         if (length $key > $longestName) {  
             $longestName = length $key;  
         }  
         $parseOptions{$key} = $options->{$key}->[0];  
     }  
     # Parse the command line.  
     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);  
     # Get the logfile suffix.  
     my $suffix = $retOptions->{user};  
     # Check for background mode.  
     if ($retOptions->{background}) {  
         my $outFileName = "$FIG_Config::temp/out$suffix.log";  
         my $errFileName = "$FIG_Config::temp/err$suffix.log";  
         open STDOUT, ">$outFileName";  
         open STDERR, ">$errFileName";  
     }  
     # Now we want to set up tracing. First, we need to know if the user  
     # wants emergency tracing.  
     if ($retOptions->{trace} eq 'E') {  
         ETracing($retOptions->{user});  
     } else {  
         # Here the tracing is controlled from the command line.  
         my @cats = @{$categories};  
         if ($retOptions->{sql}) {  
             push @cats, "SQL";  
         }  
         # Add the default categories.  
         push @cats, "Tracer";  
         # Next, we create the category string by joining the categories.  
         my $cats = join(" ", @cats);  
         # Check to determine whether or not the caller wants to turn off tracing  
         # to the standard output.  
         my $traceLevel = $retOptions->{trace};  
         my $textOKFlag = 1;  
         if ($traceLevel =~ /^(.)-/) {  
             $traceLevel = $1;  
             $textOKFlag = 0;  
         }  
         # Now we set up the trace mode.  
         my $traceMode;  
         # Verify that we can open a file in the FIG temporary directory.  
         my $traceFileName = "$FIG_Config::temp/trace$suffix.log";  
         if (open TESTTRACE, ">$traceFileName") {  
             # Here we can trace to a file.  
             $traceMode = ">$traceFileName";  
             if ($textOKFlag) {  
                 # Echo to standard output if the text-OK flag is set.  
                 $traceMode = "+$traceMode";  
             }  
             # Close the test file.  
             close TESTTRACE;  
         } else {  
             # Here we can't trace to a file. We trace to the standard output if it's  
             # okay, and the error log otherwise.  
             if ($textOKFlag) {  
                 $traceMode = "TEXT";  
551              } else {              } else {
552                  $traceMode = "WARN";                  my @cats = split /::/, $package;
553              }                  $category = $cats[$#cats];
         }  
         # Now set up the tracing.  
         TSetup("$traceLevel $cats", $traceMode);  
554      }      }
     # Check for the "h" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($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] . ")";  
555              }              }
556              print "  $name $desc\n";          # Save the category name and level.
557            $LastCategory = $category;
558            $LastLevel = $traceLevel;
559            # Convert it to lower case before we hash it.
560            $category = lc $category;
561            # Validate the trace level.
562            if (ref $traceLevel) {
563                Confess("Bad trace level.");
564            } elsif (ref $TraceLevel) {
565                Confess("Bad trace config.");
566          }          }
567          exit(0);          # Make the check. Note that level 0 shows even if the category is turned off.
568            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
569      }      }
570      # Return the parsed parameters.      # Return the computed result.
571      return ($retOptions, @retParameters);      return $retVal;
572  }  }
573    
574  =head3 Setups  =head3 QTrace
   
 C<< my $count = Tracer::Setups(); >>  
   
 Return the number of times L</TSetup> has been called.  
   
 This method allows for the creation of conditional tracing setups where, for example, we  
 may want to set up tracing if nobody else has done it before us.  
   
 =cut  
575    
576  sub Setups {      my $data = QTrace($format);
     return $SetupCount;  
 }  
577    
578  =head3 Open  Return the queued trace data in the specified format.
579    
580  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  =over 4
581    
582  Open a file.  =item format
583    
584  The I<$fileSpec> is essentially the second argument of the PERL C<open>  C<html> to format the data as an HTML list, C<text> to format it as straight text.
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
585    
586      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =back
587    
588  would open for output appended to the specified file, and  =cut
589    
590      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  sub QTrace {
591        # Get the parameter.
592        my ($format) = @_;
593        # Create the return variable.
594        my $retVal = "";
595        # Only proceed if there is an actual queue.
596        if (@Queue) {
597            # Process according to the format.
598            if ($format =~ m/^HTML$/i) {
599                # Convert the queue into an HTML list.
600                $retVal = "<ul>\n";
601                for my $line (@Queue) {
602                    my $escapedLine = CGI::escapeHTML($line);
603                    $retVal .= "<li>$escapedLine</li>\n";
604                }
605                $retVal .= "</ul>\n";
606            } elsif ($format =~ m/^TEXT$/i) {
607                # Convert the queue into a list of text lines.
608                $retVal = join("\n", @Queue) . "\n";
609            }
610            # Clear the queue.
611            @Queue = ();
612        }
613        # Return the formatted list.
614        return $retVal;
615    }
616    
617  would open a pipe that sorts the records written and removes duplicates. Note  =head3 Confess
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
618    
619      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");      Confess($message);
620    
621  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  Trace the call stack and abort the program with the specified message. When used with
622  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
623  failed open will throw an exception and the third parameter will be used to construct  So, for example
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
624    
625      Could not open "/usr/spool/news/twitlog"      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
626    
627  Note that the mode characters are automatically cleaned from the file name.  Will abort the program with a stack trace if the value of C<$recNum> is negative.
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
628    
629      Could not open "/usr/spool/news/twitlog": file not found.  =over 4
630    
631  In some versions of PERL the only error message we get is a number, which  =item message
 corresponds to the C++ C<errno> value.  
632    
633      Could not open "/usr/spool/news/twitlog": 6.  Message to include in the trace.
634    
635  =over 4  =back
636    
637  =item fileHandle  =cut
638    
639  File handle. If this parameter is C<undef>, a file handle will be generated  sub Confess {
640  and returned as the value of this method.      # Get the parameters.
641        my ($message) = @_;
642        # Set up the category and level.
643        $LastCategory = "(confess)";
644        $LastLevel = 0;
645        if (! defined($FIG_Config::no_tool_hdr)) {
646            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
647            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
648            # Only proceed if the tool header file is actually present.
649            if (-f $toolHeaderFile) {
650                my $fh;
651                if (open $fh, "<$toolHeaderFile") {
652                    my @lines = <$fh>;
653                    Trace("Tool header has " . scalar(@lines) . " lines.");
654                }
655            }
656        }
657        # Trace the call stack.
658        Cluck($message);
659        # Abort the program.
660        croak(">>> $message");
661    }
662    
663  =item fileSpec  =head3 Warn
664    
665  File name and mode, as per the PERL C<open> function.      Warn($message);
666    
667  =item message (optional)  This method traces an important message. If an RSS feed is configured
668    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
669    then the message will be echoed to the feed. In general, a tracing
670    destination of C<WARN> indicates that the caller is running as a web
671    service in a production environment; however, this is not a requirement.
672    
673    The L</Cluck> method calls this one for its final message. Since
674    L</Confess> calls L</Cluck>, this means that any error which is caught
675    and confessed will put something in the feed. This insures that someone
676    will be alerted relatively quickly when a failure occurs.
677    
678  Error message to use if the open fails. If omitted, a standard error message  =over 4
 will be generated. In either case, the error information from the file system  
 is appended to the message. To specify a conditional open that does not throw  
 an error if it fails, use C<0>.  
679    
680  =item RETURN  =item message
681    
682  Returns the name of the file handle assigned to the file, or C<undef> if the  Message to be traced.
 open failed.  
683    
684  =back  =back
685    
686  =cut  =cut
687    
688  sub Open {  sub Warn {
689      # Get the parameters.      # Get the parameters.
690      my ($fileHandle, $fileSpec, $message) = @_;      my ($message) = @_;
691      # Attempt to open the file.      # Trace the message.
692      my $rv = open $fileHandle, $fileSpec;      Trace($message);
693      # If the open failed, generate an error message.      # An error here would be disastrous. Note, however, that we aren't too worried
694      if (! $rv) {      # about losing events. The error log is always available for the occasions where
695          # Save the system error message.      # we mess up.
696          my $sysMessage = $!;      eval {
697          # See if we need a default message.          # Do we need to put this in the RSS feed?
698          if (!$message) {          if ($FIG_Config::error_feed && $Destination eq 'WARN') {
699              # Clean any obvious mode characters and leading spaces from the              # Yes. We now need to compute the date, the link, and the title.
700              # filename.              # First, the date, in a very specific format.
701              my ($fileName) = FindNamePart($fileSpec);              my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
702              $message = "Could not open \"$fileName\"";                  (tz_local_offset() / 30);
703                # We'll put the link and title in here.
704                my ($link, $title);
705                # Environment data goes in here.
706                my $environment;
707                # HTML-escape the message.
708                my $escaped = CGI::escapeHTML($message);
709                # If we have a CGI object, then this is a web error. Otherwise, it's
710                # command-line.
711                if (defined $SavedCGI) {
712                    # We're in a web service. The title is the user's IP, and the link
713                    # is the URL that got us here.
714                    my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
715                    $title = "Event Reported at IP address $key: $escaped";
716                    $link = $SavedCGI->url(-full => 1, -query => 1);
717                    # We need the user agent string and (if available) the referrer.
718                    $environment = "User Agent $ENV{HTTP_USER_AGENT}";
719                    if ($ENV{HTTP_REFERER}) {
720                        $environment .= " referred from $ENV{HTTP_REFERER}"
721                    }
722                    # Close off the sentence.
723                    $environment .= ". ";
724                } else {
725                    # No CGI object, so we're a command-line tool. Use the tracing
726                    # key and the PID as the user identifier.
727                    my $key = EmergencyKey();
728                    $title = "Event Reported by $key Process $$: $escaped";
729                    # Set the link to the development NMPDR. There is really no good
730                    # choice here.
731                    $link = "http://$FIG_Config::dev_server";
732                    # We need the command
733                    $environment = "Command $ENV{_}.";
734                }
735                # Build a GUID. We use the current time, the title, and the process ID,
736                # then digest the result.
737                my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
738                # Finally, the description. This is a stack trace plus various environmental stuff.
739                my @trace = LongMess();
740                my $trace = join "; ", @trace;
741                my $description = CGI::escapeHTML("$environment Stack trace: $trace");
742                # Okay, we have all the pieces. Create a hash of the new event.
743                my $newItem = { title => $title,
744                                description => $description,
745                                link => $link,
746                                category => $LastCategory,
747                                pubDate => $date,
748                                guid => $guid,
749                               };
750                # We need XML capability for this.
751                require XML::Simple;
752                # The RSS document goes in here.
753                my $rss;
754                # Get the name of the RSS file. It's in the FIG temporary directory.
755                my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
756                # Does it exist?
757                if (-s $fileName) {
758                    # Slurp it in.
759                    $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
760                } else {
761                    my $size = -s $fileName;
762                    # Create an empty channel.
763                    $rss = {
764                        channel => {
765                            title => 'NMPDR Warning Feed',
766                            link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
767                            description => "Important messages regarding the status of the NMPDR.",
768                            generator => "NMPDR Trace Facility",
769                            docs => "http://blogs.law.harvard.edu/tech/rss",
770                            item => []
771                        },
772                    };
773          }          }
774          # Terminate with an error using the supplied message and the              # Get the channel object.
775          # error message from the file system.              my $channel = $rss->{channel};
776          Confess("$message: $!");              # Update the last-build date.
777                $channel->{lastBuildDate} = $date;
778                # Get the item array.
779                my $items = $channel->{item};
780                # Insure it has only 100 entries.
781                while (scalar @{$items} > 100) {
782                    pop @{$items};
783                }
784                # Add our new item at the front.
785                unshift @{$items}, $newItem;
786                # Replace the file.
787                my $xml = XML::Simple::XMLout($rss, NoAttr => 1, RootName => 'rss', XmlDecl => '<?xml version="1.0" encoding="utf-8"?>',
788                                              NoEscape => 1);
789                # We don't use Open here because we can't afford an error.
790                if (open XMLOUT, ">$fileName") {
791                    print XMLOUT $xml;
792                    close XMLOUT;
793      }      }
794      # Return the file handle.          }
795      return $fileHandle;      };
796        # There's no "if ($@)" here, because putting an error message in the log
797        # saying that we missed putting an error message in the feed of messages
798        # in the log is not going to help anybody.
799  }  }
800    
801  =head3 FindNamePart  =head3 Assert
802    
803  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>      Assert($condition1, $condition2, ... $conditionN);
804    
805  Extract the portion of a file specification that contains the file name.  Return TRUE if all the conditions are true. This method can be used in conjunction with
806    the OR operator and the L</Confess> method as a debugging assert.
807    So, for example
808    
809  A file specification is the string passed to an C<open> call. It specifies the file      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
 mode and name. In a truly complex situation, it can specify a pipe sequence. This  
 method assumes that the file name is whatever follows the first angle bracket  
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
810    
811      >>/usr/fig/myfile.txt  Will abort the program with a stack trace if the value of C<$recNum> is negative.
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
812    
813  If the method cannot find a file name using its normal methods, it will return the  =cut
814  whole incoming string.  sub Assert {
815        my $retVal = 1;
816        LOOP: for my $condition (@_) {
817            if (! $condition) {
818                $retVal = 0;
819                last LOOP;
820            }
821        }
822        return $retVal;
823    }
824    
825  =over 4  =head3 Cluck
826    
827  =item fileSpec      Cluck($message);
828    
829  File specification string from which the file name is to be extracted.  Trace the call stack. Note that for best results, you should qualify the call with a
830    trace condition. For example,
831    
832  =item RETURN      Cluck("Starting record parse.") if T(3);
833    
834  Returns a three-element list. The first element contains the file name portion of  will only trace the stack if the trace level for the package is 3 or more.
835  the specified string, or the whole string if a file name cannot be found via normal  
836  methods. The second element contains the start position of the file name portion and  =over 4
837  the third element contains the length.  
838    =item message
839    
840    Message to include in the trace.
841    
842  =back  =back
843    
844  =cut  =cut
845  #: Return Type $;  
846  sub FindNamePart {  sub Cluck {
847      # Get the parameters.      # Get the parameters.
848      my ($fileSpec) = @_;      my ($message) = @_;
849      # Default to the whole input string.      # Trace what's happening.
850      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);      Trace("Stack trace for event: $message");
851      # Parse out the file name if we can.      # Get the stack trace.
852      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {      my @trace = LongMess();
853          $retVal = $2;      # Convert the trace to a series of messages.
854          $len = length $retVal;      for my $line (@trace) {
855          $pos = (length $fileSpec) - (length $3) - $len;          # Replace the tab at the beginning with spaces.
856            $line =~ s/^\t/    /;
857            # Trace the line.
858            Trace($line);
859      }      }
860      # Return the result.      # Issue a warning. This displays the event message and inserts it into the RSS error feed.
861      return ($retVal, $pos, $len);      Warn($message);
862  }  }
863    
864  =head3 OpenDir  =head3 LongMess
865    
866  C<< my @files = OpenDir($dirName, $filtered, $flag); >>      my @lines = Tracer::LongMess();
867    
868  Open a directory and return all the file names. This function essentially performs  Return a stack trace with all tracing methods removed. The return will be in the form of a list
869  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  of message strings.
 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,  
870    
871      my @files = OpenDir("/Volumes/fig/contigs", 1);  =cut
872    
873  is effectively the same as  sub LongMess {
874        # Declare the return variable.
875        my @retVal = ();
876        my $confession = longmess("");
877        for my $line (split /\s*\n/, $confession) {
878            unless ($line =~ /Tracer\.pm/) {
879                # Here we have a line worth keeping. Push it onto the result list.
880                push @retVal, $line;
881            }
882        }
883        # Return the result.
884        return @retVal;
885    }
886    
887      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  =head3 ScriptSetup (deprecated)
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
888    
889  Similarly, the following code      my ($cgi, $varHash) = ScriptSetup($noTrace);
890    
891      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  Perform standard tracing and debugging setup for scripts. The value returned is
892    the CGI object followed by a pre-built variable hash. At the end of the script,
893    the client should call L</ScriptFinish> to output the web page.
894    
895  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  This method calls L</ETracing> to configure tracing, which allows the tracing
896  automatically returns an empty list if the directory fails to open.  to be configured via the emergency tracing form on the debugging control panel.
897    Tracing will then be turned on automatically for all programs that use the L</ETracing>
898    method, which includes every program that uses this method or L</StandardSetup>.
899    
900  =over 4  =over 4
901    
902  =item dirName  =item noTrace (optional)
903    
904  Name of the directory to open.  If specified, tracing will be suppressed. This is useful if the script wants to set up
905    tracing manually.
906    
907  =item filtered  =item RETURN
908    
909  TRUE if files whose names begin with a period (C<.>) should be automatically removed  Returns a two-element list consisting of a CGI query object and a variable hash for
910  from the list, else FALSE.  the output page.
911    
912  =item flag  =back
913    
914  TRUE if a failure to open is okay, else FALSE  =cut
915    
916    sub ScriptSetup {
917        # Get the parameters.
918        my ($noTrace) = @_;
919        # Get the CGI query object.
920        my $cgi = CGI->new();
921        # Set up tracing if it's not suppressed.
922        ETracing($cgi) unless $noTrace;
923        # Create the variable hash.
924        my $varHash = { results => '' };
925        # Return the query object and variable hash.
926        return ($cgi, $varHash);
927    }
928    
929    =head3 ETracing
930    
931        ETracing($parameter);
932    
933    Set up emergency tracing. Emergency tracing is tracing that is turned
934    on automatically for any program that calls this method. The emergency
935    tracing parameters are stored in a a file identified by a tracing key.
936    If this method is called with a CGI object, then the tracing key is
937    taken from a cookie. If it is called with no parameters, then the tracing
938    key is taken from an environment variable. If it is called with a string,
939    the tracing key is that string.
940    
941    =over 4
942    
943    =item parameter
944    
945    A parameter from which the tracing key is computed. If it is a scalar,
946    that scalar is used as the tracing key. If it is a CGI object, the
947    tracing key is taken from the C<IP> cookie. If it is omitted, the
948    tracing key is taken from the C<TRACING> environment variable. If it
949    is a CGI object and emergency tracing is not on, the C<Trace> and
950    C<TF> parameters will be used to determine the type of tracing.
951    
952  =back  =back
953    
954  =cut  =cut
955  #: Return Type @;  
956  sub OpenDir {  sub ETracing {
957      # Get the parameters.      # Get the parameter.
958      my ($dirName, $filtered, $flag) = @_;      my ($parameter) = @_;
959      # Declare the return variable.      # Check for CGI mode.
960      my @retVal = ();      if (defined $parameter && ref $parameter eq 'CGI') {
961      # Open the directory.          $SavedCGI = $parameter;
     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;  
962          } else {          } else {
963              @retVal = readdir $dirHandle;          $SavedCGI = undef;
964        }
965        # Default to no tracing except errors.
966        my ($tracing, $dest) = ("0", "WARN");
967        # Check for emergency tracing.
968        my $tkey = EmergencyKey($parameter);
969        my $emergencyFile = EmergencyFileName($tkey);
970        if (-e $emergencyFile) {
971            # We have the file. Read in the data.
972            my @tracing = GetFile($emergencyFile);
973            # Pull off the time limit.
974            my $expire = shift @tracing;
975            # Convert it to seconds.
976            $expire *= 3600;
977            # Check the file data.
978            my $stat = stat($emergencyFile);
979            my ($now) = gettimeofday;
980            if ($now - $stat->mtime > $expire) {
981                # Delete the expired file.
982                unlink $emergencyFile;
983            } else {
984                # Emergency tracing is on. Pull off the destination and
985                # the trace level;
986                $dest = shift @tracing;
987                my $level = shift @tracing;
988                # Convert the destination to a real tracing destination.
989                # temp directory.
990                $dest = EmergencyTracingDest($tkey, $dest);
991                # Insure Tracer is specified.
992                my %moduleHash = map { $_ => 1 } @tracing;
993                $moduleHash{Tracer} = 1;
994                # Set the trace parameter.
995                $tracing = join(" ", $level, sort keys %moduleHash);
996            }
997        } elsif (defined $SavedCGI) {
998            # There's no emergency tracing, but we have a CGI object, so check
999            # for tracing from the form parameters.
1000            if ($SavedCGI->param('Trace')) {
1001                # Here the user has requested tracing via a form.
1002                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1003                $tracing = $SavedCGI->param('Trace') . " Tracer";
1004            }
1005        }
1006        # Setup the tracing we've determined from all the stuff above.
1007        TSetup($tracing, $dest);
1008        # Check to see if we're a web script.
1009        if (defined $SavedCGI) {
1010            # Yes we are. Trace the form and environment data.
1011            TraceParms($SavedCGI);
1012            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1013            # emitted by the script in its raw form.
1014            if (T(Raw => 3)) {
1015                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1016          }          }
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
1017      }      }
     # Return the result.  
     return @retVal;  
1018  }  }
1019    
1020  =head3 SetLevel  =head3 EmergencyFileName
1021    
1022  C<< Tracer::SetLevel($newLevel); >>      my $fileName = Tracer::EmergencyFileName($tkey);
1023    
1024  Modify the trace level. A higher trace level will cause more messages to appear.  Return the emergency tracing file name. This is the file that specifies
1025    the tracing information.
1026    
1027  =over 4  =over 4
1028    
1029  =item newLevel  =item tkey
1030    
1031  Proposed new trace level.  Tracing key for the current program.
1032    
1033    =item RETURN
1034    
1035    Returns the name of the file to contain the emergency tracing information.
1036    
1037  =back  =back
1038    
1039  =cut  =cut
1040    
1041  sub SetLevel {  sub EmergencyFileName {
1042      $TraceLevel = $_[0];      # Get the parameters.
1043        my ($tkey) = @_;
1044        # Compute the emergency tracing file name.
1045        return "$FIG_Config::temp/Emergency$tkey.txt";
1046  }  }
1047    
1048  =head3 Now  =head3 EmergencyFileTarget
1049    
1050        my $fileName = Tracer::EmergencyFileTarget($tkey);
1051    
1052    Return the emergency tracing target file name. This is the file that receives
1053    the tracing output for file-based tracing.
1054    
1055    =over 4
1056    
1057    =item tkey
1058    
1059    Tracing key for the current program.
1060    
1061    =item RETURN
1062    
1063  C<< my $string = Tracer::Now(); >>  Returns the name of the file to contain the trace output.
1064    
1065  Return a displayable time stamp containing the local time.  =back
1066    
1067  =cut  =cut
1068    
1069  sub Now {  sub EmergencyFileTarget {
1070      my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);      # Get the parameters.
1071      my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .      my ($tkey) = @_;
1072                   _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);      # Compute the emergency tracing file name.
1073      return $retVal;      return "$FIG_Config::temp/trace$tkey.log";
1074    }
1075    
1076    =head3 EmergencyTracingDest
1077    
1078        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1079    
1080    This method converts an emergency tracing destination to a real
1081    tracing destination. The main difference is that if the
1082    destination is C<FILE> or C<APPEND>, we convert it to file
1083    output. If the destination is C<DUAL>, we convert it to file
1084    and standard output.
1085    
1086    =over 4
1087    
1088    =item tkey
1089    
1090    Tracing key for this environment.
1091    
1092    =item myDest
1093    
1094    Destination from the emergency tracing file.
1095    
1096    =item RETURN
1097    
1098    Returns a destination that can be passed into L</TSetup>.
1099    
1100    =back
1101    
1102    =cut
1103    
1104    sub EmergencyTracingDest {
1105        # Get the parameters.
1106        my ($tkey, $myDest) = @_;
1107        # Declare the return variable.
1108        my $retVal = $myDest;
1109        # Process according to the destination value.
1110        if ($myDest eq 'FILE') {
1111            $retVal = ">" . EmergencyFileTarget($tkey);
1112        } elsif ($myDest eq 'APPEND') {
1113            $retVal = ">>" . EmergencyFileTarget($tkey);
1114        } elsif ($myDest eq 'DUAL') {
1115            $retVal = "+>" . EmergencyFileTarget($tkey);
1116        } elsif ($myDest eq 'WARN') {
1117            $retVal = "WARN";
1118        }
1119        # Return the result.
1120        return $retVal;
1121    }
1122    
1123    =head3 Emergency
1124    
1125        Emergency($key, $hours, $dest, $level, @modules);
1126    
1127    Turn on emergency tracing. This method is normally invoked over the web from
1128    a debugging console, but it can also be called by the C<trace.pl> script.
1129    The caller specifies the duration of the emergency in hours, the desired tracing
1130    destination, the trace level, and a list of the trace modules to activate.
1131    For the length of the duration, when a program in an environment with the
1132    specified tracing key active invokes a Sprout CGI script, tracing will be
1133    turned on automatically. See L</TSetup> for more about tracing setup and
1134    L</ETracing> for more about emergency tracing.
1135    
1136    =over 4
1137    
1138    =item tkey
1139    
1140    The tracing key. This is used to identify the control file and the trace file.
1141    
1142    =item hours
1143    
1144    Number of hours to keep emergency tracing alive.
1145    
1146    =item dest
1147    
1148    Tracing destination. If no path information is specified for a file
1149    destination, it is put in the FIG temporary directory.
1150    
1151    =item level
1152    
1153    Tracing level. A higher level means more trace messages.
1154    
1155    =item modules
1156    
1157    A list of the tracing modules to activate.
1158    
1159    =back
1160    
1161    =cut
1162    
1163    sub Emergency {
1164        # Get the parameters.
1165        my ($tkey, $hours, $dest, $level, @modules) = @_;
1166        # Create the emergency file.
1167        my $specFile = EmergencyFileName($tkey);
1168        my $outHandle = Open(undef, ">$specFile");
1169        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1170    }
1171    
1172    =head3 EmergencyKey
1173    
1174        my $tkey = EmergencyKey($parameter);
1175    
1176    Return the Key to be used for emergency tracing. This could be an IP address,
1177     a session ID, or a user name, depending on the environment.
1178    
1179    =over 4
1180    
1181    =item parameter
1182    
1183    Parameter defining the method for finding the tracing key. If it is a scalar,
1184    then it is presumed to be the tracing key itself. If it is a CGI object, then
1185    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1186    taken from the C<TRACING> environment variable.
1187    
1188    =item RETURN
1189    
1190    Returns the key to be used for labels in emergency tracing.
1191    
1192    =back
1193    
1194    =cut
1195    
1196    sub EmergencyKey {
1197        # Get the parameters.
1198        my ($parameter) = @_;
1199        # Declare the return variable.
1200        my $retVal;
1201        # Determine the parameter type.
1202        if (! defined $parameter) {
1203            # Here we're supposed to check the environment. If that fails, we
1204            # get the effective login ID.
1205            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1206        } else {
1207            my $ptype = ref $parameter;
1208            if ($ptype eq 'CGI') {
1209                # Here we were invoked from a web page. Look for a cookie.
1210                $retVal = $parameter->cookie('IP');
1211            } elsif (! $ptype) {
1212                # Here the key was passed in.
1213                $retVal = $parameter;
1214            }
1215        }
1216        # If no luck finding a key, use the PID.
1217        if (! defined $retVal) {
1218            $retVal = $$;
1219        }
1220        # Return the result.
1221        return $retVal;
1222    }
1223    
1224    
1225    =head3 TraceParms
1226    
1227        Tracer::TraceParms($cgi);
1228    
1229    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1230    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1231    
1232    =over 4
1233    
1234    =item cgi
1235    
1236    CGI query object containing the parameters to trace.
1237    
1238    =back
1239    
1240    =cut
1241    
1242    sub TraceParms {
1243        # Get the parameters.
1244        my ($cgi) = @_;
1245        if (T(CGI => 2)) {
1246            # Here we trace the GET-style URL for the script.
1247            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1248        }
1249        if (T(CGI => 3)) {
1250            # Here we want to trace the parameter data.
1251            my @names = $cgi->param;
1252            for my $parmName (sort @names) {
1253                # Note we skip the Trace parameters, which are for our use only.
1254                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1255                    my @values = $cgi->param($parmName);
1256                    Trace("[CGI] $parmName = " . join(", ", @values));
1257                }
1258            }
1259            # Display the request method.
1260            my $method = $cgi->request_method();
1261            Trace("Method: $method");
1262        }
1263        if (T(CGI => 4)) {
1264            # Here we want the environment data too.
1265            for my $envName (sort keys %ENV) {
1266                Trace("[ENV] $envName = $ENV{$envName}");
1267            }
1268        }
1269    }
1270    
1271    =head3 TraceImages
1272    
1273        Tracer::TraceImages($htmlString);
1274    
1275    Trace information about all of an html document's images. The tracing
1276    will be for type "IMG" at level 3. The image's source string
1277    will be displayed. This is generally either the URL of the image or
1278    raw data for the image itself. If the source is too long, only the first 300
1279    characters will be shown at trace level 3. The entire source will be shown,
1280    however, at trace level 4. This method is not very smart, and might catch
1281    Javascript code, but it is still useful when debugging the arcane
1282    behavior of images in multiple browser environments.
1283    
1284    =over 4
1285    
1286    =item htmlString
1287    
1288    HTML text for an outgoing web page.
1289    
1290    =back
1291    
1292    =cut
1293    
1294    sub TraceImages {
1295        # Only proceed if we're at the proper trace level.
1296        if (T(IMG => 3)) {
1297            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1298            # into a variable called "$htmlString". This is because we expect html strings to be
1299            # long, and don't want to copy them any more than we have to.
1300            Trace(length($_[0]) . " characters in web page.");
1301            # Loop through the HTML, culling image tags.
1302            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1303                # Extract the source string and determine whether or not it's too long.
1304                my $srcString = $1;
1305                my $pos = pos($_[0]) - length($srcString);
1306                my $excess = length($srcString) - 300;
1307                # We'll put the display string in here.
1308                my $srcDisplay = $srcString;
1309                # If it's a data string, split it at the comma.
1310                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1311                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1312                # a long string, however, we only show the first 300 characters.
1313                if ($excess > 0 && ! T(IMG => 4)) {
1314                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1315                }
1316                # Output the trace message.
1317                Trace("Image tag at position $pos:\n$srcDisplay");
1318            }
1319        }
1320    }
1321    
1322    
1323    =head3 ScriptFinish (deprecated)
1324    
1325        ScriptFinish($webData, $varHash);
1326    
1327    Output a web page at the end of a script. Either the string to be output or the
1328    name of a template file can be specified. If the second parameter is omitted,
1329    it is assumed we have a string to be output; otherwise, it is assumed we have the
1330    name of a template file. The template should have the variable C<DebugData>
1331    specified in any form that invokes a standard script. If debugging mode is turned
1332    on, a form field will be put in that allows the user to enter tracing data.
1333    Trace messages will be placed immediately before the terminal C<BODY> tag in
1334    the output, formatted as a list.
1335    
1336    A typical standard script would loook like the following.
1337    
1338        BEGIN {
1339            # Print the HTML header.
1340            print "CONTENT-TYPE: text/html\n\n";
1341        }
1342        use Tracer;
1343        use CGI;
1344        use FIG;
1345        # ... more uses ...
1346    
1347        my ($cgi, $varHash) = ScriptSetup();
1348        eval {
1349            # ... get data from $cgi, put it in $varHash ...
1350        };
1351        if ($@) {
1352            Trace("Script Error: $@") if T(0);
1353        }
1354        ScriptFinish("Html/MyTemplate.html", $varHash);
1355    
1356    The idea here is that even if the script fails, you'll see trace messages and
1357    useful output.
1358    
1359    =over 4
1360    
1361    =item webData
1362    
1363    A string containing either the full web page to be written to the output or the
1364    name of a template file from which the page is to be constructed. If the name
1365    of a template file is specified, then the second parameter must be present;
1366    otherwise, it must be absent.
1367    
1368    =item varHash (optional)
1369    
1370    If specified, then a reference to a hash mapping variable names for a template
1371    to their values. The template file will be read into memory, and variable markers
1372    will be replaced by data in this hash reference.
1373    
1374    =back
1375    
1376    =cut
1377    
1378    sub ScriptFinish {
1379        # Get the parameters.
1380        my ($webData, $varHash) = @_;
1381        # Check for a template file situation.
1382        my $outputString;
1383        if (defined $varHash) {
1384            # Here we have a template file. We need to determine the template type.
1385            my $template;
1386            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1387                $template = "$FIG_Config::template_url/$webData";
1388            } else {
1389                $template = "<<$webData";
1390            }
1391            $outputString = PageBuilder::Build($template, $varHash, "Html");
1392        } else {
1393            # Here the user gave us a raw string.
1394            $outputString = $webData;
1395        }
1396        # Check for trace messages.
1397        if ($Destination ne "NONE" && $TraceLevel > 0) {
1398            # We have trace messages, so we want to put them at the end of the body. This
1399            # is either at the end of the whole string or at the beginning of the BODY
1400            # end-tag.
1401            my $pos = length $outputString;
1402            if ($outputString =~ m#</body>#gi) {
1403                $pos = (pos $outputString) - 7;
1404            }
1405            # If the trace messages were queued, we unroll them. Otherwise, we display the
1406            # destination.
1407            my $traceHtml;
1408            if ($Destination eq "QUEUE") {
1409                $traceHtml = QTrace('Html');
1410            } elsif ($Destination =~ /^>>(.+)$/) {
1411                # Here the tracing output it to a file. We code it as a hyperlink so the user
1412                # can copy the file name into the clipboard easily.
1413                my $actualDest = $1;
1414                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1415            } else {
1416                # Here we have one of the special destinations.
1417                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1418            }
1419            substr $outputString, $pos, 0, $traceHtml;
1420        }
1421        # Write the output string.
1422        print $outputString;
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 PID.
1630    
1631    Finally, if the special option C<-help> is specified, the option
1632    names will be traced at level 0 and the program will exit without processing.
1633    This provides a limited help capability. For example, if the user enters
1634    
1635        TransactFeatures -help
1636    
1637    he would see the following output.
1638    
1639        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1640            -trace    tracing level (default E)
1641            -sql      trace SQL commands
1642            -safe     use database transactions
1643            -noAlias  do not expect aliases in CHANGE transactions
1644            -start    start with this genome
1645            -tblFiles output TBL files containing the corrected IDs
1646    
1647    The caller has the option of modifying the tracing scheme by placing a value
1648    for C<trace> in the incoming options hash. The default value can be overridden,
1649    or the tracing to the standard output can be turned off by suffixing a minus
1650    sign to the trace level. So, for example,
1651    
1652        { trace => [0, "tracing level (default 0)"],
1653           ...
1654    
1655    would set the default trace level to 0 instead of E, while
1656    
1657        { trace => ["2-", "tracing level (default 2)"],
1658           ...
1659    
1660    would set the default to 2, but trace only to the log file, not to the
1661    standard output.
1662    
1663    The parameters to this method are as follows.
1664    
1665    =over 4
1666    
1667    =item categories
1668    
1669    Reference to a list of tracing category names. These should be names of
1670    packages whose internal workings will need to be debugged to get the
1671    command working.
1672    
1673    =item options
1674    
1675    Reference to a hash containing the legal options for the current command mapped
1676    to their default values and descriptions. The user can override the defaults
1677    by specifying the options as command-line switches prefixed by a hyphen.
1678    Tracing-related options may be added to this hash. If the C<-h> option is
1679    specified on the command line, the option descriptions will be used to
1680    explain the options. To turn off tracing to the standard output, add a
1681    minus sign to the value for C<trace> (see above).
1682    
1683    =item parmHelp
1684    
1685    A string that vaguely describes the positional parameters. This is used
1686    if the user specifies the C<-h> option.
1687    
1688    =item argv
1689    
1690    List of command line parameters, including the option switches, which must
1691    precede the positional parameters and be prefixed by a hyphen.
1692    
1693    =item RETURN
1694    
1695    Returns a list. The first element of the list is the reference to a hash that
1696    maps the command-line option switches to their values. These will either be the
1697    default values or overrides specified on the command line. The remaining
1698    elements of the list are the position parameters, in order.
1699    
1700    =back
1701    
1702    =cut
1703    
1704    sub StandardSetup {
1705        # Get the parameters.
1706        my ($categories, $options, $parmHelp, @argv) = @_;
1707        # Get the default tracing key.
1708        my $tkey = EmergencyKey();
1709        # Add the tracing options.
1710        if (! exists $options->{trace}) {
1711            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1712        }
1713        $options->{sql} = [0, "turn on SQL tracing"];
1714        $options->{help} = [0, "display command-line options"];
1715        $options->{user} = [$tkey, "tracing key"];
1716        $options->{background} = [0, "spool standard and error output"];
1717        # Create a parsing hash from the options hash. The parsing hash
1718        # contains the default values rather than the default value
1719        # and the description. While we're at it, we'll memorize the
1720        # length of the longest option name.
1721        my $longestName = 0;
1722        my %parseOptions = ();
1723        for my $key (keys %{$options}) {
1724            if (length $key > $longestName) {
1725                $longestName = length $key;
1726            }
1727            $parseOptions{$key} = $options->{$key}->[0];
1728        }
1729        # Parse the command line.
1730        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1731        # Get the logfile suffix.
1732        my $suffix = $retOptions->{user};
1733        # Check for background mode.
1734        if ($retOptions->{background}) {
1735            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1736            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1737            open STDOUT, ">$outFileName";
1738            open STDERR, ">$errFileName";
1739            # Check for phone support. If we have phone support and a phone number,
1740            # we want to turn it on.
1741            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1742                $retOptions->{phone} = $ENV{PHONE};
1743            }
1744        }
1745        # Now we want to set up tracing. First, we need to know if the user
1746        # wants emergency tracing.
1747        if ($retOptions->{trace} eq 'E') {
1748            ETracing($retOptions->{user});
1749        } else {
1750            # Here the tracing is controlled from the command line.
1751            my @cats = @{$categories};
1752            if ($retOptions->{sql}) {
1753                push @cats, "SQL";
1754            }
1755            # Add the default categories.
1756            push @cats, "Tracer";
1757            # Next, we create the category string by joining the categories.
1758            my $cats = join(" ", @cats);
1759            # Check to determine whether or not the caller wants to turn off tracing
1760            # to the standard output.
1761            my $traceLevel = $retOptions->{trace};
1762            my $textOKFlag = 1;
1763            if ($traceLevel =~ /^(.)-/) {
1764                $traceLevel = $1;
1765                $textOKFlag = 0;
1766            }
1767            # Now we set up the trace mode.
1768            my $traceMode;
1769            # Verify that we can open a file in the FIG temporary directory.
1770            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1771            if (open TESTTRACE, ">$traceFileName") {
1772                # Here we can trace to a file.
1773                $traceMode = ">$traceFileName";
1774                if ($textOKFlag) {
1775                    # Echo to standard output if the text-OK flag is set.
1776                    $traceMode = "+$traceMode";
1777                }
1778                # Close the test file.
1779                close TESTTRACE;
1780            } else {
1781                # Here we can't trace to a file. Complain about this.
1782                warn "Could not open trace file $traceFileName: $!\n";
1783                # We trace to the standard output if it's
1784                # okay, and the error log otherwise.
1785                if ($textOKFlag) {
1786                    $traceMode = "TEXT";
1787                } else {
1788                    $traceMode = "WARN";
1789                }
1790            }
1791            # Now set up the tracing.
1792            TSetup("$traceLevel $cats", $traceMode);
1793        }
1794        # Check for the "help" option. If it is specified, dump the command-line
1795        # options and exit the program.
1796        if ($retOptions->{help}) {
1797            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1798            print "$1 [options] $parmHelp\n";
1799            for my $key (sort keys %{$options}) {
1800                my $name = Pad($key, $longestName, 0, ' ');
1801                my $desc = $options->{$key}->[1];
1802                if ($options->{$key}->[0]) {
1803                    $desc .= " (default " . $options->{$key}->[0] . ")";
1804  }  }
1805                print "  $name $desc\n";
 # Pad a number to 2 digits.  
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
1806  }  }
1807            exit(0);
1808  =head3 LogErrors      }
1809        # Trace the options, if applicable.
1810  C<< Tracer::LogErrors($fileName); >>      if (T(3)) {
1811            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1812  Route the standard error output to a log file.          Trace("Selected options: " . join(", ", sort @parms) . ".");
1813        }
1814  =over 4      # Return the parsed parameters.
1815        return ($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, '>', $fileName;  
1816  }  }
1817    
1818  =head3 ReadOptions  =head3 ReadOptions
1819    
1820  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1821    
1822  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
1823  format  format
# Line 1017  Line 1878 
1878    
1879  =head3 GetOptions  =head3 GetOptions
1880    
1881  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1882    
1883  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
1884  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 1026  Line 1887 
1887    
1888  Consider the following example.  Consider the following example.
1889    
1890  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1891    
1892  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1893  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 1034  Line 1895 
1895  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1896  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1897    
1898  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1899    
1900  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1901    
# Line 1078  Line 1939 
1939    
1940  =head3 MergeOptions  =head3 MergeOptions
1941    
1942  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
1943    
1944  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
1945  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 1110  Line 1971 
1971      }      }
1972  }  }
1973    
 =head3 Trace  
   
 C<< Trace($message); >>  
   
 Write a trace message to the target location specified in L</TSetup>. If there has not been  
 any prior call to B<TSetup>.  
   
 =over 4  
   
 =item message  
   
 Message to write.  
   
 =back  
   
 =cut  
   
 sub Trace {  
     # Get the parameters.  
     my ($message) = @_;  
     # Get the timestamp.  
     my $timeStamp = Now();  
     # Format the message. Note we strip off any line terminators at the end.  
     my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);  
     # Process according to the destination.  
     if ($Destination eq "TEXT") {  
         # Write the message to the standard output.  
         print "$formatted\n";  
     } elsif ($Destination eq "ERROR") {  
         # Write the message to the error output.  
         print STDERR "$formatted\n";  
     } elsif ($Destination eq "QUEUE") {  
         # Push the message into the queue.  
         push @Queue, "$formatted";  
     } elsif ($Destination eq "HTML") {  
         # Convert the message to HTML and write it to the standard output.  
         my $escapedMessage = CGI::escapeHTML($message);  
         print "<p>$formatted</p>\n";  
     } elsif ($Destination eq "WARN") {  
        # Emit the message as a warning.  
        warn $message;  
     } elsif ($Destination =~ m/^>>/) {  
         # Write the trace message to an output file.  
         (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";  
         print TRACING "$formatted\n";  
         close TRACING;  
         # If the Tee flag is on, echo it to the standard output.  
         if ($TeeFlag) {  
             print "$formatted\n";  
         }  
     }  
 }  
   
 =head3 T  
   
 C<< my $switch = T($category, $traceLevel); >>  
   
     or  
   
 C<< my $switch = T($traceLevel); >>  
   
 Return TRUE if the trace level is at or above a specified value and the specified category  
 is active, else FALSE. If no category is specified, the caller's package name is used.  
   
 =over 4  
   
 =item category  
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
   
 Relevant tracing level.  
   
 =item RETURN  
   
 TRUE if a message at the specified trace level would appear in the trace, else FALSE.  
   
 =back  
   
 =cut  
   
 sub T {  
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
         # Get the parameters.  
         my ($category, $traceLevel) = @_;  
         if (!defined $traceLevel) {  
             # Here we have no category, so we need to get the calling package.  
             # The calling package is normally the first parameter. If it is  
             # omitted, the first parameter will be the tracelevel. So, the  
             # first thing we do is shift the so-called category into the  
             # $traceLevel variable where it belongs.  
             $traceLevel = $category;  
             my ($package, $fileName, $line) = caller;  
             # If there is no calling package, we default to "main".  
             if (!$package) {  
                 $category = "main";  
             } else {  
                 $category = $package;  
             }  
         }  
         # Save the category name.  
         $LastCategory = $category;  
         # Convert it to lower case before we hash it.  
         $category = lc $category;  
         # Use the category and tracelevel to compute the result.  
         if (ref $traceLevel) {  
             Confess("Bad trace level.");  
         } elsif (ref $TraceLevel) {  
             Confess("Bad trace config.");  
         }  
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
     }  
     # Return the computed result.  
     return $retVal;  
 }  
   
1974  =head3 ParseCommand  =head3 ParseCommand
1975    
1976  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1977    
1978  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
1979  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
1980  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
1981  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.
1982    
1983  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1984    
1985  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,
1986  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
1987    
1988  C<< -logFile=error.log apple orange rutabaga >>      -logFile=error.log apple orange rutabaga
1989    
1990  then at the end of the invocation, C<$options> will be  then at the end of the invocation, C<$options> will be
1991    
1992  C<< { errors => 0, logFile => 'error.log' } >>      { errors => 0, logFile => 'error.log' }
1993    
1994  and C<@arguments> will contain  and C<@arguments> will contain
1995    
1996  C<< apple orange rutabaga >>      apple orange rutabaga
1997    
1998  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
1999  support for quote characters.  support for quote characters. Options can be specified with single or double hyphens.
2000    
2001  =over 4  =over 4
2002    
# Line 1281  Line 2021 
2021      my ($optionTable, @inputList) = @_;      my ($optionTable, @inputList) = @_;
2022      # Process any options in the input list.      # Process any options in the input list.
2023      my %overrides = ();      my %overrides = ();
2024      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2025          # Get the current option.          # Get the current option.
2026          my $arg = shift @inputList;          my $arg = shift @inputList;
2027          # Pull out the option name.          # Pull out the option name.
2028          $arg =~ /^-([^=]*)/g;          $arg =~ /^--?([^=]*)/g;
2029          my $name = $1;          my $name = $1;
2030          # Check for an option value.          # Check for an option value.
2031          if ($arg =~ /\G=(.*)$/g) {          if ($arg =~ /\G=(.*)$/g) {
# Line 1307  Line 2047 
2047      return ($optionTable, @retVal);      return ($optionTable, @retVal);
2048  }  }
2049    
 =head3 Escape  
2050    
2051  C<< my $codedString = Tracer::Escape($realString); >>  =head2 File Utility Methods
2052    
2053  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  =head3 GetFile
2054  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
2055  result is to reverse the effect of L</UnEscape>.      my @fileContents = Tracer::GetFile($fileName);
2056    
2057        or
2058    
2059        my $fileContents = Tracer::GetFile($fileName);
2060    
2061    Return the entire contents of a file. In list context, line-ends are removed and
2062    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2063    
2064  =over 4  =over 4
2065    
2066  =item realString  =item fileName
2067    
2068  String to escape.  Name of the file to read.
2069    
2070  =item RETURN  =item RETURN
2071    
2072  Escaped equivalent of the real string.  In a list context, returns the entire file as a list with the line terminators removed.
2073    In a scalar context, returns the entire file as a string. If an error occurs opening
2074    the file, an empty list will be returned.
2075    
2076  =back  =back
2077    
2078  =cut  =cut
2079    
2080  sub Escape {  sub GetFile {
2081      # Get the parameter.      # Get the parameters.
2082      my ($realString) = @_;      my ($fileName) = @_;
2083      # Initialize the return variable.      # Declare the return variable.
2084      my $retVal = "";      my @retVal = ();
2085      # Loop through the parameter string, looking for sequences to escape.      # Open the file for input.
2086      while (length $realString > 0) {      my $handle = Open(undef, "<$fileName");
2087          # Look for the first sequence to escape.      # Read the whole file into the return variable, stripping off any terminator
2088          if ($realString =~ /^(.*?)([\n\t\r\\])/) {      # characters.
2089              # Here we found it. The text preceding the sequence is in $1. The sequence      my $lineCount = 0;
2090              # itself is in $2. First, move the clear text to the return variable.      while (my $line = <$handle>) {
2091              $retVal .= $1;          $lineCount++;
2092              # Strip the processed section off the real string.          $line = Strip($line);
2093              $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;  
2094              }              }
2095        # Close it.
2096        close $handle;
2097        my $actualLines = @retVal;
2098        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2099        # Return the file's contents in the desired format.
2100        if (wantarray) {
2101            return @retVal;
2102          } else {          } else {
2103              # Here there are no more escape sequences. The rest of the string is          return join "\n", @retVal;
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
         }  
2104      }      }
     # Return the result.  
     return $retVal;  
2105  }  }
2106    
2107  =head3 UnEscape  =head3 PutFile
   
 C<< my $realString = Tracer::UnEscape($codedString); >>  
   
 Replace escape sequences with their actual equivalents. C<\t> will be replaced by  
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
   
 =over 4  
   
 =item codedString  
   
 String to un-escape.  
   
 =item RETURN  
   
 Returns a copy of the original string with the escape sequences converted to their actual  
 values.  
2108    
2109  =back      Tracer::PutFile($fileName, \@lines);
2110    
2111  =cut  Write out a file from a list of lines of text.
2112    
2113  sub UnEscape {  =over 4
2114      # Get the parameter.  
2115      my ($codedString) = @_;  =item fileName
2116      # Initialize the return variable.  
2117      my $retVal = "";  Name of the output file.
2118      # Only proceed if the incoming string is nonempty.  
2119      if (defined $codedString) {  =item lines
2120          # Loop through the parameter string, looking for escape sequences. We can't do  
2121          # translating because it causes problems with the escaped slash. ("\\t" becomes  Reference to a list of text lines. The lines will be written to the file in order, with trailing
2122          # "\<tab>" no matter what we do.)  new-line characters. Alternatively, may be a string, in which case the string will be written without
2123          while (length $codedString > 0) {  modification.
2124              # Look for the first escape sequence.  
2125              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {  =back
2126                  # Here we found it. The text preceding the sequence is in $1. The sequence  
2127                  # itself is in $2. First, move the clear text to the return variable.  =cut
2128                  $retVal .= $1;  
2129                  $codedString = substr $codedString, (2 + length $1);  sub PutFile {
2130                  # Get the escape value.      # Get the parameters.
2131                  my $char = $2;      my ($fileName, $lines) = @_;
2132                  # If we have a "\r", we are done.      # Open the output file.
2133                  if ($char ne 'r') {      my $handle = Open(undef, ">$fileName");
2134                      # Here it's not an 'r', so we convert it.      # Count the lines written.
2135                      $char =~ tr/\\tn/\\\t\n/;      if (ref $lines ne 'ARRAY') {
2136                      $retVal .= $char;          # Here we have a scalar, so we write it raw.
2137                  }          print $handle $lines;
2138            Trace("Scalar put to file $fileName.") if T(File => 3);
2139              } else {              } else {
2140                  # Here there are no more escape sequences. The rest of the string is          # Write the lines one at a time.
2141                  # transferred unmodified.          my $count = 0;
2142                  $retVal .= $codedString;          for my $line (@{$lines}) {
2143                  $codedString = "";              print $handle "$line\n";
2144              }              $count++;
2145          }          }
2146            Trace("$count lines put to file $fileName.") if T(File => 3);
2147      }      }
2148      # Return the result.      # Close the output file.
2149      return $retVal;      close $handle;
2150  }  }
2151    
2152  =head3 ParseRecord  =head3 ParseRecord
2153    
2154  C<< my @fields = Tracer::ParseRecord($line); >>      my @fields = Tracer::ParseRecord($line);
2155    
2156  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
2157  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 1469  Line 2196 
2196    
2197  =head3 Merge  =head3 Merge
2198    
2199  C<< my @mergedList = Tracer::Merge(@inputList); >>      my @mergedList = Tracer::Merge(@inputList);
2200    
2201  Sort a list of strings and remove duplicates.  Sort a list of strings and remove duplicates.
2202    
# Line 1515  Line 2242 
2242      return @inputList;      return @inputList;
2243  }  }
2244    
2245  =head3 Percent  =head3 Open
   
 C<< my $percent = Tracer::Percent($number, $base); >>  
   
 Returns the percent of the base represented by the given number. If the base  
 is zero, returns zero.  
   
 =over 4  
2246    
2247  =item number      my $handle = Open($fileHandle, $fileSpec, $message);
2248    
2249  Percent numerator.  Open a file.
2250    
2251  =item base  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2252    function. The mode is specified using Unix-like shell information. So, for
2253    example,
2254    
2255  Percent base.      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2256    
2257  =item RETURN  would open for output appended to the specified file, and
2258    
2259  Returns the percentage of the base represented by the numerator.      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2260    
2261  =back  would open a pipe that sorts the records written and removes duplicates. Note
2262    the use of file handle syntax in the Open call. To use anonymous file handles,
2263    code as follows.
2264    
2265  =cut      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2266    
2267  sub Percent {  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2268      # Get the parameters.  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2269      my ($number, $base) = @_;  failed open will throw an exception and the third parameter will be used to construct
2270      # Declare the return variable.  an error message. If the parameter is omitted, a standard message is constructed
2271      my $retVal = 0;  using the file spec.
     # Compute the percent.  
     if ($base != 0) {  
         $retVal = $number * 100 / $base;  
     }  
     # Return the result.  
     return $retVal;  
 }  
2272    
2273  =head3 GetFile      Could not open "/usr/spool/news/twitlog"
2274    
2275  C<< my @fileContents = Tracer::GetFile($fileName); >>  Note that the mode characters are automatically cleaned from the file name.
2276    The actual error message from the file system will be captured and appended to the
2277    message in any case.
2278    
2279      or      Could not open "/usr/spool/news/twitlog": file not found.
2280    
2281  C<< my $fileContents = Tracer::GetFile($fileName); >>  In some versions of PERL the only error message we get is a number, which
2282    corresponds to the C++ C<errno> value.
2283    
2284  Return the entire contents of a file. In list context, line-ends are removed and      Could not open "/usr/spool/news/twitlog": 6.
 each line is a list element. In scalar context, line-ends are replaced by C<\n>.  
2285    
2286  =over 4  =over 4
2287    
2288  =item fileName  =item fileHandle
   
 Name of the file to read.  
   
 =item RETURN  
   
 In a list context, returns the entire file as a list with the line terminators removed.  
 In a scalar context, returns the entire file as a string. If an error occurs opening  
 the file, an empty list will be returned.  
   
 =back  
   
 =cut  
   
 sub GetFile {  
     # Get the parameters.  
     my ($fileName) = @_;  
     # Declare the return variable.  
     my @retVal = ();  
     # Open the file for input.  
     my $handle = Open(undef, "<$fileName");  
     # Read the whole file into the return variable, stripping off any terminator  
     # characters.  
     my $lineCount = 0;  
     while (my $line = <$handle>) {  
         $lineCount++;  
         $line = Strip($line);  
         push @retVal, $line;  
     }  
     # Close it.  
     close $handle;  
     my $actualLines = @retVal;  
     # Return the file's contents in the desired format.  
     if (wantarray) {  
         return @retVal;  
     } else {  
         return join "\n", @retVal;  
     }  
 }  
   
 =head3 PutFile  
2289    
2290  C<< Tracer::PutFile($fileName, \@lines); >>  File handle. If this parameter is C<undef>, a file handle will be generated
2291    and returned as the value of this method.
2292    
2293  Write out a file from a list of lines of text.  =item fileSpec
2294    
2295  =over 4  File name and mode, as per the PERL C<open> function.
2296    
2297  =item fileName  =item message (optional)
2298    
2299  Name of the output file.  Error message to use if the open fails. If omitted, a standard error message
2300    will be generated. In either case, the error information from the file system
2301    is appended to the message. To specify a conditional open that does not throw
2302    an error if it fails, use C<0>.
2303    
2304  =item lines  =item RETURN
2305    
2306  Reference to a list of text lines. The lines will be written to the file in order, with trailing  Returns the name of the file handle assigned to the file, or C<undef> if the
2307  new-line characters. Alternatively, may be a string, in which case the string will be written without  open failed.
 modification.  
2308    
2309  =back  =back
2310    
2311  =cut  =cut
2312    
2313  sub PutFile {  sub Open {
2314      # Get the parameters.      # Get the parameters.
2315      my ($fileName, $lines) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2316      # Open the output file.      # Attempt to open the file.
2317      my $handle = Open(undef, ">$fileName");      my $rv = open $fileHandle, $fileSpec;
2318      if (ref $lines ne 'ARRAY') {      # If the open failed, generate an error message.
2319          # Here we have a scalar, so we write it raw.      if (! $rv) {
2320          print $handle $lines;          # Save the system error message.
2321      } else {          my $sysMessage = $!;
2322          # Write the lines one at a time.          # See if we need a default message.
2323          for my $line (@{$lines}) {          if (!$message) {
2324              print $handle "$line\n";              # Clean any obvious mode characters and leading spaces from the
2325                # filename.
2326                my ($fileName) = FindNamePart($fileSpec);
2327                $message = "Could not open \"$fileName\"";
2328          }          }
2329            # Terminate with an error using the supplied message and the
2330            # error message from the file system.
2331            Confess("$message: $!");
2332      }      }
2333      # Close the output file.      # Return the file handle.
2334      close $handle;      return $fileHandle;
2335  }  }
2336    
2337  =head3 QTrace  =head3 FindNamePart
   
 C<< my $data = QTrace($format); >>  
   
 Return the queued trace data in the specified format.  
   
 =over 4  
   
 =item format  
   
 C<html> to format the data as an HTML list, C<text> to format it as straight text.  
   
 =back  
2338    
2339  =cut      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2340    
2341  sub QTrace {  Extract the portion of a file specification that contains the file name.
     # Get the parameter.  
     my ($format) = @_;  
     # Create the return variable.  
     my $retVal = "";  
     # Only proceed if there is an actual queue.  
     if (@Queue) {  
         # Process according to the format.  
         if ($format =~ m/^HTML$/i) {  
             # Convert the queue into an HTML list.  
             $retVal = "<ul>\n";  
             for my $line (@Queue) {  
                 my $escapedLine = CGI::escapeHTML($line);  
                 $retVal .= "<li>$escapedLine</li>\n";  
             }  
             $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
             # Convert the queue into a list of text lines.  
             $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
     }  
     # Return the formatted list.  
     return $retVal;  
 }  
2342    
2343  =head3 Confess  A file specification is the string passed to an C<open> call. It specifies the file
2344    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2345    method assumes that the file name is whatever follows the first angle bracket
2346    sequence.  So, for example, in the following strings the file name is
2347    C</usr/fig/myfile.txt>.
2348    
2349  C<< Confess($message); >>      >>/usr/fig/myfile.txt
2350        </usr/fig/myfile.txt
2351        | sort -u > /usr/fig/myfile.txt
2352    
2353  Trace the call stack and abort the program with the specified message. When used with  If the method cannot find a file name using its normal methods, it will return the
2354  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  whole incoming string.
 So, for example  
2355    
2356  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
2357    
2358  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item fileSpec
2359    
2360  =over 4  File specification string from which the file name is to be extracted.
2361    
2362  =item message  =item RETURN
2363    
2364  Message to include in the trace.  Returns a three-element list. The first element contains the file name portion of
2365    the specified string, or the whole string if a file name cannot be found via normal
2366    methods. The second element contains the start position of the file name portion and
2367    the third element contains the length.
2368    
2369  =back  =back
2370    
2371  =cut  =cut
2372    #: Return Type $;
2373  sub Confess {  sub FindNamePart {
2374      # Get the parameters.      # Get the parameters.
2375      my ($message) = @_;      my ($fileSpec) = @_;
2376      # Trace the call stack.      # Default to the whole input string.
2377      Cluck($message);      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2378      # Abort the program.      # Parse out the file name if we can.
2379      croak(">>> $message");      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2380            $retVal = $2;
2381            $len = length $retVal;
2382            $pos = (length $fileSpec) - (length $3) - $len;
2383        }
2384        # Return the result.
2385        return ($retVal, $pos, $len);
2386  }  }
2387    
2388  =head3 Assert  =head3 OpenDir
2389    
2390  C<< Assert($condition1, $condition2, ... $conditionN); >>      my @files = OpenDir($dirName, $filtered, $flag);
2391    
2392  Return TRUE if all the conditions are true. This method can be used in conjunction with  Open a directory and return all the file names. This function essentially performs
2393  the OR operator and the L</Confess> method as a debugging assert.  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2394  So, for example  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2395    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2396    filtered out of the return list. If the directory does not open and I<$flag> is not
2397    set, an exception is thrown. So, for example,
2398    
2399  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my @files = OpenDir("/Volumes/fig/contigs", 1);
2400    
2401  Will abort the program with a stack trace if the value of C<$recNum> is negative.  is effectively the same as
2402    
2403  =cut      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2404  sub Assert {      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
2405    
2406  =head3 Cluck  Similarly, the following code
2407    
2408  C<< Cluck($message); >>      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2409    
2410  Trace the call stack. Note that for best results, you should qualify the call with a  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2411  trace condition. For example,  automatically returns an empty list if the directory fails to open.
2412    
2413  C<< Cluck("Starting record parse.") if T(3); >>  =over 4
2414    
2415  will only trace the stack if the trace level for the package is 3 or more.  =item dirName
2416    
2417  =over 4  Name of the directory to open.
2418    
2419  =item message  =item filtered
2420    
2421  Message to include in the trace.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2422    from the list, else FALSE.
2423    
2424    =item flag
2425    
2426    TRUE if a failure to open is okay, else FALSE
2427    
2428  =back  =back
2429    
2430  =cut  =cut
2431    #: Return Type @;
2432  sub Cluck {  sub OpenDir {
2433      # Get the parameters.      # Get the parameters.
2434      my ($message) = @_;      my ($dirName, $filtered, $flag) = @_;
2435      # Trace what's happening.      # Declare the return variable.
2436      Trace("Stack trace for event: $message");      my @retVal = ();
2437      my $confession = longmess($message);      # Open the directory.
2438      # Convert the confession to a series of trace messages. Note we skip any      if (opendir(my $dirHandle, $dirName)) {
2439      # messages relating to calls into Tracer.          # The directory opened successfully. Get the appropriate list according to the
2440      for my $line (split /\s*\n/, $confession) {          # strictures of the filter parameter.
2441          Trace($line) if ($line !~ /Tracer\.pm/);          if ($filtered) {
2442                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2443            } else {
2444                @retVal = readdir $dirHandle;
2445            }
2446        } elsif (! $flag) {
2447            # Here the directory would not open and it's considered an error.
2448            Confess("Could not open directory $dirName.");
2449      }      }
2450        # Return the result.
2451        return @retVal;
2452  }  }
2453    
 =head3 Min  
2454    
2455  C<< my $min = Min($value1, $value2, ... $valueN); >>  =head3 Insure
2456    
2457        Insure($dirName, $chmod);
2458    
2459  Return the minimum argument. The arguments are treated as numbers.  Insure a directory is present.
2460    
2461  =over 4  =over 4
2462    
2463  =item $value1, $value2, ... $valueN  =item dirName
2464    
2465  List of numbers to compare.  Name of the directory to check. If it does not exist, it will be created.
2466    
2467  =item RETURN  =item chmod (optional)
2468    
2469  Returns the lowest number in the list.  Security privileges to be given to the directory if it is created.
2470    
2471  =back  =back
2472    
2473  =cut  =cut
2474    
2475  sub Min {  sub Insure {
2476      # Get the parameters. Note that we prime the return value with the first parameter.      my ($dirName, $chmod) = @_;
2477      my ($retVal, @values) = @_;      if (! -d $dirName) {
2478      # Loop through the remaining parameters, looking for the lowest.          Trace("Creating $dirName directory.") if T(2);
2479      for my $value (@values) {          eval {
2480          if ($value < $retVal) {              mkpath $dirName;
2481              $retVal = $value;              # If we have permissions specified, set them here.
2482                if (defined($chmod)) {
2483                    chmod $chmod, $dirName;
2484                }
2485            };
2486            if ($@) {
2487                Confess("Error creating $dirName: $@");
2488          }          }
2489      }      }
     # Return the minimum found.  
     return $retVal;  
2490  }  }
2491    
2492  =head3 Max  =head3 ChDir
2493    
2494  C<< my $max = Max($value1, $value2, ... $valueN); >>      ChDir($dirName);
2495    
2496  Return the maximum argument. The arguments are treated as numbers.  Change to the specified directory.
2497    
2498  =over 4  =over 4
2499    
2500  =item $value1, $value2, ... $valueN  =item dirName
   
 List of numbers to compare.  
   
 =item RETURN  
2501    
2502  Returns the highest number in the list.  Name of the directory to which we want to change.
2503    
2504  =back  =back
2505    
2506  =cut  =cut
2507    
2508  sub Max {  sub ChDir {
2509      # Get the parameters. Note that we prime the return value with the first parameter.      my ($dirName) = @_;
2510      my ($retVal, @values) = @_;      if (! -d $dirName) {
2511      # Loop through the remaining parameters, looking for the highest.          Confess("Cannot change to directory $dirName: no such directory.");
2512      for my $value (@values) {      } else {
2513          if ($value > $retVal) {          Trace("Changing to directory $dirName.") if T(File => 4);
2514              $retVal = $value;          my $okFlag = chdir $dirName;
2515            if (! $okFlag) {
2516                Confess("Error switching to directory $dirName.");
2517          }          }
2518      }      }
     # Return the maximum found.  
     return $retVal;  
2519  }  }
2520    
2521  =head3 AddToListMap  =head3 SetPermissions
2522    
2523        Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2524    
2525  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>  Set the permissions for a directory and all the files and folders inside it.
2526    In addition, the group ownership will be changed to the specified value.
2527    
2528  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  This method is more vulnerable than most to permission and compatability
2529  is created for the key. Otherwise, the new value is pushed onto the list.  problems, so it does internal error recovery.
2530    
2531  =over 4  =over 4
2532    
2533  =item hash  =item dirName
2534    
2535  Reference to the target hash.  Name of the directory to process.
2536    
2537  =item key  =item group
2538    
2539  Key for which the value is to be added.  Name of the group to be assigned.
2540    
2541  =item value1, value2, ... valueN  =item mask
2542    
2543  List of values to add to the key's value list.  Permission mask. Bits that are C<1> in this mask will be ORed into the
2544    permission bits of any file or directory that does not already have them
2545    set to 1.
2546    
2547  =back  =item otherMasks
2548    
2549  =cut  Map of search patterns to permission masks. If a directory name matches
2550    one of the patterns, that directory and all its members and subdirectories
2551    will be assigned the new pattern. For example, the following would
2552    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2553    
2554  sub AddToListMap {      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
     # Get the parameters.  
     my ($hash, $key, @values) = @_;  
     # Process according to whether or not the key already has a value.  
     if (! exists $hash->{$key}) {  
         $hash->{$key} = [@values];  
     } else {  
         push @{$hash->{$key}}, @values;  
     }  
 }  
2555    
2556  =head3 DebugMode  The list is ordered, so the following would use 0777 for C<tmp1> and
2557    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2558    
2559  C<< if (Tracer::DebugMode) { ...code... } >>      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2560                                                       '^tmp' => 0666);
2561    
2562  Return TRUE if debug mode has been turned on, else abort.  Note that the pattern matches are all case-insensitive, and only directory
2563    names are matched, not file names.
2564    
2565  Certain CGI scripts are too dangerous to exist in the production  =back
 environment. This method provides a simple way to prevent them  
 from working unless they are explicitly turned on by creating a password  
 cookie via the B<SetPassword> script.  If debugging mode  
 is not turned on, an error will occur.  
2566    
2567  =cut  =cut
2568    
2569  sub DebugMode {  sub SetPermissions {
2570      # Declare the return variable.      # Get the parameters.
2571      my $retVal = 0;      my ($dirName, $group, $mask, @otherMasks) = @_;
2572      # Check the debug configuration.      # Set up for error recovery.
2573      my $password = CGI::cookie("DebugMode");      eval {
2574      my $encrypted = Digest::MD5::md5_hex($password);          # Switch to the specified directory.
2575      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {          ChDir($dirName);
2576          $retVal = 1;          # Get the group ID.
2577            my $gid = getgrnam($group);
2578            # Get the mask for tracing.
2579            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2580            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2581            my $fixCount = 0;
2582            my $lookCount = 0;
2583            # @dirs will be a stack of directories to be processed.
2584            my @dirs = (getcwd());
2585            while (scalar(@dirs) > 0) {
2586                # Get the current directory.
2587                my $dir = pop @dirs;
2588                # Check for a match to one of the specified directory names. To do
2589                # that, we need to pull the individual part of the name off of the
2590                # whole path.
2591                my $simpleName = $dir;
2592                if ($dir =~ m!/([^/]+)$!) {
2593                    $simpleName = $1;
2594                }
2595                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2596                # Search for a match.
2597                my $match = 0;
2598                my $i;
2599                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2600                    my $pattern = $otherMasks[$i];
2601                    if ($simpleName =~ /$pattern/i) {
2602                        $match = 1;
2603                    }
2604                }
2605                # Check for a match. Note we use $i-1 because the loop added 2
2606                # before terminating due to the match.
2607                if ($match && $otherMasks[$i-1] != $mask) {
2608                    # This directory matches one of the incoming patterns, and it's
2609                    # a different mask, so we process it recursively with that mask.
2610                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2611      } else {      } else {
2612          # Here debug mode is off, so we generate an error.                  # Here we can process normally. Get all of the non-hidden members.
2613          Confess("Cannot use this facility without logging in.");                  my @submems = OpenDir($dir, 1);
2614                    for my $submem (@submems) {
2615                        # Get the full name.
2616                        my $thisMem = "$dir/$submem";
2617                        Trace("Checking member $thisMem.") if T(4);
2618                        $lookCount++;
2619                        if ($lookCount % 1000 == 0) {
2620                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2621                        }
2622                        # Fix the group.
2623                        chown -1, $gid, $thisMem;
2624                        # Insure this member is not a symlink.
2625                        if (! -l $thisMem) {
2626                            # Get its info.
2627                            my $fileInfo = stat $thisMem;
2628                            # Only proceed if we got the info. Otherwise, it's a hard link
2629                            # and we want to skip it anyway.
2630                            if ($fileInfo) {
2631                                my $fileMode = $fileInfo->mode;
2632                                if (($fileMode & $mask) != $mask) {
2633                                    # Fix this member.
2634                                    $fileMode |= $mask;
2635                                    chmod $fileMode, $thisMem;
2636                                    $fixCount++;
2637                                }
2638                                # If it's a subdirectory, stack it.
2639                                if (-d $thisMem) {
2640                                    push @dirs, $thisMem;
2641                                }
2642                            }
2643                        }
2644                    }
2645                }
2646            }
2647            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2648        };
2649        # Check for an error.
2650        if ($@) {
2651            Confess("SetPermissions error: $@");
2652      }      }
     # Return the determination indicator.  
     return $retVal;  
2653  }  }
2654    
2655  =head3 Strip  =head3 GetLine
2656    
2657  C<< my $string = Tracer::Strip($line); >>      my @data = Tracer::GetLine($handle);
2658    
2659  Strip all line terminators off a string. This is necessary when dealing with files  Read a line of data from a tab-delimited file.
 that may have been transferred back and forth several times among different  
 operating environments.  
2660    
2661  =over 4  =over 4
2662    
2663  =item line  =item handle
2664    
2665  Line of text to be stripped.  Open file handle from which to read.
2666    
2667  =item RETURN  =item RETURN
2668    
2669  The same line of text with all the line-ending characters chopped from the end.  Returns a list of the fields in the record read. The fields are presumed to be
2670    tab-delimited. If we are at the end of the file, then an empty list will be
2671    returned. If an empty line is read, a single list item consisting of a null
2672    string will be returned.
2673    
2674  =back  =back
2675    
2676  =cut  =cut
2677    
2678  sub Strip {  sub GetLine {
2679      # Get a copy of the parameter string.      # Get the parameters.
2680      my ($string) = @_;      my ($handle) = @_;
2681      my $retVal = (defined $string ? $string : "");      # Declare the return variable.
2682      # Strip the line terminator characters.      my @retVal = ();
2683      $retVal =~ s/(\r|\n)+$//g;      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2684        # Read from the file.
2685        my $line = <$handle>;
2686        # Only proceed if we found something.
2687        if (defined $line) {
2688            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2689            # upload control and have a nonstandard EOL combination.
2690            $line =~ s/(\r|\n)+$//;
2691            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2692            if (T(File => 4)) {
2693                my $escapedLine = $line;
2694                $escapedLine =~ s/\n/\\n/g;
2695                $escapedLine =~ s/\r/\\r/g;
2696                $escapedLine =~ s/\t/\\t/g;
2697                Trace("Line read: -->$escapedLine<--");
2698            }
2699            # If the line is empty, return a single empty string; otherwise, parse
2700            # it into fields.
2701            if ($line eq "") {
2702                push @retVal, "";
2703            } else {
2704                push @retVal, split /\t/,$line;
2705            }
2706        } else {
2707            # Trace the reason the read failed.
2708            Trace("End of file: $!") if T(File => 3);
2709        }
2710      # Return the result.      # Return the result.
2711      return $retVal;      return @retVal;
2712  }  }
2713    
2714  =head3 Pad  =head3 PutLine
2715    
2716  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      Tracer::PutLine($handle, \@fields, $eol);
2717    
2718  Pad a string to a specified length. The pad character will be a  Write a line of data to a tab-delimited file. The specified field values will be
2719  space, and the padding will be on the right side unless specified  output in tab-separated form, with a trailing new-line.
 in the third parameter.  
2720    
2721  =over 4  =over 4
2722    
2723  =item string  =item handle
   
 String to be padded.  
   
 =item len  
   
 Desired length of the padded string.  
   
 =item left (optional)  
2724    
2725  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  Output file handle.
2726    
2727  =item padChar (optional)  =item fields
2728    
2729  Character to use for padding. The default is a space.  List of field values.
2730    
2731  =item RETURN  =item eol (optional)
2732    
2733  Returns a copy of the original string with the pad character added to the  End-of-line character (default is "\n").
 specified end so that it achieves the desired length.  
2734    
2735  =back  =back
2736    
2737  =cut  =cut
2738    
2739  sub Pad {  sub PutLine {
2740      # Get the parameters.      # Get the parameters.
2741      my ($string, $len, $left, $padChar) = @_;      my ($handle, $fields, $eol) = @_;
2742      # Compute the padding character.      # Write the data.
2743      if (! defined $padChar) {      print $handle join("\t", @{$fields}) . ($eol || "\n");
         $padChar = " ";  
     }  
     # Compute the number of spaces needed.  
     my $needed = $len - length $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;  
         }  
     }  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 EOF  
   
 This is a constant that is lexically greater than any useful string.  
   
 =cut  
   
 sub EOF {  
     return "\xFF\xFF\xFF\xFF\xFF";  
2744  }  }
2745    
 =head3 TICK  
   
 C<< my @results = TICK($commandString); >>  
2746    
2747  Perform a back-tick operation on a command. If this is a Windows environment, any leading  =head3 PrintLine
 dot-slash (C<./> will be removed. So, for example, if you were doing  
   
     `./protein.cgi`  
2748    
2749  from inside a CGI script, it would work fine in Unix, but would issue an error message      Tracer::PrintLine($line);
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
   
     TICK("./protein.cgi")  
2750    
2751  it will work correctly in both environments.  Print a line of text with a trailing new-line.
2752    
2753  =over 4  =over 4
2754    
2755  =item commandString  =item line
   
 The command string to pass to the system.  
   
 =item RETURN  
2756    
2757  Returns the standard output from the specified command, as a list.  Line of text to print.
2758    
2759  =back  =back
2760    
2761  =cut  =cut
2762  #: Return Type @;  
2763  sub TICK {  sub PrintLine {
2764      # Get the parameters.      # Get the parameters.
2765      my ($commandString) = @_;      my ($line) = @_;
2766      # Chop off the dot-slash if this is Windows.      # Print the line.
2767      if ($FIG_Config::win_mode) {      print "$line\n";
         $commandString =~ s!^\./!!;  
     }  
     # Activate the command and return the result.  
     return `$commandString`;  
2768  }  }
2769    
 =head3 ScriptSetup  
2770    
2771  C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  =head2 Other Useful Methods
2772    
2773  Perform standard tracing and debugging setup for scripts. The value returned is  =head3 ParseParm
 the CGI object followed by a pre-built variable hash.  
2774    
2775  The C<Trace> form parameter is used to determine whether or not tracing is active and      my $listValue = Tracer::ParseParm($string);
 which trace modules (other than C<Tracer> itself) should be turned on. Specifying  
 the C<CGI> trace module will trace parameter and environment information. Parameters are  
 traced at level 3 and environment variables at level 4. To trace to a file instead of to  
 the web page, set C<TF> to 1. At the end of the script, the client should call  
 L</ScriptFinish> to output the web page.  
2776    
2777  In some situations, it is not practical to invoke tracing via form parameters. For this  Convert a parameter into a list reference. If the parameter is undefined,
2778  situation, you can turn on emergency tracing from the debugging control panel.  an undefined value will be returned. Otherwise, it will be parsed as a
2779  Tracing will then be turned on automatically for all programs that use the L</ETracing>  comma-separated list of values.
 method, which includes every program that uses this method or L</StandardSetup>.  
2780    
2781  =over 4  =over 4
2782    
2783  =item noTrace (optional)  =item string
2784    
2785  If specified, tracing will be suppressed. This is useful if the script wants to set up  Incoming string.
 tracing manually.  
2786    
2787  =item RETURN  =item RETURN
2788    
2789  Returns a two-element list consisting of a CGI query object and a variable hash for  Returns a reference to a list of values, or C<undef> if the incoming value
2790  the output page.  was undefined.
2791    
2792  =back  =back
2793    
2794  =cut  =cut
2795    
2796  sub ScriptSetup {  sub ParseParm {
2797      # Get the parameters.      # Get the parameters.
2798      my ($noTrace) = @_;      my ($string) = @_;
2799      # Get the CGI query object.      # Declare the return variable.
2800      my $cgi = CGI->new();      my $retVal;
2801      # Set up tracing if it's not suppressed.      # Check for data.
2802      ETracing($cgi) unless $noTrace;      if (defined $string) {
2803      # Create the variable hash.          # We have some, so split it into a list.
2804      my $varHash = { results => '' };          $retVal = [ split /\s*,\s*/, $string];
     # Return the query object and variable hash.  
     return ($cgi, $varHash);  
 }  
   
 =head3 ETracing  
   
 C<< ETracing($parameter); >>  
   
 Set up emergency tracing. Emergency tracing is tracing that is turned  
 on automatically for any program that calls this method. The emergency  
 tracing parameters are stored in a a file identified by a tracing key.  
 If this method is called with a CGI object, then the tracing key is  
 taken from a cookie. If it is called with no parameters, then the tracing  
 key is taken from an environment variable. If it is called with a string,  
 the tracing key is that string.  
   
 =over 4  
   
 =item parameter  
   
 A parameter from which the tracing key is computed. If it is a scalar,  
 that scalar is used as the tracing key. If it is a CGI object, the  
 tracing key is taken from the C<IP> cookie. If it is omitted, the  
 tracing key is taken from the C<TRACING> environment variable. If it  
 is a CGI object and emergency tracing is not on, the C<Trace> and  
 C<TF> parameters will be used to determine the type of tracing.  
   
 =back  
   
 =cut  
   
 sub ETracing {  
     # Get the parameter.  
     my ($parameter) = @_;  
     # Check for CGI mode.  
     my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);  
     # Default to no tracing except errors.  
     my ($tracing, $dest) = ("0", "WARN");  
     # Check for emergency tracing.  
     my $tkey = EmergencyKey($parameter);  
     my $emergencyFile = EmergencyFileName($tkey);  
     if (-e $emergencyFile) {  
         # We have the file. Read in the data.  
         my @tracing = GetFile($emergencyFile);  
         # Pull off the time limit.  
         my $expire = shift @tracing;  
         # Convert it to seconds.  
         $expire *= 3600;  
         # Check the file data.  
         my $stat = stat($emergencyFile);  
         my ($now) = gettimeofday;  
         if ($now - $stat->mtime > $expire) {  
             # Delete the expired file.  
             unlink $emergencyFile;  
         } else {  
             # Emergency tracing is on. Pull off the destination and  
             # the trace level;  
             $dest = shift @tracing;  
             my $level = shift @tracing;  
             # Convert the destination to a real tracing destination.  
             # temp directory.  
             $dest = EmergencyTracingDest($tkey, $dest);  
             # Insure Tracer is specified.  
             my %moduleHash = map { $_ => 1 } @tracing;  
             $moduleHash{Tracer} = 1;  
             # Set the trace parameter.  
             $tracing = join(" ", $level, sort keys %moduleHash);  
         }  
     } elsif (defined $cgi) {  
         # There's no emergency tracing, but we have a CGI object, so check  
         # for tracing from the form parameters.  
         if ($cgi->param('Trace')) {  
             # Here the user has requested tracing via a form.  
             $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");  
             $tracing = $cgi->param('Trace') . " Tracer";  
         }  
     }  
     # Setup the tracing we've determined from all the stuff above.  
     TSetup($tracing, $dest);  
     # If we're a web script, trace the parameter and environment data.  
     if (defined $cgi) {  
         TraceParms($cgi);  
2805      }      }
2806        # Return the result.
2807        return $retVal;
2808  }  }
2809    
2810  =head3 EmergencyFileName  =head3 Now
   
 C<< my $fileName = Tracer::EmergencyFileName($tkey); >>  
   
 Return the emergency tracing file name. This is the file that specifies  
 the tracing information.  
   
 =over 4  
   
 =item tkey  
   
 Tracing key for the current program.  
   
 =item RETURN  
2811    
2812  Returns the name of the file to contain the emergency tracing information.      my $string = Tracer::Now();
2813    
2814  =back  Return a displayable time stamp containing the local time. Whatever format this
2815    method produces must be parseable by L</ParseDate>.
2816    
2817  =cut  =cut
2818    
2819  sub EmergencyFileName {  sub Now {
2820      # Get the parameters.      return DisplayTime(time);
     my ($tkey) = @_;  
     # Compute the emergency tracing file name.  
     return "$FIG_Config::temp/Emergency$tkey.txt";  
2821  }  }
2822    
2823  =head3 EmergencyFileTarget  =head3 DisplayTime
2824    
2825  C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>      my $string = Tracer::DisplayTime($time);
2826    
2827  Return the emergency tracing target file name. This is the file that receives  Convert a time value to a displayable time stamp. Whatever format this
2828  the tracing output for file-based tracing.  method produces must be parseable by L</ParseDate>.
2829    
2830  =over 4  =over 4
2831    
2832  =item tkey  =item time
2833    
2834  Tracing key for the current program.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2835    
2836  =item RETURN  =item RETURN
2837    
2838  Returns the name of the file to contain the trace output.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2839    
2840  =back  =back
2841    
2842  =cut  =cut
2843    
2844  sub EmergencyFileTarget {  sub DisplayTime {
2845      # Get the parameters.      my ($time) = @_;
2846      my ($tkey) = @_;      my $retVal = "(n/a)";
2847      # Compute the emergency tracing file name.      if (defined $time) {
2848      return "$FIG_Config::temp/trace$tkey.log";          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2849            $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2850                      _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2851        }
2852        return $retVal;
2853  }  }
2854    
2855  =head3 EmergencyTracingDest  # Pad a number to 2 digits.
2856    sub _p2 {
2857  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>      my ($value) = @_;
2858        $value = "0$value" if ($value < 10);
2859        return $value;
2860    }
2861    
2862  This method converts an emergency tracing destination to a real  =head3 Escape
 tracing destination. The main difference is that if the  
 destination is C<FILE> or C<APPEND>, we convert it to file  
 output.  
2863    
2864  =over 4      my $codedString = Tracer::Escape($realString);
2865    
2866  =item tkey  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2867    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2868    result is to reverse the effect of L</UnEscape>.
2869    
2870  Tracing key for this environment.  =over 4
2871    
2872  =item myDest  =item realString
2873    
2874  Destination from the emergency tracing file.  String to escape.
2875    
2876  =item RETURN  =item RETURN
2877    
2878  Returns a destination that can be passed into L</TSetup>.  Escaped equivalent of the real string.
2879    
2880  =back  =back
2881    
2882  =cut  =cut
2883    
2884  sub EmergencyTracingDest {  sub Escape {
2885      # Get the parameters.      # Get the parameter.
2886      my ($tkey, $myDest) = @_;      my ($realString) = @_;
2887      # Declare the return variable.      # Initialize the return variable.
2888      my $retVal;      my $retVal = "";
2889      # Process according to the destination value.      # Loop through the parameter string, looking for sequences to escape.
2890      if ($myDest eq 'FILE') {      while (length $realString > 0) {
2891          $retVal = ">" . EmergencyFileTarget($tkey);          # Look for the first sequence to escape.
2892      } elsif ($myDest eq 'APPEND') {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2893          $retVal = ">>" . EmergencyFileTarget($tkey);              # Here we found it. The text preceding the sequence is in $1. The sequence
2894                # itself is in $2. First, move the clear text to the return variable.
2895                $retVal .= $1;
2896                # Strip the processed section off the real string.
2897                $realString = substr $realString, (length $2) + (length $1);
2898                # Get the matched character.
2899                my $char = $2;
2900                # If we have a CR, we are done.
2901                if ($char ne "\r") {
2902                    # It's not a CR, so encode the escape sequence.
2903                    $char =~ tr/\t\n/tn/;
2904                    $retVal .= "\\" . $char;
2905                }
2906      } else {      } else {
2907          $retVal = $myDest;              # Here there are no more escape sequences. The rest of the string is
2908                # transferred unmodified.
2909                $retVal .= $realString;
2910                $realString = "";
2911            }
2912      }      }
2913      # Return the result.      # Return the result.
2914      return $retVal;      return $retVal;
2915  }  }
2916    
2917  =head3 Emergency  =head3 UnEscape
2918    
2919  C<< Emergency($key, $hours, $dest, $level, @modules); >>      my $realString = Tracer::UnEscape($codedString);
2920    
2921  Turn on emergency tracing. This method can only be invoked over the web and is  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2922  should not be called if debug mode is off. The caller specifies the duration of the  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2923  emergency in hours, the desired tracing destination, the trace level,  be deleted.
 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.  
2924    
2925  =over 4  =over 4
2926    
2927  =item tkey  =item codedString
   
 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  
2928    
2929  Tracing level. A higher level means more trace messages.  String to un-escape.
2930    
2931  =item modules  =item RETURN
2932    
2933  A list of the tracing modules to activate.  Returns a copy of the original string with the escape sequences converted to their actual
2934    values.
2935    
2936  =back  =back
2937    
2938  =cut  =cut
2939    
2940  sub Emergency {  sub UnEscape {
2941      # Get the parameters.      # Get the parameter.
2942      my ($tkey, $hours, $dest, $level, @modules) = @_;      my ($codedString) = @_;
2943      # Create the emergency file.      # Initialize the return variable.
2944      my $specFile = EmergencyFileName($tkey);      my $retVal = "";
2945      my $outHandle = Open(undef, ">$specFile");      # Only proceed if the incoming string is nonempty.
2946      print $outHandle join("\n", $hours, $dest, $level, @modules, "");      if (defined $codedString) {
2947            # Loop through the parameter string, looking for escape sequences. We can't do
2948            # translating because it causes problems with the escaped slash. ("\\t" becomes
2949            # "\<tab>" no matter what we do.)
2950            while (length $codedString > 0) {
2951                # Look for the first escape sequence.
2952                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2953                    # Here we found it. The text preceding the sequence is in $1. The sequence
2954                    # itself is in $2. First, move the clear text to the return variable.
2955                    $retVal .= $1;
2956                    $codedString = substr $codedString, (2 + length $1);
2957                    # Get the escape value.
2958                    my $char = $2;
2959                    # If we have a "\r", we are done.
2960                    if ($char ne 'r') {
2961                        # Here it's not an 'r', so we convert it.
2962                        $char =~ tr/\\tn/\\\t\n/;
2963                        $retVal .= $char;
2964                    }
2965                } else {
2966                    # Here there are no more escape sequences. The rest of the string is
2967                    # transferred unmodified.
2968                    $retVal .= $codedString;
2969                    $codedString = "";
2970                }
2971            }
2972        }
2973        # Return the result.
2974        return $retVal;
2975  }  }
2976    
2977  =head3 EmergencyKey  =head3 Percent
2978    
2979  C<< my $tkey = EmergencyKey($parameter); >>      my $percent = Tracer::Percent($number, $base);
2980    
2981  Return the Key to be used for emergency tracing. This could be an IP address,  Returns the percent of the base represented by the given number. If the base
2982   a session ID, or a user name, depending on the environment.  is zero, returns zero.
2983    
2984  =over 4  =over 4
2985    
2986  =item parameter  =item number
2987    
2988  Parameter defining the method for finding the tracing key. If it is a scalar,  Percent numerator.
2989  then it is presumed to be the tracing key itself. If it is a CGI object, then  
2990  the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is  =item base
2991  taken from the C<TRACING> environment variable.  
2992    Percent base.
2993    
2994  =item RETURN  =item RETURN
2995    
2996  Returns the key to be used for labels in emergency tracing.  Returns the percentage of the base represented by the numerator.
2997    
2998  =back  =back
2999    
3000  =cut  =cut
3001    
3002  sub EmergencyKey {  sub Percent {
3003      # Get the parameters.      # Get the parameters.
3004      my ($parameter) = @_;      my ($number, $base) = @_;
3005      # Declare the return variable.      # Declare the return variable.
3006      my $retVal;      my $retVal = 0;
3007      # Determine the parameter type.      # Compute the percent.
3008      if (! defined $parameter) {      if ($base != 0) {
3009          # Here we're supposed to check the environment.          $retVal = $number * 100 / $base;
         $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;  
         }  
     }  
     # If no luck finding a key, use the PID.  
     if (! defined $retVal) {  
         $retVal = $$;  
3010      }      }
3011      # Return the result.      # Return the result.
3012      return $retVal;      return $retVal;
3013  }  }
3014    
3015    =head3 Constrain
3016    
3017  =head3 TraceParms      my $constrained = Constrain($value, $min, $max);
   
 C<< Tracer::TraceParms($cgi); >>  
3018    
3019  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Modify a numeric value to bring it to a point in between a maximum and a minimum.
 at level CGI => 4.  
3020    
3021  =over 4  =over 4
3022    
3023  =item cgi  =item value
3024    
3025  CGI query object containing the parameters to trace.  Value to constrain.
3026    
3027  =back  =item min (optional)
3028    
3029  =cut  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3030    
3031  sub TraceParms {  =item max (optional)
     # Get the parameters.  
     my ($cgi) = @_;  
     if (T(CGI => 3)) {  
         # Here we want to trace the parameter data.  
         my @names = $cgi->param;  
         for my $parmName (sort @names) {  
             # Note we skip the Trace parameters, which are for our use only.  
             if ($parmName ne 'Trace' && $parmName ne 'TF') {  
                 my @values = $cgi->param($parmName);  
                 Trace("CGI: $parmName = " . join(", ", @values));  
             }  
         }  
         # Display the request method.  
         my $method = $cgi->request_method();  
         Trace("Method: $method");  
     }  
     if (T(CGI => 4)) {  
         # Here we want the environment data too.  
         for my $envName (sort keys %ENV) {  
             Trace("ENV: $envName = $ENV{$envName}");  
         }  
     }  
 }  
3032    
3033  =head3 ScriptFinish  Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3034    
3035  C<< ScriptFinish($webData, $varHash); >>  =item RETURN
3036    
3037  Output a web page at the end of a script. Either the string to be output or the  Returns the incoming value, constrained according to the other parameters.
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
3038    
3039  A typical standard script would loook like the following.  =back
3040    
3041      BEGIN {  =cut
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
3042    
3043      my ($cgi, $varHash) = ScriptSetup();  sub Constrain {
3044      eval {      # Get the parameters.
3045          # ... get data from $cgi, put it in $varHash ...      my ($value, $min, $max) = @_;
3046      };      # Declare the return variable.
3047      if ($@) {      my $retVal = $value;
3048          Trace("Script Error: $@") if T(0);      # Apply the minimum constraint.
3049        if (defined $min && $retVal < $min) {
3050            $retVal = $min;
3051        }
3052        # Apply the maximum constraint.
3053        if (defined $max && $retVal > $max) {
3054            $retVal = $max;
3055        }
3056        # Return the result.
3057        return $retVal;
3058      }      }
     ScriptFinish("Html/MyTemplate.html", $varHash);  
3059    
3060  The idea here is that even if the script fails, you'll see trace messages and  =head3 Min
3061  useful output.  
3062        my $min = Min($value1, $value2, ... $valueN);
3063    
3064    Return the minimum argument. The arguments are treated as numbers.
3065    
3066  =over 4  =over 4
3067    
3068  =item webData  =item $value1, $value2, ... $valueN
3069    
3070  A string containing either the full web page to be written to the output or the  List of numbers to compare.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3071    
3072  =item varHash (optional)  =item RETURN
3073    
3074  If specified, then a reference to a hash mapping variable names for a template  Returns the lowest number in the list.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3075    
3076  =back  =back
3077    
3078  =cut  =cut
3079    
3080  sub ScriptFinish {  sub Min {
3081      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3082      my ($webData, $varHash) = @_;      my ($retVal, @values) = @_;
3083      # Check for a template file situation.      # Loop through the remaining parameters, looking for the lowest.
3084      my $outputString;      for my $value (@values) {
3085      if (defined $varHash) {          if ($value < $retVal) {
3086          # Here we have a template file. We need to determine the template type.              $retVal = $value;
         my $template;  
         if ($FIG_Config::template_url && $webData =~ /\.php$/) {  
             $template = "$FIG_Config::template_url/$webData";  
         } else {  
             $template = "<<$webData";  
         }  
         $outputString = PageBuilder::Build($template, $varHash, "Html");  
     } else {  
         # Here the user gave us a raw string.  
         $outputString = $webData;  
     }  
     # Check for trace messages.  
     if ($Destination ne "NONE" && $TraceLevel > 0) {  
         # We have trace messages, so we want to put them at the end of the body. This  
         # is either at the end of the whole string or at the beginning of the BODY  
         # end-tag.  
         my $pos = length $outputString;  
         if ($outputString =~ m#</body>#gi) {  
             $pos = (pos $outputString) - 7;  
         }  
         # If the trace messages were queued, we unroll them. Otherwise, we display the  
         # destination.  
         my $traceHtml;  
         if ($Destination eq "QUEUE") {  
             $traceHtml = QTrace('Html');  
         } elsif ($Destination =~ /^>>(.+)$/) {  
             # Here the tracing output it to a file. We code it as a hyperlink so the user  
             # can copy the file name into the clipboard easily.  
             my $actualDest = $1;  
             $traceHtml = "<p>Tracing output to $actualDest.</p>\n";  
         } else {  
             # Here we have one of the special destinations.  
             $traceHtml = "<P>Tracing output type is $Destination.</p>\n";  
3087          }          }
         substr $outputString, $pos, 0, $traceHtml;  
3088      }      }
3089      # Write the output string.      # Return the minimum found.
3090      print $outputString;      return $retVal;
3091  }  }
3092    
3093  =head3 Insure  =head3 Max
3094    
3095  C<< Insure($dirName); >>      my $max = Max($value1, $value2, ... $valueN);
3096    
3097  Insure a directory is present.  Return the maximum argument. The arguments are treated as numbers.
3098    
3099  =over 4  =over 4
3100    
3101  =item dirName  =item $value1, $value2, ... $valueN
3102    
3103  Name of the directory to check. If it does not exist, it will be created.  List of numbers to compare.
3104    
3105    =item RETURN
3106    
3107    Returns the highest number in the list.
3108    
3109  =back  =back
3110    
3111  =cut  =cut
3112    
3113  sub Insure {  sub Max {
3114      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
3115      if (! -d $dirName) {      my ($retVal, @values) = @_;
3116          Trace("Creating $dirName directory.") if T(2);      # Loop through the remaining parameters, looking for the highest.
3117          eval { mkpath $dirName; };      for my $value (@values) {
3118          if ($@) {          if ($value > $retVal) {
3119              Confess("Error creating $dirName: $@");              $retVal = $value;
3120          }          }
3121      }      }
3122        # Return the maximum found.
3123        return $retVal;
3124  }  }
3125    
 =head3 ChDir  
3126    
3127  C<< ChDir($dirName); >>  =head3 Strip
3128    
3129        my $string = Tracer::Strip($line);
3130    
3131  Change to the specified directory.  Strip all line terminators off a string. This is necessary when dealing with files
3132    that may have been transferred back and forth several times among different
3133    operating environments.
3134    
3135  =over 4  =over 4
3136    
3137  =item dirName  =item line
3138    
3139  Name of the directory to which we want to change.  Line of text to be stripped.
3140    
3141    =item RETURN
3142    
3143    The same line of text with all the line-ending characters chopped from the end.
3144    
3145  =back  =back
3146    
3147  =cut  =cut
3148    
3149  sub ChDir {  sub Strip {
3150      my ($dirName) = @_;      # Get a copy of the parameter string.
3151      if (! -d $dirName) {      my ($string) = @_;
3152          Confess("Cannot change to directory $dirName: no such directory.");      my $retVal = (defined $string ? $string : "");
3153      } else {      # Strip the line terminator characters.
3154          Trace("Changing to directory $dirName.") if T(4);      $retVal =~ s/(\r|\n)+$//g;
3155          my $okFlag = chdir $dirName;      # Return the result.
3156          if (! $okFlag) {      return $retVal;
             Confess("Error switching to directory $dirName.");  
         }  
     }  
3157  }  }
3158    
3159  =head3 SendSMS  =head3 Pad
3160    
3161  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3162    
3163  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  Pad a string to a specified length. The pad character will be a
3164  user name, password, and API ID for the relevant account in the hash reference variable  space, and the padding will be on the right side unless specified
3165  I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For  in the third parameter.
 example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID  
 is C<2561022>, then the FIG_Config file must contain  
3166    
3167      $phone =  { user => 'BruceTheHumanPet',  =over 4
                 password => 'silly',  
                 api_id => '2561022' };  
3168    
3169  The original purpose of this method was to insure Bruce would be notified immediately when the  =item string
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3170    
3171  The message ID will be returned if successful, and C<undef> if an error occurs.  String to be padded.
3172    
3173  =over 4  =item len
3174    
3175  =item phoneNumber  Desired length of the padded string.
3176    
3177  Phone number to receive the message, in international format. A United States phone number  =item left (optional)
 would be prefixed by "1". A British phone number would be prefixed by "44".  
3178    
3179  =item msg  TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3180    
3181  Message to send to the specified phone.  =item padChar (optional)
3182    
3183    Character to use for padding. The default is a space.
3184    
3185  =item RETURN  =item RETURN
3186    
3187  Returns the message ID if successful, and C<undef> if the message could not be sent.  Returns a copy of the original string with the pad character added to the
3188    specified end so that it achieves the desired length.
3189    
3190  =back  =back
3191    
3192  =cut  =cut
3193    
3194  sub SendSMS {  sub Pad {
3195      # Get the parameters.      # Get the parameters.
3196      my ($phoneNumber, $msg) = @_;      my ($string, $len, $left, $padChar) = @_;
3197      # Declare the return variable. If we do not change it, C<undef> will be returned.      # Compute the padding character.
3198      my $retVal;      if (! defined $padChar) {
3199      # Only proceed if we have phone support.          $padChar = " ";
3200      if (! defined $FIG_Config::phone) {      }
3201          Trace("Phone support not present in FIG_Config.") if T(1);      # Compute the number of spaces needed.
3202      } else {      my $needed = $len - length $string;
3203          # Get the phone data.      # Copy the string into the return variable.
3204          my $parms = $FIG_Config::phone;      my $retVal = $string;
3205          # Get the Clickatell URL.      # Only proceed if padding is needed.
3206          my $url = "http://api.clickatell.com/http/";      if ($needed > 0) {
3207          # Create the user agent.          # Create the pad string.
3208          my $ua = LWP::UserAgent->new;          my $pad = $padChar x $needed;
3209          # Request a Clickatell session.          # Affix it to the return value.
3210          my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},          if ($left) {
3211                                       password => $parms->{password},              $retVal = $pad . $retVal;
                                      api_id => $parms->{api_id},  
                                      to => $phoneNumber,  
                                      text => $msg});  
         # Check for an error.  
         if (! $resp->is_success) {  
             Trace("Alert failed.") if T(1);  
         } else {  
             # Get the message ID.  
             my $rstring = $resp->content;  
             if ($rstring =~ /^ID:\s+(.*)$/) {  
                 $retVal = $1;  
3212              } else {              } else {
3213                  Trace("Phone attempt failed with $rstring") if T(1);              $retVal .= $pad;
3214              }              }
3215          }          }
3216        # Return the result.
3217        return $retVal;
3218    }
3219    
3220    =head3 EOF
3221    
3222    This is a constant that is lexically greater than any useful string.
3223    
3224    =cut
3225    
3226    sub EOF {
3227        return "\xFF\xFF\xFF\xFF\xFF";
3228    }
3229    
3230    =head3 TICK
3231    
3232        my @results = TICK($commandString);
3233    
3234    Perform a back-tick operation on a command. If this is a Windows environment, any leading
3235    dot-slash (C<./> will be removed. So, for example, if you were doing
3236    
3237        `./protein.cgi`
3238    
3239    from inside a CGI script, it would work fine in Unix, but would issue an error message
3240    in Windows complaining that C<'.'> is not a valid command. If instead you code
3241    
3242        TICK("./protein.cgi")
3243    
3244    it will work correctly in both environments.
3245    
3246    =over 4
3247    
3248    =item commandString
3249    
3250    The command string to pass to the system.
3251    
3252    =item RETURN
3253    
3254    Returns the standard output from the specified command, as a list.
3255    
3256    =back
3257    
3258    =cut
3259    #: Return Type @;
3260    sub TICK {
3261        # Get the parameters.
3262        my ($commandString) = @_;
3263        # Chop off the dot-slash if this is Windows.
3264        if ($FIG_Config::win_mode) {
3265            $commandString =~ s!^\./!!;
3266      }      }
3267      # Return the result.      # Activate the command and return the result.
3268      return $retVal;      return `$commandString`;
3269  }  }
3270    
3271    
3272  =head3 CommaFormat  =head3 CommaFormat
3273    
3274  C<< my $formatted = Tracer::CommaFormat($number); >>      my $formatted = Tracer::CommaFormat($number);
3275    
3276  Insert commas into a number.  Insert commas into a number.
3277    
# Line 2695  Line 3304 
3304      # Return the result.      # Return the result.
3305      return $retVal;      return $retVal;
3306  }  }
 =head3 SetPermissions  
   
 C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  
   
 Set the permissions for a directory and all the files and folders inside it.  
 In addition, the group ownership will be changed to the specified value.  
   
 This method is more vulnerable than most to permission and compatability  
 problems, so it does internal error recovery.  
   
 =over 4  
   
 =item dirName  
   
 Name of the directory to process.  
   
 =item group  
   
 Name of the group to be assigned.  
   
 =item mask  
   
 Permission mask. Bits that are C<1> in this mask will be ORed into the  
 permission bits of any file or directory that does not already have them  
 set to 1.  
   
 =item otherMasks  
3307    
 Map of search patterns to permission masks. If a directory name matches  
 one of the patterns, that directory and all its members and subdirectories  
 will be assigned the new pattern. For example, the following would  
 assign 01664 to most files, but would use 01777 for directories named C<tmp>.  
   
     Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  
   
 The list is ordered, so the following would use 0777 for C<tmp1> and  
 0666 for C<tmp>, C<tmp2>, or C<tmp3>.  
   
     Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  
                                                    '^tmp' => 0666);  
   
 Note that the pattern matches are all case-insensitive, and only directory  
 names are matched, not file names.  
   
 =back  
   
 =cut  
   
 sub SetPermissions {  
     # Get the parameters.  
     my ($dirName, $group, $mask, @otherMasks) = @_;  
     # Set up for error recovery.  
     eval {  
         # Switch to the specified directory.  
         ChDir($dirName);  
         # Get the group ID.  
         my $gid = getgrnam($group);  
         # Get the mask for tracing.  
         my $traceMask = sprintf("%04o", $mask) . "($mask)";  
         Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(2);  
         my $fixCount = 0;  
         my $lookCount = 0;  
         # @dirs will be a stack of directories to be processed.  
         my @dirs = (getcwd());  
         while (scalar(@dirs) > 0) {  
             # Get the current directory.  
             my $dir = pop @dirs;  
             # Check for a match to one of the specified directory names. To do  
             # that, we need to pull the individual part of the name off of the  
             # whole path.  
             my $simpleName = $dir;  
             if ($dir =~ m!/([^/]+)$!) {  
                 $simpleName = $1;  
             }  
             Trace("Simple directory name for $dir is $simpleName.") if T(4);  
             # Search for a match.  
             my $match = 0;  
             my $i;  
             for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {  
                 my $pattern = $otherMasks[$i];  
                 if ($simpleName =~ /$pattern/i) {  
                     $match = 1;  
                 }  
             }  
             # Check for a match. Note we use $i-1 because the loop added 2  
             # before terminating due to the match.  
             if ($match && $otherMasks[$i-1] != $mask) {  
                 # This directory matches one of the incoming patterns, and it's  
                 # a different mask, so we process it recursively with that mask.  
                 SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);  
             } else {  
                 # Here we can process normally. Get all of the non-hidden members.  
                 my @submems = OpenDir($dir, 1);  
                 for my $submem (@submems) {  
                     # Get the full name.  
                     my $thisMem = "$dir/$submem";  
                     Trace("Checking member $thisMem.") if T(4);  
                     $lookCount++;  
                     if ($lookCount % 1000 == 0) {  
                         Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(3);  
                     }  
                     # Fix the group.  
                     chown -1, $gid, $thisMem;  
                     # Insure this member is not a symlink.  
                     if (! -l $thisMem) {  
                         # Get its info.  
                         my $fileInfo = stat $thisMem;  
                         # Only proceed if we got the info. Otherwise, it's a hard link  
                         # and we want to skip it anyway.  
                         if ($fileInfo) {  
                             my $fileMode = $fileInfo->mode;  
                             if (($fileMode & $mask) != $mask) {  
                                 # Fix this member.  
                                 $fileMode |= $mask;  
                                 chmod $fileMode, $thisMem;  
                                 $fixCount++;  
                             }  
                             # If it's a subdirectory, stack it.  
                             if (-d $thisMem) {  
                                 push @dirs, $thisMem;  
                             }  
                         }  
                     }  
                 }  
             }  
         }  
         Trace("$lookCount files and directories processed, $fixCount fixed.") if T(2);  
     };  
     # Check for an error.  
     if ($@) {  
         Confess("SetPermissions error: $@");  
     }  
 }  
3308    
3309  =head3 CompareLists  =head3 CompareLists
3310    
3311  C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3312    
3313  Compare two lists of tuples, and return a hash analyzing the differences. The lists  Compare two lists of tuples, and return a hash analyzing the differences. The lists
3314  are presumed to be sorted alphabetically by the value in the $keyIndex column.  are presumed to be sorted alphabetically by the value in the $keyIndex column.
# Line 2896  Line 3373 
3373      return ($inserted, $deleted);      return ($inserted, $deleted);
3374  }  }
3375    
3376  =head3 GetLine  =head3 GenerateURL
3377    
3378  C<< my @data = Tracer::GetLine($handle); >>      my $queryUrl = Tracer::GenerateURL($page, %parameters);
3379    
3380  Read a line of data from a tab-delimited file.  Generate a GET-style URL for the specified page with the specified parameter
3381    names and values. The values will be URL-escaped automatically. So, for
3382    example
3383    
3384        Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3385    
3386    would return
3387    
3388        form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3389    
3390  =over 4  =over 4
3391    
3392  =item handle  =item page
3393    
3394  Open file handle from which to read.  Page URL.
3395    
3396    =item parameters
3397    
3398    Hash mapping parameter names to parameter values.
3399    
3400  =item RETURN  =item RETURN
3401    
3402  Returns a list of the fields in the record read. The fields are presumed to be  Returns a GET-style URL that goes to the specified page and passes in the
3403  tab-delimited. If we are at the end of the file, then an empty list will be  specified parameters and values.
 returned. If an empty line is read, a single list item consisting of a null  
 string will be returned.  
3404    
3405  =back  =back
3406    
3407  =cut  =cut
3408    
3409  sub GetLine {  sub GenerateURL {
3410      # Get the parameters.      # Get the parameters.
3411      my ($handle) = @_;      my ($page, %parameters) = @_;
3412      # Declare the return variable.      # Prime the return variable with the page URL.
3413      my @retVal = ();      my $retVal = $page;
3414      # Read from the file.      # Loop through the parameters, creating parameter elements in a list.
3415      my $line = <$handle>;      my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3416      # Only proceed if we found something.      # If the list is nonempty, tack it on.
3417      if (defined $line) {      if (@parmList) {
3418          # Remove the new-line.          $retVal .= "?" . join(";", @parmList);
         chomp $line;  
         # If the line is empty, return a single empty string; otherwise, parse  
         # it into fields.  
         if ($line eq "") {  
             push @retVal, "";  
         } else {  
             push @retVal, split /\t/,$line;  
         }  
3419      }      }
3420      # Return the result.      # Return the result.
3421      return @retVal;      return $retVal;
3422  }  }
3423    
3424  =head3 PutLine  =head3 ApplyURL
3425    
3426  C<< Tracer::PutLine($handle, \@fields); >>      Tracer::ApplyURL($table, $target, $url);
3427    
3428  Write a line of data to a tab-delimited file. The specified field values will be  Run through a two-dimensional table (or more accurately, a list of lists), converting the
3429  output in tab-separated form, with a trailing new-line.  I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3430    URL column will be deleted by this process and the target column will be HTML-escaped.
3431    
3432    This provides a simple way to process the results of a database query into something
3433    displayable by combining a URL with text.