[Bio] / FigKernelPackages / Tracer.pm Repository:
ViewVC logotype

Diff of /FigKernelPackages/Tracer.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.79, Thu Nov 9 21:12:46 2006 UTC revision 1.106, Fri May 16 08:32:02 2008 UTC
# Line 1  Line 1 
1  #  # -*- perl -*-
2    ########################################################################
3  # Copyright (c) 2003-2006 University of Chicago and Fellowship  # Copyright (c) 2003-2006 University of Chicago and Fellowship
4  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
5  #  #
# Line 13  Line 14 
14  # at info@ci.uchicago.edu or the Fellowship for Interpretation of  # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15  # Genomes at veronika@thefig.info or download a copy from  # Genomes at veronika@thefig.info or download a copy from
16  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
17  #  ########################################################################
18    
19  package Tracer;  package Tracer;
20    
21      require Exporter;      require Exporter;
22      @ISA = ('Exporter');      @ISA = ('Exporter');
23      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn);
24      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
25      use strict;      use strict;
26      use Carp qw(longmess croak);      use Carp qw(longmess croak carp);
27      use CGI;      use CGI;
28      use Cwd;      use Cwd;
29      use FIG_Config;      use FIG_Config;
# Line 35  Line 36 
36      use Time::HiRes 'gettimeofday';      use Time::HiRes 'gettimeofday';
37      use URI::Escape;      use URI::Escape;
38      use Time::Local;      use Time::Local;
39        use POSIX qw(strftime);
40        use Time::Zone;
41        use Fcntl ':flock';
42    
43    
44  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
45    
# Line 159  Line 164 
164    
165  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
166  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
167  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
168  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
169  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
170  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
171  the tracing in your environment without stepping on other users.  the tracing in your environment without stepping on other users.
# Line 183  Line 188 
188    
189  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
190  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
191  using the L</StandardScript> or L</StandardSetup> methods, emergency tracing  using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
192  will be configured automatically.  will be configured automatically.
193    
 =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.  
   
194  =cut  =cut
195    
196  # Declare the configuration variables.  # Declare the configuration variables.
197    
198  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
199  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
200                              # standard output                              # standard output
201  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
202                              # hash of active category names                              # hash of active category names
203    my @LevelNames = qw(error warn notice info detail);
204  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
205                              # messages                              # messages
206  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
207  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
208    my $LastLevel = 0;          # level of the last test call
209  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
210  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
211    my $SavedCGI;               # CGI object passed to ETracing
212    my $CommandLine;            # Command line passed to StandardSetup
213    umask 2;                    # Fix the damn umask so everything is group-writable.
214    
215  =head2 Public Methods  =head2 Tracing Methods
216    
217    =head3 Setups
218    
219        my $count = Tracer::Setups();
220    
221    Return the number of times L</TSetup> has been called.
222    
223    This method allows for the creation of conditional tracing setups where, for example, we
224    may want to set up tracing if nobody else has done it before us.
225    
226    =cut
227    
228    sub Setups {
229        return $SetupCount;
230    }
231    
232  =head3 TSetup  =head3 TSetup
233    
234  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
235    
236  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
237  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 347  Line 281 
281          }          }
282      }      }
283      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
284      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
285      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
286        # the standard output (tee mode).
287      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
288          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
289              $TeeFlag = 1;              $TeeFlag = 1;
290              $target = substr($target, 1);              $target = substr($target, 1);
291          }          }
292          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
293                # We need to initialize the file (which clears it).
294              open TRACEFILE, $target;              open TRACEFILE, $target;
295              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
296              close TRACEFILE;              close TRACEFILE;
297                # Set to append mode now that the file has been cleared.
298              $Destination = ">$target";              $Destination = ">$target";
299          } else {          } else {
300              $Destination = $target;              $Destination = $target;
# Line 369  Line 306 
306      $SetupCount++;      $SetupCount++;
307  }  }
308    
309  =head3 StandardSetup  =head3 SetLevel
310    
311  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
312    
313  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.  
314    
315  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.  
316    
317  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  
318    
319      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
320    
321  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.  
322    
323  =over 4  =cut
324    
325  =item SQL  sub SetLevel {
326        $TraceLevel = $_[0];
327    }
328    
329  Traces SQL commands and activity.  =head3 ParseDate
330    
331  =item Tracer      my $time = Tracer::ParseDate($dateString);
332    
333  Traces error messages and call stacks.  Convert a date into a PERL time number. This method expects a date-like string
334    and parses it into a number. The string must be vaguely date-like or it will
335    return an undefined value. Our requirement is that a month and day be
336    present and that three pieces of the date string (time of day, month and day,
337    year) be separated by likely delimiters, such as spaces, commas, and such-like.
338    
339  =back  If a time of day is present, it must be in military time with two digits for
340    everything but the hour.
341    
342  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.  
343    
344      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
345    equally innocuous. This means, however, that a sufficiently long sentence with date-like
346    parts in it may be interpreted as a date. Hopefully this will not be a problem.
347    
348  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  
349    
350  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.  
351    
352      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  =over 4
353    
354  would send the trace output to C<traceBruce.log> in the temporary directory.  =item dateString
355    
356  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.  
357    
358  You can specify a different default trace level by setting C<$options->{trace}>  =item RETURN
 prior to calling this method.  
359    
360  An example at this point would help. Consider, for example, the command-line utility  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
361  C<TransactFeatures>. It accepts a list of positional parameters plus the options  the date string is invalid. A valid date string must contain a month and day.
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
362    
363      my ($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);  
364    
365    =cut
366    
367  The call to C<ParseCommand> specifies the default values for the options and  # Universal month conversion table.
368  stores the actual options in a hash that is returned as C<$options>. The  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
369  positional parameters are returned in C<@parameters>.                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
370                                Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
371                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
372                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
373                                Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
374                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
375                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
376                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
377                                Oct =>  9, October  =>   9, '10' =>  9,
378                                Nov => 10, November =>  10, '11' => 10,
379                                Dec => 11, December =>  11, '12' => 11
380                            };
381    
382  The following is a sample command line for C<TransactFeatures>.  sub ParseDate {
383        # Get the parameters.
384        my ($dateString) = @_;
385        # Declare the return variable.
386        my $retVal;
387        # Find the month and day of month. There are two ways that can happen. We check for the
388        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
389        # won't be fooled into thinking the month is Sunday.
390        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
391            my ($mon, $mday) = (MONTHS->{$1}, $2);
392            # Insist that the month and day are valid.
393            if (defined($mon) && $2 >= 1 && $2 <= 31) {
394                # Find the time.
395                my ($hour, $min, $sec) = (0, 0, 0);
396                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
397                    ($hour, $min, $sec) = ($1, $2, $3);
398                }
399                # Find the year.
400                my $year;
401                if ($dateString =~ /\b(\d{4})\b/) {
402                    $year = $1;
403                } else {
404                    # Get the default year, which is this one. Note we must convert it to
405                    # the four-digit value expected by "timelocal".
406                    (undef, undef, undef, undef, undef, $year) = localtime();
407                    $year += 1900;
408                }
409                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
410            }
411        }
412        # Return the result.
413        return $retVal;
414    }
415    
416      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  =head3 LogErrors
417    
418  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional      Tracer::LogErrors($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<$options> hash would be  
419    
420      { trace => 2, sql => 0, safe => 0,  Route the standard error output to a log file.
       noAlias => 1, start => ' ', tblFiles => 0 }  
421    
422  Use of C<StandardSetup> in this way provides a simple way of performing  =over 4
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
423    
424  If the C<background> option is specified on the command line, then the  =item fileName
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
425    
426      -user=Bruce -background  Name of the file to receive the error output.
427    
428  then the trace output would go to C<traceBruce.log>, the standard output to  =back
 C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to  
 simplify starting a command in the background.  
429    
430  The user name is also used as the tracing key for L</Emergency Tracing>.  =cut
 Specifying a value of C<E> for the trace level causes emergency tracing to  
 be used instead of custom tracing. If the user name is not specified,  
 the tracing key is taken from the C<Tracing> environment variable. If there  
 is no value for that variable, the tracing key will be computed from the PID.  
431    
432  Finally, if the special option C<-h> is specified, the option names will  sub LogErrors {
433  be traced at level 0 and the program will exit without processing.      # Get the file name.
434  This provides a limited help capability. For example, if the user enters      my ($fileName) = @_;
435        # Open the file as the standard error output.
436        open STDERR, '>', $fileName;
437    }
438    
439      TransactFeatures -h  =head3 Trace
440    
441  he would see the following output.      Trace($message);
442    
443      TransactFeatures [options] command transactionDirectory IDfile  Write a trace message to the target location specified in L</TSetup>. If there has not been
444          -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  
445    
446  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,  
447    
448      { trace => [0, "tracing level (default 0)"],  =item message
        ...  
449    
450  would set the default trace level to 0 instead of E, while  Message to write.
451    
452      { trace => ["2-", "tracing level (default 2)"],  =back
        ...  
453    
454  would set the default to 2, but trace only to the log file, not to the  =cut
 standard output.  
455    
456  The parameters to this method are as follows.  sub Trace {
457        # Get the parameters.
458        my ($message) = @_;
459        # Strip off any line terminators at the end of the message. We will add
460        # new-line stuff ourselves.
461        my $stripped = Strip($message);
462        # Compute the caller information.
463        my ($callPackage, $callFile, $callLine) = caller();
464        my $callFileTitle = basename($callFile);
465        # Check the caller.
466        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
467        # Get the timestamp.
468        my $timeStamp = Now();
469        # Build the prefix.
470        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
471        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
472        # Format the message.
473        my $formatted = "$prefix $stripped";
474        # Process according to the destination.
475        if ($Destination eq "TEXT") {
476            # Write the message to the standard output.
477            print "$formatted\n";
478        } elsif ($Destination eq "ERROR") {
479            # Write the message to the error output. Here, we want our prefix fields.
480            print STDERR "$formatted\n";
481        } elsif ($Destination eq "WARN") {
482            # Emit the message to the standard error output. It is presumed that the
483            # error logger will add its own prefix fields, the notable exception being
484            # the caller info.
485            print STDERR "$callerInfo$stripped\n";
486        } elsif ($Destination eq "QUEUE") {
487            # Push the message into the queue.
488            push @Queue, "$formatted";
489        } elsif ($Destination eq "HTML") {
490            # Convert the message to HTML and write it to the standard output.
491            my $escapedMessage = CGI::escapeHTML($stripped);
492            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
493        } elsif ($Destination =~ m/^>>/) {
494            # Write the trace message to an output file.
495            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
496            print TRACING "$formatted\n";
497            close TRACING;
498            # If the Tee flag is on, echo it to the standard output.
499            if ($TeeFlag) {
500                print "$formatted\n";
501            }
502        }
503    }
504    
505  =over 4  =head3 T
506    
507  =item categories      my $switch = T($category, $traceLevel);
508    
509  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.  
510    
511  =item options      my $switch = T($traceLevel);
512    
513  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
514  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).  
515    
516  =item parmHelp  =over 4
517    
518  A string that vaguely describes the positional parameters. This is used  =item category
 if the user specifies the C<-h> option.  
519    
520  =item argv  Category to which the message belongs. If not specified, the caller's package name is
521    used.
522    
523  List of command line parameters, including the option switches, which must  =item traceLevel
524  precede the positional parameters and be prefixed by a hyphen.  
525    Relevant tracing level.
526    
527  =item RETURN  =item RETURN
528    
529  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.  
530    
531  =back  =back
532    
533  =cut  =cut
534    
535  sub StandardSetup {  sub T {
536        # Declare the return variable.
537        my $retVal = 0;
538        # Only proceed if tracing is turned on.
539        if ($Destination ne "NONE") {
540      # Get the parameters.      # Get the parameters.
541      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
542      # Get the default tracing key.          if (!defined $traceLevel) {
543      my $tkey = EmergencyKey();              # Here we have no category, so we need to get the calling package.
544      # Add the tracing options.              # The calling package is normally the first parameter. If it is
545      if (! exists $options->{trace}) {              # omitted, the first parameter will be the tracelevel. So, the
546          $options->{trace} = ['E', "tracing level (E for emergency tracing)"];              # first thing we do is shift the so-called category into the
547      }              # $traceLevel variable where it belongs.
548      $options->{sql} = [0, "turn on SQL tracing"];              $traceLevel = $category;
549      $options->{h} = [0, "display command-line options"];              my ($package, $fileName, $line) = caller;
550      $options->{user} = [$tkey, "tracing key"];              # If there is no calling package, we default to "main".
551      $options->{background} = [0, "spool standard and error output"];              if (!$package) {
552      # 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});  
553      } else {      } else {
554          # Here the tracing is controlled from the command line.                  my @cats = split /::/, $package;
555          my @cats = @{$categories};                  $category = $cats[$#cats];
         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;  
556          }          }
         # 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";  
557              }              }
558              # Close the test file.          # Save the category name and level.
559              close TESTTRACE;          $LastCategory = $category;
560          } else {          $LastLevel = $traceLevel;
561              # Here we can't trace to a file. We trace to the standard output if it's          # Convert it to lower case before we hash it.
562              # okay, and the error log otherwise.          $category = lc $category;
563              if ($textOKFlag) {          # Validate the trace level.
564                  $traceMode = "TEXT";          if (ref $traceLevel) {
565              } else {              Confess("Bad trace level.");
566                  $traceMode = "WARN";          } elsif (ref $TraceLevel) {
567                Confess("Bad trace config.");
568              }              }
569            # Make the check. Note that level 0 shows even if the category is turned off.
570            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
571          }          }
572          # Now set up the tracing.      # Return the computed result.
573          TSetup("$traceLevel $cats", $traceMode);      return $retVal;
574      }      }
575      # Check for the "h" option. If it is specified, dump the command-line  
576      # options and exit the program.  =head3 QTrace
577      if ($retOptions->{h}) {  
578          $0 =~ m#[/\\](\w+)(\.pl)?$#i;      my $data = QTrace($format);
579          print "$1 [options] $parmHelp\n";  
580          for my $key (sort keys %{$options}) {  Return the queued trace data in the specified format.
581              my $name = Pad($key, $longestName, 0, ' ');  
582              my $desc = $options->{$key}->[1];  =over 4
583              if ($options->{$key}->[0]) {  
584                  $desc .= " (default " . $options->{$key}->[0] . ")";  =item format
585    
586    C<html> to format the data as an HTML list, C<text> to format it as straight text.
587    
588    =back
589    
590    =cut
591    
592    sub QTrace {
593        # Get the parameter.
594        my ($format) = @_;
595        # Create the return variable.
596        my $retVal = "";
597        # Only proceed if there is an actual queue.
598        if (@Queue) {
599            # Process according to the format.
600            if ($format =~ m/^HTML$/i) {
601                # Convert the queue into an HTML list.
602                $retVal = "<ul>\n";
603                for my $line (@Queue) {
604                    my $escapedLine = CGI::escapeHTML($line);
605                    $retVal .= "<li>$escapedLine</li>\n";
606              }              }
607              print "  $name $desc\n";              $retVal .= "</ul>\n";
608            } elsif ($format =~ m/^TEXT$/i) {
609                # Convert the queue into a list of text lines.
610                $retVal = join("\n", @Queue) . "\n";
611          }          }
612          exit(0);          # Clear the queue.
613            @Queue = ();
614      }      }
615      # Return the parsed parameters.      # Return the formatted list.
616      return ($retOptions, @retParameters);      return $retVal;
617  }  }
618    
619  =head3 Setups  =head3 Confess
620    
621  C<< my $count = Tracer::Setups(); >>      Confess($message);
622    
623  Return the number of times L</TSetup> has been called.  Trace the call stack and abort the program with the specified message. When used with
624    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
625    So, for example
626    
627  This method allows for the creation of conditional tracing setups where, for example, we      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
628  may want to set up tracing if nobody else has done it before us.  
629    Will abort the program with a stack trace if the value of C<$recNum> is negative.
630    
631    =over 4
632    
633    =item message
634    
635    Message to include in the trace.
636    
637    =back
638    
639  =cut  =cut
640    
641  sub Setups {  sub Confess {
642      return $SetupCount;      # Get the parameters.
643        my ($message) = @_;
644        # Set up the category and level.
645        $LastCategory = "(confess)";
646        $LastLevel = 0;
647        if (! defined($FIG_Config::no_tool_hdr)) {
648            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
649            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
650            # Only proceed if the tool header file is actually present.
651            if (-f $toolHeaderFile) {
652                my $fh;
653                if (open $fh, "<$toolHeaderFile") {
654                    my @lines = <$fh>;
655                    Trace("Tool header has " . scalar(@lines) . " lines.");
656                }
657            }
658        }
659        # Trace the call stack.
660        Cluck($message);
661        # Abort the program.
662        croak(">>> $message");
663  }  }
664    
665  =head3 Open  =head3 SaveCGI
   
 C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  
666    
667  Open a file.      Tracer::SaveCGI($cgi);
668    
669  The I<$fileSpec> is essentially the second argument of the PERL C<open>  This method saves the CGI object but does not activate emergency tracing.
670  function. The mode is specified using Unix-like shell information. So, for  It is used to allow L</Warn> to work in situations where emergency
671  example,  tracing is contra-indicated (e.g. the wiki).
672    
673      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =over 4
674    
675  would open for output appended to the specified file, and  =item cgi
676    
677      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  Active CGI query object.
678    
679  would open a pipe that sorts the records written and removes duplicates. Note  =back
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
680    
681      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =cut
682    
683  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  sub SaveCGI {
684  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a      $SavedCGI = $_[0];
685  failed open will throw an exception and the third parameter will be used to construct  }
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
686    
687      Could not open "/usr/spool/news/twitlog"  =head3 Warn
688    
689  Note that the mode characters are automatically cleaned from the file name.      Warn($message, @options);
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
690    
691      Could not open "/usr/spool/news/twitlog": file not found.  This method traces an important message. If an RSS feed is configured
692    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
693    then the message will be echoed to the feed. In general, a tracing
694    destination of C<WARN> indicates that the caller is running as a web
695    service in a production environment; however, this is not a requirement.
696    
697  In some versions of PERL the only error message we get is a number, which  To force warnings into the RSS feed even when the tracing destination
698  corresponds to the C++ C<errno> value.  is not C<WARN>, simply specify the C<Feed> tracing module. This can be
699    configured automatically when L</StandardSetup> is used.
700    
701      Could not open "/usr/spool/news/twitlog": 6.  The L</Cluck> method calls this one for its final message. Since
702    L</Confess> calls L</Cluck>, this means that any error which is caught
703    and confessed will put something in the feed. This insures that someone
704    will be alerted relatively quickly when a failure occurs.
705    
706  =over 4  =over 4
707    
708  =item fileHandle  =item message
709    
710  File handle. If this parameter is C<undef>, a file handle will be generated  Message to be traced.
 and returned as the value of this method.  
711    
712  =item fileSpec  =item options
713    
714  File name and mode, as per the PERL C<open> function.  A list containing zero or more options.
715    
716  =item message (optional)  =back
717    
718  Error message to use if the open fails. If omitted, a standard error message  The permissible options are as follows.
 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>.  
719    
720  =item RETURN  =over 4
721    
722  Returns the name of the file handle assigned to the file, or C<undef> if the  =item noStack
723  open failed.  
724    If specified, then the stack trace is not included in the output.
725    
726  =back  =back
727    
728  =cut  =cut
729    
730  sub Open {  sub Warn {
731      # Get the parameters.      # Get the parameters.
732      my ($fileHandle, $fileSpec, $message) = @_;      my $message = shift @_;
733      # Attempt to open the file.      my %options = map { $_ => 1 } @_;
734      my $rv = open $fileHandle, $fileSpec;      # Trace the message.
735      # If the open failed, generate an error message.      Trace($message);
736      if (! $rv) {      # This will contain the lock handle. If it's defined, it means we need to unlock.
737          # Save the system error message.      my $lock;
738          my $sysMessage = $!;      # Check for feed forcing.
739          # See if we need a default message.      my $forceFeed = exists $Categories{feed};
740          if (!$message) {      # An error here would be disastrous. Note that if debug mode is specified,
741              # Clean any obvious mode characters and leading spaces from the      # we do this stuff even in a test environment.
742              # filename.      eval {
743              my ($fileName) = FindNamePart($fileSpec);          # Do we need to put this in the RSS feed?
744              $message = "Could not open \"$fileName\"";          if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
745                # Yes. We now need to compute the date, the link, and the title.
746                # First, the date, in a very specific format.
747                my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
748                    (tz_local_offset() / 30);
749                # Environment data goes in here. We start with the date.
750                my $environment = "$date.  ";
751                # If we need to recap the message (because it's too long to be a title), we'll
752                # put it in here.
753                my $recap;
754                # Copy the message and remove excess space.
755                my $title = $message;
756                $title =~ s/\s+/ /gs;
757                # If it's too long, we have to split it up.
758                if (length $title > 60) {
759                    # Put the full message in the environment string.
760                    $recap = $title;
761                    # Excerpt it as the title.
762                    $title = substr($title, 0, 50) . "...";
763                }
764                # If we have a CGI object, then this is a web error. Otherwise, it's
765                # command-line.
766                if (defined $SavedCGI) {
767                    # We're in a web service. The environment is the user's IP, and the link
768                    # is the URL that got us here.
769                    my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
770                    $environment .= "Event Reported at IP address $key process $$.";
771                    my $url = $SavedCGI->self_url();
772                    # We need the user agent string and (if available) the referrer.
773                    # The referrer will be the link.
774                    $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
775                    if ($ENV{HTTP_REFERER}) {
776                        my $link = $ENV{HTTP_REFERER};
777                        $environment .= " referred from <a href=\"$link\">$link</a>.";
778                    } else {
779                        $environment .= " referrer unknown.";
780                    }
781                    # Close off the sentence with the original link.
782                    $environment .= " URL of event is <a href=\"$url\">$url</a>.";
783                } else {
784                    # No CGI object, so we're a command-line tool. Use the tracing
785                    # key and the PID as the user identifier, and add the command.
786                    my $key = EmergencyKey();
787                    $environment .= "Event Reported by $key process $$.";
788                    if ($CommandLine) {
789                        # We're in a StandardSetup script, so we have the real command line.
790                        $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
791                    } elsif ($ENV{_}) {
792                        # We're in a BASH script, so the command has been stored in the _ variable.
793                        $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
794                    }
795                }
796                # Build a GUID. We use the current time, the title, and the process ID,
797                # then digest the result.
798                my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
799                # Finally, the description. This is a stack trace plus various environmental stuff.
800                # The trace is optional.
801                my $stackTrace;
802                if ($options{noStack}) {
803                    $stackTrace = "";
804                } else {
805                    my @trace = LongMess();
806                    # Only proceed if we got something back.
807                    if (scalar(@trace) > 0) {
808                        $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
809                        $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
810                    }
811                }
812                # We got the stack trace. Now it's time to put it all together.
813                # We have a goofy thing here in that we need to HTML-escape some sections of the description
814                # twice. They will be escaped once here, and then once when written by XML::Simple. They are
815                # unescaped once when processed by the RSS reader, and stuff in the description is treated as
816                # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
817                # our <br>s and <pre>s are used to format the description.
818                $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
819                my $description = "$recap$environment  $stackTrace";
820                # Okay, we have all the pieces. Create a hash of the new event.
821                my $newItem = { title => $title,
822                                description => $description,
823                                category => $LastCategory,
824                                pubDate => $date,
825                                guid => $guid,
826                              };
827                # We need XML capability for this.
828                require XML::Simple;
829                # The RSS document goes in here.
830                my $rss;
831                # Get the name of the RSS file. It's in the FIG temporary directory.
832                my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
833                # Open the config file and lock it.
834                $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
835                flock $lock, LOCK_EX;
836                # Does it exist?
837                if (-s $fileName) {
838                    # Slurp it in.
839                    $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
840                } else {
841                    my $size = -s $fileName;
842                    # Create an empty channel.
843                    $rss = {
844                        channel => {
845                            title => 'NMPDR Warning Feed',
846                            link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
847                            description => "Important messages regarding the status of the NMPDR.",
848                            generator => "NMPDR Trace Facility",
849                            docs => "http://blogs.law.harvard.edu/tech/rss",
850                            item => []
851                        },
852                    };
853          }          }
854          # Terminate with an error using the supplied message and the              # Get the channel object.
855          # error message from the file system.              my $channel = $rss->{channel};
856          Confess("$message: $!");              # Update the last-build date.
857                $channel->{lastBuildDate} = $date;
858                # Get the item array.
859                my $items = $channel->{item};
860                # Insure it has only 100 entries.
861                while (scalar @{$items} > 100) {
862                    pop @{$items};
863                }
864                # Add our new item at the front.
865                unshift @{$items}, $newItem;
866                # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
867                # the requirements for those.
868                my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
869                # Here we put in the root and declaration. The problem is that the root has to have the version attribute
870                # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
871                $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
872                # We don't use Open here because we can't afford an error.
873                if (open XMLOUT, ">$fileName") {
874                    print XMLOUT $xml;
875                    close XMLOUT;
876                }
877            }
878        };
879        if ($@) {
880            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
881            # (which is a good thing).
882            my $error = $@;
883            Trace("Feed Error: $error") if T(Feed => 0);
884        }
885        # Be sure to unlock.
886        if ($lock) {
887            flock $lock, LOCK_UN;
888            undef $lock;
889      }      }
     # Return the file handle.  
     return $fileHandle;  
890  }  }
891    
 =head3 FindNamePart  
   
 C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>  
   
 Extract the portion of a file specification that contains the file name.  
   
 A file specification is the string passed to an C<open> call. It specifies the file  
 mode and name. In a truly complex situation, it can specify a pipe sequence. This  
 method assumes that the file name is whatever follows the first angle bracket  
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
   
     >>/usr/fig/myfile.txt  
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
892    
 If the method cannot find a file name using its normal methods, it will return the  
 whole incoming string.  
893    
 =over 4  
894    
895  =item fileSpec  =head3 Assert
896    
897  File specification string from which the file name is to be extracted.      Assert($condition1, $condition2, ... $conditionN);
898    
899  =item RETURN  Return TRUE if all the conditions are true. This method can be used in conjunction with
900    the OR operator and the L</Confess> method as a debugging assert.
901    So, for example
902    
903  Returns a three-element list. The first element contains the file name portion of      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
 the specified string, or the whole string if a file name cannot be found via normal  
 methods. The second element contains the start position of the file name portion and  
 the third element contains the length.  
904    
905  =back  Will abort the program with a stack trace if the value of C<$recNum> is negative.
906    
907  =cut  =cut
908  #: Return Type $;  sub Assert {
909  sub FindNamePart {      my $retVal = 1;
910      # Get the parameters.      LOOP: for my $condition (@_) {
911      my ($fileSpec) = @_;          if (! $condition) {
912      # Default to the whole input string.              $retVal = 0;
913      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);              last LOOP;
     # Parse out the file name if we can.  
     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {  
         $retVal = $2;  
         $len = length $retVal;  
         $pos = (length $fileSpec) - (length $3) - $len;  
914      }      }
915      # Return the result.      }
916      return ($retVal, $pos, $len);      return $retVal;
917  }  }
918    
919  =head3 OpenDir  =head3 Cluck
   
 C<< my @files = OpenDir($dirName, $filtered, $flag); >>  
   
 Open a directory and return all the file names. This function essentially performs  
 the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  
 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  
 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be  
 filtered out of the return list. If the directory does not open and I<$flag> is not  
 set, an exception is thrown. So, for example,  
   
     my @files = OpenDir("/Volumes/fig/contigs", 1);  
   
 is effectively the same as  
920    
921      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");      Cluck($message);
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
922    
923  Similarly, the following code  Trace the call stack. Note that for best results, you should qualify the call with a
924    trace condition. For example,
925    
926      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);      Cluck("Starting record parse.") if T(3);
927    
928  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  will only trace the stack if the trace level for the package is 3 or more.
 automatically returns an empty list if the directory fails to open.  
929    
930  =over 4  =over 4
931    
932  =item dirName  =item message
933    
934  Name of the directory to open.  Message to include in the trace.
935    
936  =item filtered  =back
937    
938  TRUE if files whose names begin with a period (C<.>) should be automatically removed  =cut
 from the list, else FALSE.  
939    
940  =item flag  sub Cluck {
941        # Get the parameters.
942        my ($message) = @_;
943        # Trace what's happening.
944        Trace("Stack trace for event: $message");
945        # Get the stack trace.
946        my @trace = LongMess();
947        # Convert the trace to a series of messages.
948        for my $line (@trace) {
949            # Replace the tab at the beginning with spaces.
950            $line =~ s/^\t/    /;
951            # Trace the line.
952            Trace($line);
953        }
954        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
955        Warn($message);
956    }
957    
958  TRUE if a failure to open is okay, else FALSE  =head3 LongMess
959    
960  =back      my @lines = Tracer::LongMess();
961    
962    Return a stack trace with all tracing methods removed. The return will be in the form of a list
963    of message strings.
964    
965  =cut  =cut
966  #: Return Type @;  
967  sub OpenDir {  sub LongMess {
     # Get the parameters.  
     my ($dirName, $filtered, $flag) = @_;  
968      # Declare the return variable.      # Declare the return variable.
969      my @retVal = ();      my @retVal = ();
970      # Open the directory.      my $confession = longmess("");
971      if (opendir(my $dirHandle, $dirName)) {      for my $line (split /\s*\n/, $confession) {
972          # The directory opened successfully. Get the appropriate list according to the          unless ($line =~ /Tracer\.pm/) {
973          # strictures of the filter parameter.              # Here we have a line worth keeping. Push it onto the result list.
974          if ($filtered) {              push @retVal, $line;
             @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;  
         } else {  
             @retVal = readdir $dirHandle;  
975          }          }
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
976      }      }
977      # Return the result.      # Return the result.
978      return @retVal;      return @retVal;
979  }  }
980    
981  =head3 SetLevel  =head3 ETracing
982    
983  C<< Tracer::SetLevel($newLevel); >>      ETracing($parameter);
984    
985  Modify the trace level. A higher trace level will cause more messages to appear.  Set up emergency tracing. Emergency tracing is tracing that is turned
986    on automatically for any program that calls this method. The emergency
987    tracing parameters are stored in a a file identified by a tracing key.
988    If this method is called with a CGI object, then the tracing key is
989    taken from a cookie. If it is called with no parameters, then the tracing
990    key is taken from an environment variable. If it is called with a string,
991    the tracing key is that string.
992    
993  =over 4  =over 4
994    
995  =item newLevel  =item parameter
996    
997  Proposed new trace level.  A parameter from which the tracing key is computed. If it is a scalar,
998    that scalar is used as the tracing key. If it is a CGI object, the
999    tracing key is taken from the C<IP> cookie. If it is omitted, the
1000    tracing key is taken from the C<TRACING> environment variable. If it
1001    is a CGI object and emergency tracing is not on, the C<Trace> and
1002    C<TF> parameters will be used to determine the type of tracing.
1003    
1004  =back  =back
1005    
1006  =cut  =cut
1007    
1008  sub SetLevel {  sub ETracing {
1009      $TraceLevel = $_[0];      # Get the parameter.
1010        my ($parameter) = @_;
1011        # Check for CGI mode.
1012        if (defined $parameter && ref $parameter eq 'CGI') {
1013            $SavedCGI = $parameter;
1014        } else {
1015            $SavedCGI = undef;
1016        }
1017        # Default to no tracing except errors.
1018        my ($tracing, $dest) = ("0", "WARN");
1019        # Check for emergency tracing.
1020        my $tkey = EmergencyKey($parameter);
1021        my $emergencyFile = EmergencyFileName($tkey);
1022        if (-e $emergencyFile) {
1023            # We have the file. Read in the data.
1024            my @tracing = GetFile($emergencyFile);
1025            # Pull off the time limit.
1026            my $expire = shift @tracing;
1027            # Convert it to seconds.
1028            $expire *= 3600;
1029            # Check the file data.
1030            my $stat = stat($emergencyFile);
1031            my ($now) = gettimeofday;
1032            if ($now - $stat->mtime > $expire) {
1033                # Delete the expired file.
1034                unlink $emergencyFile;
1035            } else {
1036                # Emergency tracing is on. Pull off the destination and
1037                # the trace level;
1038                $dest = shift @tracing;
1039                my $level = shift @tracing;
1040                # Convert the destination to a real tracing destination.
1041                # temp directory.
1042                $dest = EmergencyTracingDest($tkey, $dest);
1043                # Insure Tracer is specified.
1044                my %moduleHash = map { $_ => 1 } @tracing;
1045                $moduleHash{Tracer} = 1;
1046                # Set the trace parameter.
1047                $tracing = join(" ", $level, sort keys %moduleHash);
1048            }
1049        } elsif (defined $SavedCGI) {
1050            # There's no emergency tracing, but we have a CGI object, so check
1051            # for tracing from the form parameters.
1052            if ($SavedCGI->param('Trace')) {
1053                # Here the user has requested tracing via a form.
1054                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1055                $tracing = $SavedCGI->param('Trace') . " Tracer";
1056            }
1057        }
1058        # Setup the tracing we've determined from all the stuff above.
1059        TSetup($tracing, $dest);
1060        # Check to see if we're a web script.
1061        if (defined $SavedCGI) {
1062            # Yes we are. Trace the form and environment data.
1063            TraceParms($SavedCGI);
1064            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1065            # emitted by the script in its raw form.
1066            if (T(Raw => 3)) {
1067                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1068  }  }
   
 =head3 Now  
   
 C<< my $string = Tracer::Now(); >>  
   
 Return a displayable time stamp containing the local time.  
   
 =cut  
   
 sub Now {  
     my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);  
     my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .  
                  _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);  
     return $retVal;  
1069  }  }
   
 # Pad a number to 2 digits.  
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
1070  }  }
1071    
1072  =head3 ParseTraceDate  =head3 EmergencyFileName
1073    
1074  C<< my $time = Tracer::ParseTraceDate($dateString); >>      my $fileName = Tracer::EmergencyFileName($tkey);
1075    
1076  Convert a date from the trace file into a PERL timestamp.  Return the emergency tracing file name. This is the file that specifies
1077    the tracing information.
1078    
1079  =over 4  =over 4
1080    
1081  =item dateString  =item tkey
1082    
1083  The date string from the trace file. The format of the string is determined by the  Tracing key for the current program.
 L</Now> method.  
1084    
1085  =item RETURN  =item RETURN
1086    
1087  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if  Returns the name of the file to contain the emergency tracing information.
 the time string is invalid.  
1088    
1089  =back  =back
1090    
1091  =cut  =cut
1092    
1093  sub ParseTraceDate {  sub EmergencyFileName {
1094      # Get the parameters.      # Get the parameters.
1095      my ($dateString) = @_;      my ($tkey) = @_;
1096      # Declare the return variable.      # Compute the emergency tracing file name.
1097      my $retVal;      return "$FIG_Config::temp/Emergency$tkey.txt";
     # Parse the date.  
     if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {  
         # Create a time object. Note we need to convert the day, month,  
         # and year to a different base. Years count from 1900, and  
         # the internal month value is relocated to January = 0.  
         $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);  
     }  
     # Return the result.  
     return $retVal;  
1098  }  }
1099    
1100  =head3 LogErrors  =head3 EmergencyFileTarget
1101    
1102  C<< Tracer::LogErrors($fileName); >>      my $fileName = Tracer::EmergencyFileTarget($tkey);
1103    
1104  Route the standard error output to a log file.  Return the emergency tracing target file name. This is the file that receives
1105    the tracing output for file-based tracing.
1106    
1107  =over 4  =over 4
1108    
1109  =item fileName  =item tkey
1110    
1111  Name of the file to receive the error output.  Tracing key for the current program.
1112    
1113    =item RETURN
1114    
1115    Returns the name of the file to contain the trace output.
1116    
1117  =back  =back
1118    
1119  =cut  =cut
1120    
1121  sub LogErrors {  sub EmergencyFileTarget {
1122      # Get the file name.      # Get the parameters.
1123      my ($fileName) = @_;      my ($tkey) = @_;
1124      # Open the file as the standard error output.      # Compute the emergency tracing file name.
1125      open STDERR, '>', $fileName;      return "$FIG_Config::temp/trace$tkey.log";
1126  }  }
1127    
1128  =head3 ReadOptions  =head3 EmergencyTracingDest
   
 C<< my %options = Tracer::ReadOptions($fileName); >>  
   
 Read a set of options from a file. Each option is encoded in a line of text that has the  
 format  
1129    
1130  I<optionName>C<=>I<optionValue>C<; >I<comment>      my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1131    
1132  The option name must consist entirely of letters, digits, and the punctuation characters  This method converts an emergency tracing destination to a real
1133  C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  tracing destination. The main difference is that if the
1134  character is a semi-colon will be ignored. The return hash will map each option name to  destination is C<FILE> or C<APPEND>, we convert it to file
1135  the corresponding option value.  output. If the destination is C<DUAL>, we convert it to file
1136    and standard output.
1137    
1138  =over 4  =over 4
1139    
1140  =item fileName  =item tkey
1141    
1142  Name of the file containing the option data.  Tracing key for this environment.
1143    
1144    =item myDest
1145    
1146    Destination from the emergency tracing file.
1147    
1148  =item RETURN  =item RETURN
1149    
1150  Returns a hash mapping the option names specified in the file to their corresponding option  Returns a destination that can be passed into L</TSetup>.
 value.  
1151    
1152  =back  =back
1153    
1154  =cut  =cut
1155    
1156  sub ReadOptions {  sub EmergencyTracingDest {
1157      # Get the parameters.      # Get the parameters.
1158      my ($fileName) = @_;      my ($tkey, $myDest) = @_;
1159      # Open the file.      # Declare the return variable.
1160      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");      my $retVal = $myDest;
1161      # Count the number of records read.      # Process according to the destination value.
1162      my ($records, $comments) = 0;      if ($myDest eq 'FILE') {
1163      # Create the return hash.          $retVal = ">" . EmergencyFileTarget($tkey);
1164      my %retVal = ();      } elsif ($myDest eq 'APPEND') {
1165      # Loop through the file, accumulating key-value pairs.          $retVal = ">>" . EmergencyFileTarget($tkey);
1166      while (my $line = <CONFIGFILE>) {      } elsif ($myDest eq 'DUAL') {
1167          # Denote we've read a line.          $retVal = "+>" . EmergencyFileTarget($tkey);
1168          $records++;      } elsif ($myDest eq 'WARN') {
1169          # Determine the line type.          $retVal = "WARN";
         if ($line =~ /^\s*[\n\r]/) {  
             # A blank line is a comment.  
             $comments++;  
         } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {  
             # Here we have an option assignment.  
             retVal{$1} = $2;  
         } elsif ($line =~ /^\s*;/) {  
             # Here we have a text comment.  
             $comments++;  
         } else {  
             # Here we have an invalid line.  
             Trace("Invalid option statement in record $records.") if T(0);  
         }  
1170      }      }
1171      # Return the hash created.      # Return the result.
1172      return %retVal;      return $retVal;
1173  }  }
1174    
1175  =head3 GetOptions  =head3 Emergency
1176    
1177  C<< Tracer::GetOptions(\%defaults, \%options); >>      Emergency($key, $hours, $dest, $level, @modules);
1178    
1179  Merge a specified set of options into a table of defaults. This method takes two hash references  Turn on emergency tracing. This method is normally invoked over the web from
1180  as input and uses the data from the second to update the first. If the second does not exist,  a debugging console, but it can also be called by the C<trace.pl> script.
1181  there will be no effect. An error will be thrown if one of the entries in the second hash does not  The caller specifies the duration of the emergency in hours, the desired tracing
1182  exist in the first.  destination, the trace level, and a list of the trace modules to activate.
1183    For the length of the duration, when a program in an environment with the
1184    specified tracing key active invokes a Sprout CGI script, tracing will be
1185    turned on automatically. See L</TSetup> for more about tracing setup and
1186    L</ETracing> for more about emergency tracing.
1187    
1188  Consider the following example.  =over 4
1189    
1190  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  =item tkey
1191    
1192  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  The tracing key. This is used to identify the control file and the trace file.
 B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  
 B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and  
 the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  
 will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  
1193    
1194  C<< {databaseType => 'Oracle'} >>  =item hours
1195    
1196  an error will occur because the B<databaseType> option does not exist.  Number of hours to keep emergency tracing alive.
1197    
1198  =over 4  =item dest
1199    
1200  =item defaults  Tracing destination. If no path information is specified for a file
1201    destination, it is put in the FIG temporary directory.
1202    
1203  Table of default option values.  =item level
1204    
1205  =item options  Tracing level. A higher level means more trace messages.
1206    
1207  Table of overrides, if any.  =item modules
1208    
1209    A list of the tracing modules to activate.
1210    
1211    =back
1212    
1213    =cut
1214    
1215    sub Emergency {
1216        # Get the parameters.
1217        my ($tkey, $hours, $dest, $level, @modules) = @_;
1218        # Create the emergency file.
1219        my $specFile = EmergencyFileName($tkey);
1220        my $outHandle = Open(undef, ">$specFile");
1221        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1222    }
1223    
1224    =head3 EmergencyKey
1225    
1226        my $tkey = EmergencyKey($parameter);
1227    
1228    Return the Key to be used for emergency tracing. This could be an IP address,
1229     a session ID, or a user name, depending on the environment.
1230    
1231    =over 4
1232    
1233    =item parameter
1234    
1235    Parameter defining the method for finding the tracing key. If it is a scalar,
1236    then it is presumed to be the tracing key itself. If it is a CGI object, then
1237    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1238    taken from the C<TRACING> environment variable.
1239    
1240  =item RETURN  =item RETURN
1241    
1242  Returns a reference to the default table passed in as the first parameter.  Returns the key to be used for labels in emergency tracing.
1243    
1244  =back  =back
1245    
1246  =cut  =cut
1247    
1248  sub GetOptions {  sub EmergencyKey {
1249      # Get the parameters.      # Get the parameters.
1250      my ($defaults, $options) = @_;      my ($parameter) = @_;
1251      # Check for overrides.      # Declare the return variable.
1252      if ($options) {      my $retVal;
1253          # Loop through the overrides.      # Determine the parameter type.
1254          while (my ($option, $setting) = each %{$options}) {      if (! defined $parameter) {
1255              # Insure this override exists.          # Here we're supposed to check the environment. If that fails, we
1256              if (!exists $defaults->{$option}) {          # get the effective login ID.
1257                  croak "Unrecognized option $option encountered.";          $retVal = $ENV{TRACING} || scalar getpwuid($<);
1258              } else {              } else {
1259                  # Apply the override.          my $ptype = ref $parameter;
1260                  $defaults->{$option} = $setting;          if ($ptype eq 'CGI') {
1261                # Here we were invoked from a web page. Look for a cookie.
1262                $retVal = $parameter->cookie('IP');
1263            } elsif (! $ptype) {
1264                # Here the key was passed in.
1265                $retVal = $parameter;
1266              }              }
1267          }          }
1268        # If no luck finding a key, use the PID.
1269        if (! defined $retVal) {
1270            $retVal = $$;
1271      }      }
1272      # Return the merged table.      # Return the result.
1273      return $defaults;      return $retVal;
1274  }  }
1275    
 =head3 MergeOptions  
   
 C<< Tracer::MergeOptions(\%table, \%defaults); >>  
1276    
1277  Merge default values into a hash table. This method looks at the key-value pairs in the  =head3 TraceParms
 second (default) hash, and if a matching key is not found in the first hash, the default  
 pair is copied in. The process is similar to L</GetOptions>, but there is no error-  
 checking and no return value.  
1278    
1279  =over 4      Tracer::TraceParms($cgi);
1280    
1281  =item table  Trace the CGI parameters at trace level CGI => 3 and the environment variables
1282    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1283    
1284  Hash table to be updated with the default values.  =over 4
1285    
1286  =item defaults  =item cgi
1287    
1288  Default values to be merged into the first hash table if they are not already present.  CGI query object containing the parameters to trace.
1289    
1290  =back  =back
1291    
1292  =cut  =cut
1293    
1294  sub MergeOptions {  sub TraceParms {
1295      # Get the parameters.      # Get the parameters.
1296      my ($table, $defaults) = @_;      my ($cgi) = @_;
1297      # Loop through the defaults.      if (T(CGI => 2)) {
1298      while (my ($key, $value) = each %{$defaults}) {          # Here we trace the GET-style URL for the script.
1299          if (!exists $table->{$key}) {          Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1300              $table->{$key} = $value;      }
1301        if (T(CGI => 3)) {
1302            # Here we want to trace the parameter data.
1303            my @names = $cgi->param;
1304            for my $parmName (sort @names) {
1305                # Note we skip the Trace parameters, which are for our use only.
1306                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1307                    my @values = $cgi->param($parmName);
1308                    Trace("[CGI] $parmName = " . join(", ", @values));
1309                }
1310            }
1311            # Display the request method.
1312            my $method = $cgi->request_method();
1313            Trace("Method: $method");
1314        }
1315        if (T(CGI => 4)) {
1316            # Here we want the environment data too.
1317            for my $envName (sort keys %ENV) {
1318                Trace("[ENV] $envName = $ENV{$envName}");
1319          }          }
1320      }      }
1321  }  }
1322    
1323  =head3 Trace  =head3 TraceImages
1324    
1325  C<< Trace($message); >>      Tracer::TraceImages($htmlString);
1326    
1327  Write a trace message to the target location specified in L</TSetup>. If there has not been  Trace information about all of an html document's images. The tracing
1328  any prior call to B<TSetup>.  will be for type "IMG" at level 3. The image's source string
1329    will be displayed. This is generally either the URL of the image or
1330    raw data for the image itself. If the source is too long, only the first 300
1331    characters will be shown at trace level 3. The entire source will be shown,
1332    however, at trace level 4. This method is not very smart, and might catch
1333    Javascript code, but it is still useful when debugging the arcane
1334    behavior of images in multiple browser environments.
1335    
1336  =over 4  =over 4
1337    
1338  =item message  =item htmlString
1339    
1340  Message to write.  HTML text for an outgoing web page.
1341    
1342  =back  =back
1343    
1344  =cut  =cut
1345    
1346  sub Trace {  sub TraceImages {
1347      # Get the parameters.      # Only proceed if we're at the proper trace level.
1348      my ($message) = @_;      if (T(IMG => 3)) {
1349      # Get the timestamp.          # For performance reasons we're manipulating $_[0] instead of retrieving the string
1350      my $timeStamp = Now();          # into a variable called "$htmlString". This is because we expect html strings to be
1351      # Format the message. Note we strip off any line terminators at the end.          # long, and don't want to copy them any more than we have to.
1352      my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);          Trace(length($_[0]) . " characters in web page.");
1353      # Process according to the destination.          # Loop through the HTML, culling image tags.
1354      if ($Destination eq "TEXT") {          while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1355          # Write the message to the standard output.              # Extract the source string and determine whether or not it's too long.
1356          print "$formatted\n";              my $srcString = $1;
1357      } elsif ($Destination eq "ERROR") {              my $pos = pos($_[0]) - length($srcString);
1358          # Write the message to the error output.              my $excess = length($srcString) - 300;
1359          print STDERR "$formatted\n";              # We'll put the display string in here.
1360      } elsif ($Destination eq "QUEUE") {              my $srcDisplay = $srcString;
1361          # Push the message into the queue.              # If it's a data string, split it at the comma.
1362          push @Queue, "$formatted";              $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1363      } elsif ($Destination eq "HTML") {              # If there's no excess or we're at trace level 4, we're done. At level 3 with
1364          # Convert the message to HTML and write it to the standard output.              # a long string, however, we only show the first 300 characters.
1365          my $escapedMessage = CGI::escapeHTML($message);              if ($excess > 0 && ! T(IMG => 4)) {
1366          print "<p>$formatted</p>\n";                  $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1367      } elsif ($Destination eq "WARN") {              }
1368         # Emit the message as a warning.              # Output the trace message.
1369         warn $message;              Trace("Image tag at position $pos:\n$srcDisplay");
     } 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";  
1370          }          }
1371      }      }
1372  }  }
1373    
1374  =head3 T  =head2 Command-Line Utility Methods
1375    
1376    =head3 SendSMS
1377    
1378  C<< my $switch = T($category, $traceLevel); >>      my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1379    
1380      or  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1381    user name, password, and API ID for the relevant account in the hash reference variable
1382    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1383    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1384    is C<2561022>, then the FIG_Config file must contain
1385    
1386  C<< my $switch = T($traceLevel); >>      $phone =  { user => 'BruceTheHumanPet',
1387                    password => 'silly',
1388                    api_id => '2561022' };
1389    
1390  Return TRUE if the trace level is at or above a specified value and the specified category  The original purpose of this method was to insure Bruce would be notified immediately when the
1391  is active, else FALSE. If no category is specified, the caller's package name is used.  Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1392    when you call this method.
1393    
1394    The message ID will be returned if successful, and C<undef> if an error occurs.
1395    
1396  =over 4  =over 4
1397    
1398  =item category  =item phoneNumber
1399    
1400  Category to which the message belongs. If not specified, the caller's package name is  Phone number to receive the message, in international format. A United States phone number
1401  used.  would be prefixed by "1". A British phone number would be prefixed by "44".
1402    
1403  =item traceLevel  =item msg
1404    
1405  Relevant tracing level.  Message to send to the specified phone.
1406    
1407  =item RETURN  =item RETURN
1408    
1409  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  Returns the message ID if successful, and C<undef> if the message could not be sent.
1410    
1411  =back  =back
1412    
1413  =cut  =cut
1414    
1415  sub T {  sub SendSMS {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
1416          # Get the parameters.          # Get the parameters.
1417          my ($category, $traceLevel) = @_;      my ($phoneNumber, $msg) = @_;
1418          if (!defined $traceLevel) {      # Declare the return variable. If we do not change it, C<undef> will be returned.
1419              # Here we have no category, so we need to get the calling package.      my $retVal;
1420              # The calling package is normally the first parameter. If it is      # Only proceed if we have phone support.
1421              # omitted, the first parameter will be the tracelevel. So, the      if (! defined $FIG_Config::phone) {
1422              # first thing we do is shift the so-called category into the          Trace("Phone support not present in FIG_Config.") if T(1);
             # $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";  
1423              } else {              } else {
1424                  $category = $package;          # Get the phone data.
1425              }          my $parms = $FIG_Config::phone;
1426            # Get the Clickatell URL.
1427            my $url = "http://api.clickatell.com/http/";
1428            # Create the user agent.
1429            my $ua = LWP::UserAgent->new;
1430            # Request a Clickatell session.
1431            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1432                                         password => $parms->{password},
1433                                         api_id => $parms->{api_id},
1434                                         to => $phoneNumber,
1435                                         text => $msg});
1436            # Check for an error.
1437            if (! $resp->is_success) {
1438                Trace("Alert failed.") if T(1);
1439            } else {
1440                # Get the message ID.
1441                my $rstring = $resp->content;
1442                if ($rstring =~ /^ID:\s+(.*)$/) {
1443                    $retVal = $1;
1444                } else {
1445                    Trace("Phone attempt failed with $rstring") if T(1);
1446          }          }
         # 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.");  
1447          }          }
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
1448      }      }
1449      # Return the computed result.      # Return the result.
1450      return $retVal;      return $retVal;
1451  }  }
1452    
1453  =head3 ParseCommand  =head3 StandardSetup
1454    
1455  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1456    
1457  Parse a command line consisting of a list of parameters. The initial parameters may be option  This method performs standard command-line parsing and tracing setup. The return
1458  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  values are a hash of the command-line options and a list of the positional
1459  off and merged into a table of default options. The remainder of the command line is  parameters. Tracing is automatically set up and the command-line options are
1460  returned as a list of positional arguments. For example, consider the following invocation.  validated.
1461    
1462  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  This is a complex method that does a lot of grunt work. The parameters can
1463    be more easily understood, however, once they are examined individually.
1464    
1465  In this case, the list @words will be treated as a command line. There are two options available,  The I<categories> parameter is the most obtuse. It is a reference to a list of
1466  B<errors> and B<logFile>. If @words has the following format  special-purpose tracing categories. Most tracing categories are PERL package
1467    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1468    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1469    
1470  C<< -logFile=error.log apple orange rutabaga >>      ["Sprout", "SproutLoad", "ERDB"]
1471    
1472  then at the end of the invocation, C<$options> will be  This would cause trace messages in the specified three packages to appear in
1473    the output. There are two special tracing categories that are automatically
1474    handled by this method. In other words, if you used L</TSetup> you would need
1475    to include these categories manually, but if you use this method they are turned
1476    on automatically.
1477    
1478    =over 4
1479    
1480  C<< { errors => 0, logFile => 'error.log' } >>  =item SQL
1481    
1482  and C<@arguments> will contain  Traces SQL commands and activity.
1483    
1484  C<< apple orange rutabaga >>  =item Tracer
1485    
1486  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  Traces error messages and call stacks.
1487  support for quote characters.  
1488    =back
1489    
1490    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1491    The trace level is specified using the C<-trace> command-line option. For example,
1492    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1493    all tracing at level 3.
1494    
1495        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1496    
1497    Standard tracing is output to the standard output and echoed to the file
1498    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1499    process ID. You can also specify the C<user> parameter to put a user ID
1500    instead of a process ID in the trace file name. So, for example
1501    
1502    The default trace level is 2. To get all messages, specify a trace level of 4.
1503    For a genome-by-genome update, use 3.
1504    
1505        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1506    
1507    would send the trace output to C<traceBruce.log> in the temporary directory.
1508    
1509    The I<options> parameter is a reference to a hash containing the command-line
1510    options, their default values, and an explanation of what they mean. Command-line
1511    options may be in the form of switches or keywords. In the case of a switch, the
1512    option value is 1 if it is specified and 0 if it is not specified. In the case
1513    of a keyword, the value is separated from the option name by an equal sign. You
1514    can see this last in the command-line example above.
1515    
1516    You can specify a different default trace level by setting C<$options->{trace}>
1517    prior to calling this method.
1518    
1519    An example at this point would help. Consider, for example, the command-line utility
1520    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1521    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1522    the following code.
1523    
1524        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1525                            { safe => [0, "use database transactions"],
1526                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1527                              start => [' ', "start with this genome"],
1528                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1529                            "<command> <transactionDirectory> <IDfile>",
1530                          @ARGV);
1531    
1532    
1533    The call to C<ParseCommand> specifies the default values for the options and
1534    stores the actual options in a hash that is returned as C<$options>. The
1535    positional parameters are returned in C<@parameters>.
1536    
1537    The following is a sample command line for C<TransactFeatures>.
1538    
1539        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1540    
1541    Single and double hyphens are equivalent. So, you could also code the
1542    above command as
1543    
1544        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1545    
1546    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1547    parameters, and would find themselves in I<@parameters> after executing the
1548    above code fragment. The tracing would be set to level 2, and the categories
1549    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1550    and C<DocUtils> was included because it came in within the first parameter
1551    to this method. The I<$options> hash would be
1552    
1553        { trace => 2, sql => 0, safe => 0,
1554          noAlias => 1, start => ' ', tblFiles => 0 }
1555    
1556    Use of C<StandardSetup> in this way provides a simple way of performing
1557    standard tracing setup and command-line parsing. Note that the caller is
1558    not even aware of the command-line switches C<-trace> and C<-sql>, which
1559    are used by this method to control the tracing. If additional tracing features
1560    need to be added in the future, they can be processed by this method without
1561    upsetting the command-line utilities.
1562    
1563    If the C<background> option is specified on the command line, then the
1564    standard and error outputs will be directed to files in the temporary
1565    directory, using the same suffix as the trace file. So, if the command
1566    line specified
1567    
1568        -user=Bruce -background
1569    
1570    then the trace output would go to C<traceBruce.log>, the standard output to
1571    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1572    simplify starting a command in the background.
1573    
1574    The user name is also used as the tracing key for L</Emergency Tracing>.
1575    Specifying a value of C<E> for the trace level causes emergency tracing to
1576    be used instead of custom tracing. If the user name is not specified,
1577    the tracing key is taken from the C<Tracing> environment variable. If there
1578    is no value for that variable, the tracing key will be computed from the active
1579    login ID.
1580    
1581    Since the default situation in StandardSetup is to trace to the standard
1582    output, errors that occur in command-line scripts will not generate
1583    RSS events. To force the events, use the C<warn> option.
1584    
1585        TransactFeatures -background -warn register ../xacts IDs.tbl
1586    
1587    Finally, if the special option C<-help> is specified, the option
1588    names will be traced at level 0 and the program will exit without processing.
1589    This provides a limited help capability. For example, if the user enters
1590    
1591        TransactFeatures -help
1592    
1593    he would see the following output.
1594    
1595        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1596            -trace    tracing level (default E)
1597            -sql      trace SQL commands
1598            -safe     use database transactions
1599            -noAlias  do not expect aliases in CHANGE transactions
1600            -start    start with this genome
1601            -tblFiles output TBL files containing the corrected IDs
1602    
1603    The caller has the option of modifying the tracing scheme by placing a value
1604    for C<trace> in the incoming options hash. The default value can be overridden,
1605    or the tracing to the standard output can be turned off by suffixing a minus
1606    sign to the trace level. So, for example,
1607    
1608        { trace => [0, "tracing level (default 0)"],
1609           ...
1610    
1611    would set the default trace level to 0 instead of E, while
1612    
1613        { trace => ["2-", "tracing level (default 2)"],
1614           ...
1615    
1616    would set the default to 2, but trace only to the log file, not to the
1617    standard output.
1618    
1619    The parameters to this method are as follows.
1620    
1621  =over 4  =over 4
1622    
1623  =item optionTable  =item categories
1624    
1625  Table of default options.  Reference to a list of tracing category names. These should be names of
1626    packages whose internal workings will need to be debugged to get the
1627    command working.
1628    
1629  =item inputList  =item options
1630    
1631  List of words on the command line.  Reference to a hash containing the legal options for the current command mapped
1632    to their default values and descriptions. The user can override the defaults
1633    by specifying the options as command-line switches prefixed by a hyphen.
1634    Tracing-related options may be added to this hash. If the C<-h> option is
1635    specified on the command line, the option descriptions will be used to
1636    explain the options. To turn off tracing to the standard output, add a
1637    minus sign to the value for C<trace> (see above).
1638    
1639    =item parmHelp
1640    
1641    A string that vaguely describes the positional parameters. This is used
1642    if the user specifies the C<-h> option.
1643    
1644    =item argv
1645    
1646    List of command line parameters, including the option switches, which must
1647    precede the positional parameters and be prefixed by a hyphen.
1648    
1649  =item RETURN  =item RETURN
1650    
1651  Returns a reference to the option table and a list of the positional arguments.  Returns a list. The first element of the list is the reference to a hash that
1652    maps the command-line option switches to their values. These will either be the
1653    default values or overrides specified on the command line. The remaining
1654    elements of the list are the position parameters, in order.
1655    
1656  =back  =back
1657    
1658  =cut  =cut
1659    
1660  sub ParseCommand {  sub StandardSetup {
1661      # Get the parameters.      # Get the parameters.
1662      my ($optionTable, @inputList) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
1663      # Process any options in the input list.      # Get the default tracing key.
1664      my %overrides = ();      my $tkey = EmergencyKey();
1665      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      # Save the command line.
1666          # Get the current option.      $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1667          my $arg = shift @inputList;      # Add the tracing options.
1668          # Pull out the option name.      if (! exists $options->{trace}) {
1669          $arg =~ /^-([^=]*)/g;          $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1670          my $name = $1;      }
1671          # Check for an option value.      $options->{sql} = [0, "turn on SQL tracing"];
1672          if ($arg =~ /\G=(.*)$/g) {      $options->{help} = [0, "display command-line options"];
1673              # Here we have a value for the option.      $options->{user} = [$tkey, "tracing key"];
1674              $overrides{$name} = UnEscape($1);      $options->{background} = [0, "spool standard and error output"];
1675        $options->{warn} = [0, "send errors to RSS feed"];
1676        # Create a parsing hash from the options hash. The parsing hash
1677        # contains the default values rather than the default value
1678        # and the description. While we're at it, we'll memorize the
1679        # length of the longest option name.
1680        my $longestName = 0;
1681        my %parseOptions = ();
1682        for my $key (keys %{$options}) {
1683            if (length $key > $longestName) {
1684                $longestName = length $key;
1685            }
1686            $parseOptions{$key} = $options->{$key}->[0];
1687        }
1688        # Parse the command line.
1689        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1690        # Get the logfile suffix.
1691        my $suffix = $retOptions->{user};
1692        # Check for background mode.
1693        if ($retOptions->{background}) {
1694            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1695            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1696            open STDOUT, ">$outFileName";
1697            open STDERR, ">$errFileName";
1698            # Check for phone support. If we have phone support and a phone number,
1699            # we want to turn it on.
1700            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1701                $retOptions->{phone} = $ENV{PHONE};
1702            }
1703        }
1704        # Now we want to set up tracing. First, we need to know if the user
1705        # wants emergency tracing.
1706        if ($retOptions->{trace} eq 'E') {
1707            ETracing($retOptions->{user});
1708          } else {          } else {
1709              # Here there is no value, so we use 1.          # Here the tracing is controlled from the command line.
1710              $overrides{$name} = 1;          my @cats = @{$categories};
1711            if ($retOptions->{sql}) {
1712                push @cats, "SQL";
1713          }          }
1714            if ($retOptions->{warn}) {
1715                push @cats, "Feed";
1716      }      }
1717      # Merge the options into the defaults.          # Add the default categories.
1718      GetOptions($optionTable, \%overrides);          push @cats, "Tracer";
1719      # Translate the remaining parameters.          # Next, we create the category string by joining the categories.
1720      my @retVal = ();          my $cats = join(" ", @cats);
1721      for my $inputParm (@inputList) {          # Check to determine whether or not the caller wants to turn off tracing
1722          push @retVal, UnEscape($inputParm);          # to the standard output.
1723            my $traceLevel = $retOptions->{trace};
1724            my $textOKFlag = 1;
1725            if ($traceLevel =~ /^(.)-/) {
1726                $traceLevel = $1;
1727                $textOKFlag = 0;
1728      }      }
1729      # Return the results.          # Now we set up the trace mode.
1730      return ($optionTable, @retVal);          my $traceMode;
1731            # Verify that we can open a file in the FIG temporary directory.
1732            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1733            if (open TESTTRACE, ">$traceFileName") {
1734                # Here we can trace to a file.
1735                $traceMode = ">$traceFileName";
1736                if ($textOKFlag) {
1737                    # Echo to standard output if the text-OK flag is set.
1738                    $traceMode = "+$traceMode";
1739                }
1740                # Close the test file.
1741                close TESTTRACE;
1742            } else {
1743                # Here we can't trace to a file. Complain about this.
1744                warn "Could not open trace file $traceFileName: $!\n";
1745                # We trace to the standard output if it's
1746                # okay, and the error log otherwise.
1747                if ($textOKFlag) {
1748                    $traceMode = "TEXT";
1749                } else {
1750                    $traceMode = "WARN";
1751                }
1752            }
1753            # Now set up the tracing.
1754            TSetup("$traceLevel $cats", $traceMode);
1755        }
1756        # Check for the "help" option. If it is specified, dump the command-line
1757        # options and exit the program.
1758        if ($retOptions->{help}) {
1759            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1760            print "$1 [options] $parmHelp\n";
1761            for my $key (sort keys %{$options}) {
1762                my $name = Pad($key, $longestName, 0, ' ');
1763                my $desc = $options->{$key}->[1];
1764                if ($options->{$key}->[0]) {
1765                    $desc .= " (default " . $options->{$key}->[0] . ")";
1766                }
1767                print "  $name $desc\n";
1768            }
1769            exit(0);
1770        }
1771        # Trace the options, if applicable.
1772        if (T(3)) {
1773            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1774            Trace("Selected options: " . join(", ", sort @parms) . ".");
1775        }
1776        # Return the parsed parameters.
1777        return ($retOptions, @retParameters);
1778  }  }
1779    
1780  =head3 Escape  =head3 ReadOptions
1781    
1782  C<< my $codedString = Tracer::Escape($realString); >>      my %options = Tracer::ReadOptions($fileName);
1783    
1784  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  Read a set of options from a file. Each option is encoded in a line of text that has the
1785  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  format
1786  result is to reverse the effect of L</UnEscape>.  
1787    I<optionName>C<=>I<optionValue>C<; >I<comment>
1788    
1789    The option name must consist entirely of letters, digits, and the punctuation characters
1790    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1791    character is a semi-colon will be ignored. The return hash will map each option name to
1792    the corresponding option value.
1793    
1794  =over 4  =over 4
1795    
1796  =item realString  =item fileName
1797    
1798  String to escape.  Name of the file containing the option data.
1799    
1800  =item RETURN  =item RETURN
1801    
1802  Escaped equivalent of the real string.  Returns a hash mapping the option names specified in the file to their corresponding option
1803    value.
1804    
1805  =back  =back
1806    
1807  =cut  =cut
1808    
1809  sub Escape {  sub ReadOptions {
1810      # Get the parameter.      # Get the parameters.
1811      my ($realString) = @_;      my ($fileName) = @_;
1812      # Initialize the return variable.      # Open the file.
1813      my $retVal = "";      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1814      # Loop through the parameter string, looking for sequences to escape.      # Count the number of records read.
1815      while (length $realString > 0) {      my ($records, $comments) = 0;
1816          # Look for the first sequence to escape.      # Create the return hash.
1817          if ($realString =~ /^(.*?)([\n\t\r\\])/) {      my %retVal = ();
1818              # Here we found it. The text preceding the sequence is in $1. The sequence      # Loop through the file, accumulating key-value pairs.
1819              # itself is in $2. First, move the clear text to the return variable.      while (my $line = <CONFIGFILE>) {
1820              $retVal .= $1;          # Denote we've read a line.
1821              # Strip the processed section off the real string.          $records++;
1822              $realString = substr $realString, (length $2) + (length $1);          # Determine the line type.
1823              # Get the matched character.          if ($line =~ /^\s*[\n\r]/) {
1824              my $char = $2;              # A blank line is a comment.
1825              # If we have a CR, we are done.              $comments++;
1826              if ($char ne "\r") {          } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1827                  # It's not a CR, so encode the escape sequence.              # Here we have an option assignment.
1828                  $char =~ tr/\t\n/tn/;              retVal{$1} = $2;
1829                  $retVal .= "\\" . $char;          } elsif ($line =~ /^\s*;/) {
1830              }              # Here we have a text comment.
1831                $comments++;
1832          } else {          } else {
1833              # Here there are no more escape sequences. The rest of the string is              # Here we have an invalid line.
1834              # transferred unmodified.              Trace("Invalid option statement in record $records.") if T(0);
             $retVal .= $realString;  
             $realString = "";  
1835          }          }
1836      }      }
1837      # Return the result.      # Return the hash created.
1838      return $retVal;      return %retVal;
1839  }  }
1840    
1841  =head3 UnEscape  =head3 GetOptions
1842    
1843        Tracer::GetOptions(\%defaults, \%options);
1844    
1845    Merge a specified set of options into a table of defaults. This method takes two hash references
1846    as input and uses the data from the second to update the first. If the second does not exist,
1847    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1848    exist in the first.
1849    
1850    Consider the following example.
1851    
1852  C<< my $realString = Tracer::UnEscape($codedString); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1853    
1854  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1855  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1856  be deleted.  B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1857    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1858    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1859    
1860        {databaseType => 'Oracle'}
1861    
1862    an error will occur because the B<databaseType> option does not exist.
1863    
1864  =over 4  =over 4
1865    
1866  =item codedString  =item defaults
1867    
1868  String to un-escape.  Table of default option values.
1869    
1870    =item options
1871    
1872    Table of overrides, if any.
1873    
1874  =item RETURN  =item RETURN
1875    
1876  Returns a copy of the original string with the escape sequences converted to their actual  Returns a reference to the default table passed in as the first parameter.
 values.  
1877    
1878  =back  =back
1879    
1880  =cut  =cut
1881    
1882  sub UnEscape {  sub GetOptions {
1883      # Get the parameter.      # Get the parameters.
1884      my ($codedString) = @_;      my ($defaults, $options) = @_;
1885      # Initialize the return variable.      # Check for overrides.
1886      my $retVal = "";      if ($options) {
1887      # Only proceed if the incoming string is nonempty.          # Loop through the overrides.
1888      if (defined $codedString) {          while (my ($option, $setting) = each %{$options}) {
1889          # Loop through the parameter string, looking for escape sequences. We can't do              # Insure this override exists.
1890          # translating because it causes problems with the escaped slash. ("\\t" becomes              if (!exists $defaults->{$option}) {
1891          # "\<tab>" no matter what we do.)                  croak "Unrecognized option $option encountered.";
         while (length $codedString > 0) {  
             # Look for the first escape sequence.  
             if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {  
                 # Here we found it. The text preceding the sequence is in $1. The sequence  
                 # itself is in $2. First, move the clear text to the return variable.  
                 $retVal .= $1;  
                 $codedString = substr $codedString, (2 + length $1);  
                 # Get the escape value.  
                 my $char = $2;  
                 # If we have a "\r", we are done.  
                 if ($char ne 'r') {  
                     # Here it's not an 'r', so we convert it.  
                     $char =~ tr/\\tn/\\\t\n/;  
                     $retVal .= $char;  
                 }  
1892              } else {              } else {
1893                  # Here there are no more escape sequences. The rest of the string is                  # Apply the override.
1894                  # transferred unmodified.                  $defaults->{$option} = $setting;
                 $retVal .= $codedString;  
                 $codedString = "";  
1895              }              }
1896          }          }
1897      }      }
1898      # Return the result.      # Return the merged table.
1899      return $retVal;      return $defaults;
1900  }  }
1901    
1902  =head3 ParseRecord  =head3 MergeOptions
1903    
1904  C<< my @fields = Tracer::ParseRecord($line); >>      Tracer::MergeOptions(\%table, \%defaults);
1905    
1906  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Merge default values into a hash table. This method looks at the key-value pairs in the
1907  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  second (default) hash, and if a matching key is not found in the first hash, the default
1908  These will automatically be converted.  pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1909    checking and no return value.
1910    
1911  =over 4  =over 4
1912    
1913  =item line  =item table
1914    
1915  Line of data containing the tab-delimited fields.  Hash table to be updated with the default values.
1916    
1917  =item RETURN  =item defaults
1918    
1919  Returns a list of the fields found in the data line.  Default values to be merged into the first hash table if they are not already present.
1920    
1921  =back  =back
1922    
1923  =cut  =cut
1924    
1925  sub ParseRecord {  sub MergeOptions {
1926      # Get the parameter.      # Get the parameters.
1927      my ($line) = @_;      my ($table, $defaults) = @_;
1928      # Remove the trailing new-line, if any.      # Loop through the defaults.
1929      chomp $line;      while (my ($key, $value) = each %{$defaults}) {
1930      # Split the line read into pieces using the tab character.          if (!exists $table->{$key}) {
1931      my @retVal = split /\t/, $line;              $table->{$key} = $value;
1932      # Trim and fix the escapes in each piece.          }
     for my $value (@retVal) {  
         # Trim leading whitespace.  
         $value =~ s/^\s+//;  
         # Trim trailing whitespace.  
         $value =~ s/\s+$//;  
         # Delete the carriage returns.  
         $value =~ s/\r//g;  
         # Convert the escapes into their real values.  
         $value =~ s/\\t/"\t"/ge;  
         $value =~ s/\\n/"\n"/ge;  
1933      }      }
     # Return the result.  
     return @retVal;  
1934  }  }
1935    
1936  =head3 Merge  =head3 ParseCommand
   
 C<< my @mergedList = Tracer::Merge(@inputList); >>  
   
 Sort a list of strings and remove duplicates.  
   
 =over 4  
1937    
1938  =item inputList      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1939    
1940  List of scalars to sort and merge.  Parse a command line consisting of a list of parameters. The initial parameters may be option
1941    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1942    off and merged into a table of default options. The remainder of the command line is
1943    returned as a list of positional arguments. For example, consider the following invocation.
1944    
1945  =item RETURN      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1946    
1947  Returns a list containing the same elements sorted in ascending order with duplicates  In this case, the list @words will be treated as a command line and there are two options available,
1948  removed.  B<errors> and B<logFile>. If @words has the following format
1949    
1950  =back      -logFile=error.log apple orange rutabaga
1951    
1952  =cut  then at the end of the invocation, C<$options> will be
1953    
1954  sub Merge {      { errors => 0, logFile => 'error.log' }
     # Get the input list in sort order.  
     my @inputList = sort @_;  
     # Only proceed if the list has at least two elements.  
     if (@inputList > 1) {  
         # Now we want to move through the list splicing out duplicates.  
         my $i = 0;  
         while ($i < @inputList) {  
             # Get the current entry.  
             my $thisEntry = $inputList[$i];  
             # Find out how many elements duplicate the current entry.  
             my $j = $i + 1;  
             my $dup1 = $i + 1;  
             while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };  
             # If the number is nonzero, splice out the duplicates found.  
             if ($j > $dup1) {  
                 splice @inputList, $dup1, $j - $dup1;  
             }  
             # Now the element at position $dup1 is different from the element before it  
             # at position $i. We push $i forward one position and start again.  
             $i++;  
         }  
     }  
     # Return the merged list.  
     return @inputList;  
 }  
1955    
1956  =head3 Percent  and C<@arguments> will contain
1957    
1958  C<< my $percent = Tracer::Percent($number, $base); >>      apple orange rutabaga
1959    
1960  Returns the percent of the base represented by the given number. If the base  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1961  is zero, returns zero.  support for quote characters. Options can be specified with single or double hyphens.
1962    
1963  =over 4  =over 4
1964    
1965  =item number  =item optionTable
1966    
1967  Percent numerator.  Table of default options.
1968    
1969  =item base  =item inputList
1970    
1971  Percent base.  List of words on the command line.
1972    
1973  =item RETURN  =item RETURN
1974    
1975  Returns the percentage of the base represented by the numerator.  Returns a reference to the option table and a list of the positional arguments.
1976    
1977  =back  =back
1978    
1979  =cut  =cut
1980    
1981  sub Percent {  sub ParseCommand {
1982      # Get the parameters.      # Get the parameters.
1983      my ($number, $base) = @_;      my ($optionTable, @inputList) = @_;
1984      # Declare the return variable.      # Process any options in the input list.
1985      my $retVal = 0;      my %overrides = ();
1986      # Compute the percent.      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1987      if ($base != 0) {          # Get the current option.
1988          $retVal = $number * 100 / $base;          my $arg = shift @inputList;
1989            # Pull out the option name.
1990            $arg =~ /^--?([^=]*)/g;
1991            my $name = $1;
1992            # Check for an option value.
1993            if ($arg =~ /\G=(.*)$/g) {
1994                # Here we have a value for the option.
1995                $overrides{$name} = UnEscape($1);
1996            } else {
1997                # Here there is no value, so we use 1.
1998                $overrides{$name} = 1;
1999      }      }
     # Return the result.  
     return $retVal;  
2000  }  }
2001        # Merge the options into the defaults.
2002        GetOptions($optionTable, \%overrides);
2003        # Translate the remaining parameters.
2004        my @retVal = ();
2005        for my $inputParm (@inputList) {
2006            push @retVal, UnEscape($inputParm);
2007        }
2008        # Return the results.
2009        return ($optionTable, @retVal);
2010    }
2011    
2012    
2013    =head2 File Utility Methods
2014    
2015  =head3 GetFile  =head3 GetFile
2016    
2017  C<< my @fileContents = Tracer::GetFile($fileName); >>      my @fileContents = Tracer::GetFile($fileName);
2018    
2019      or      or
2020    
2021  C<< my $fileContents = Tracer::GetFile($fileName); >>      my $fileContents = Tracer::GetFile($fileName);
2022    
2023  Return the entire contents of a file. In list context, line-ends are removed and  Return the entire contents of a file. In list context, line-ends are removed and
2024  each line is a list element. In scalar context, line-ends are replaced by C<\n>.  each line is a list element. In scalar context, line-ends are replaced by C<\n>.
# Line 1648  Line 2068 
2068    
2069  =head3 PutFile  =head3 PutFile
2070    
2071  C<< Tracer::PutFile($fileName, \@lines); >>      Tracer::PutFile($fileName, \@lines);
2072    
2073  Write out a file from a list of lines of text.  Write out a file from a list of lines of text.
2074    
# Line 1691  Line 2111 
2111      close $handle;      close $handle;
2112  }  }
2113    
2114  =head3 QTrace  =head3 ParseRecord
   
 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  
   
 =cut  
   
 sub QTrace {  
     # 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;  
 }  
   
 =head3 Confess  
2115    
2116  C<< Confess($message); >>      my @fields = Tracer::ParseRecord($line);
2117    
2118  Trace the call stack and abort the program with the specified message. When used with  Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2119  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2120  So, for example  These will automatically be converted.
2121    
2122  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
2123    
2124  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item line
2125    
2126  =over 4  Line of data containing the tab-delimited fields.
2127    
2128  =item message  =item RETURN
2129    
2130  Message to include in the trace.  Returns a list of the fields found in the data line.
2131    
2132  =back  =back
2133    
2134  =cut  =cut
2135    
2136  sub Confess {  sub ParseRecord {
2137      # Get the parameters.      # Get the parameter.
2138      my ($message) = @_;      my ($line) = @_;
2139      # Trace the call stack.      # Remove the trailing new-line, if any.
2140      Cluck($message);      chomp $line;
2141      # Abort the program.      # Split the line read into pieces using the tab character.
2142      croak(">>> $message");      my @retVal = split /\t/, $line;
2143        # Trim and fix the escapes in each piece.
2144        for my $value (@retVal) {
2145            # Trim leading whitespace.
2146            $value =~ s/^\s+//;
2147            # Trim trailing whitespace.
2148            $value =~ s/\s+$//;
2149            # Delete the carriage returns.
2150            $value =~ s/\r//g;
2151            # Convert the escapes into their real values.
2152            $value =~ s/\\t/"\t"/ge;
2153            $value =~ s/\\n/"\n"/ge;
2154        }
2155        # Return the result.
2156        return @retVal;
2157  }  }
2158    
2159  =head3 Assert  =head3 Merge
2160    
2161  C<< Assert($condition1, $condition2, ... $conditionN); >>      my @mergedList = Tracer::Merge(@inputList);
2162    
2163  Return TRUE if all the conditions are true. This method can be used in conjunction with  Sort a list of strings and remove duplicates.
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
2164    
2165  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
2166    
2167  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item inputList
2168    
2169    List of scalars to sort and merge.
2170    
2171    =item RETURN
2172    
2173    Returns a list containing the same elements sorted in ascending order with duplicates
2174    removed.
2175    
2176    =back
2177    
2178  =cut  =cut
2179  sub Assert {  
2180      my $retVal = 1;  sub Merge {
2181      LOOP: for my $condition (@_) {      # Get the input list in sort order.
2182          if (! $condition) {      my @inputList = sort @_;
2183              $retVal = 0;      # Only proceed if the list has at least two elements.
2184              last LOOP;      if (@inputList > 1) {
2185            # Now we want to move through the list splicing out duplicates.
2186            my $i = 0;
2187            while ($i < @inputList) {
2188                # Get the current entry.
2189                my $thisEntry = $inputList[$i];
2190                # Find out how many elements duplicate the current entry.
2191                my $j = $i + 1;
2192                my $dup1 = $i + 1;
2193                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2194                # If the number is nonzero, splice out the duplicates found.
2195                if ($j > $dup1) {
2196                    splice @inputList, $dup1, $j - $dup1;
2197                }
2198                # Now the element at position $dup1 is different from the element before it
2199                # at position $i. We push $i forward one position and start again.
2200                $i++;
2201          }          }
2202      }      }
2203      return $retVal;      # Return the merged list.
2204        return @inputList;
2205  }  }
2206    
2207  =head3 Cluck  =head3 Open
2208    
2209  C<< Cluck($message); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2210    
2211  Trace the call stack. Note that for best results, you should qualify the call with a  Open a file.
 trace condition. For example,  
2212    
2213  C<< Cluck("Starting record parse.") if T(3); >>  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2214    function. The mode is specified using Unix-like shell information. So, for
2215    example,
2216    
2217  will only trace the stack if the trace level for the package is 3 or more.      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2218    
2219  =over 4  would open for output appended to the specified file, and
2220    
2221  =item message      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2222    
2223  Message to include in the trace.  would open a pipe that sorts the records written and removes duplicates. Note
2224    the use of file handle syntax in the Open call. To use anonymous file handles,
2225    code as follows.
2226    
2227  =back      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2228    
2229  =cut  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2230    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2231    failed open will throw an exception and the third parameter will be used to construct
2232    an error message. If the parameter is omitted, a standard message is constructed
2233    using the file spec.
2234    
2235  sub Cluck {      Could not open "/usr/spool/news/twitlog"
     # Get the parameters.  
     my ($message) = @_;  
     # Trace what's happening.  
     Trace("Stack trace for event: $message");  
     my $confession = longmess($message);  
     # Convert the confession to a series of trace messages. Note we skip any  
     # messages relating to calls into Tracer.  
     for my $line (split /\s*\n/, $confession) {  
         Trace($line) if ($line !~ /Tracer\.pm/);  
     }  
 }  
2236    
2237  =head3 Min  Note that the mode characters are automatically cleaned from the file name.
2238    The actual error message from the file system will be captured and appended to the
2239    message in any case.
2240    
2241        Could not open "/usr/spool/news/twitlog": file not found.
2242    
2243  C<< my $min = Min($value1, $value2, ... $valueN); >>  In some versions of PERL the only error message we get is a number, which
2244    corresponds to the C++ C<errno> value.
2245    
2246  Return the minimum argument. The arguments are treated as numbers.      Could not open "/usr/spool/news/twitlog": 6.
2247    
2248  =over 4  =over 4
2249    
2250  =item $value1, $value2, ... $valueN  =item fileHandle
2251    
2252  List of numbers to compare.  File handle. If this parameter is C<undef>, a file handle will be generated
2253    and returned as the value of this method.
2254    
2255    =item fileSpec
2256    
2257    File name and mode, as per the PERL C<open> function.
2258    
2259    =item message (optional)
2260    
2261    Error message to use if the open fails. If omitted, a standard error message
2262    will be generated. In either case, the error information from the file system
2263    is appended to the message. To specify a conditional open that does not throw
2264    an error if it fails, use C<0>.
2265    
2266  =item RETURN  =item RETURN
2267    
2268  Returns the lowest number in the list.  Returns the name of the file handle assigned to the file, or C<undef> if the
2269    open failed.
2270    
2271  =back  =back
2272    
2273  =cut  =cut
2274    
2275  sub Min {  sub Open {
2276      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2277      my ($retVal, @values) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2278      # Loop through the remaining parameters, looking for the lowest.      # Attempt to open the file.
2279      for my $value (@values) {      my $rv = open $fileHandle, $fileSpec;
2280          if ($value < $retVal) {      # If the open failed, generate an error message.
2281              $retVal = $value;      if (! $rv) {
2282            # Save the system error message.
2283            my $sysMessage = $!;
2284            # See if we need a default message.
2285            if (!$message) {
2286                # Clean any obvious mode characters and leading spaces from the
2287                # filename.
2288                my ($fileName) = FindNamePart($fileSpec);
2289                $message = "Could not open \"$fileName\"";
2290          }          }
2291            # Terminate with an error using the supplied message and the
2292            # error message from the file system.
2293            Confess("$message: $!");
2294      }      }
2295      # Return the minimum found.      # Return the file handle.
2296      return $retVal;      return $fileHandle;
2297  }  }
2298    
2299  =head3 Max  =head3 FindNamePart
2300    
2301  C<< my $max = Max($value1, $value2, ... $valueN); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2302    
2303  Return the maximum argument. The arguments are treated as numbers.  Extract the portion of a file specification that contains the file name.
2304    
2305    A file specification is the string passed to an C<open> call. It specifies the file
2306    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2307    method assumes that the file name is whatever follows the first angle bracket
2308    sequence.  So, for example, in the following strings the file name is
2309    C</usr/fig/myfile.txt>.
2310    
2311        >>/usr/fig/myfile.txt
2312        </usr/fig/myfile.txt
2313        | sort -u > /usr/fig/myfile.txt
2314    
2315    If the method cannot find a file name using its normal methods, it will return the
2316    whole incoming string.
2317    
2318  =over 4  =over 4
2319    
2320  =item $value1, $value2, ... $valueN  =item fileSpec
2321    
2322  List of numbers to compare.  File specification string from which the file name is to be extracted.
2323    
2324  =item RETURN  =item RETURN
2325    
2326  Returns the highest number in the list.  Returns a three-element list. The first element contains the file name portion of
2327    the specified string, or the whole string if a file name cannot be found via normal
2328    methods. The second element contains the start position of the file name portion and
2329    the third element contains the length.
2330    
2331  =back  =back
2332    
2333  =cut  =cut
2334    #: Return Type $;
2335  sub Max {  sub FindNamePart {
2336      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2337      my ($retVal, @values) = @_;      my ($fileSpec) = @_;
2338      # Loop through the remaining parameters, looking for the highest.      # Default to the whole input string.
2339      for my $value (@values) {      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2340          if ($value > $retVal) {      # Parse out the file name if we can.
2341              $retVal = $value;      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2342          }          $retVal = $2;
2343            $len = length $retVal;
2344            $pos = (length $fileSpec) - (length $3) - $len;
2345      }      }
2346      # Return the maximum found.      # Return the result.
2347      return $retVal;      return ($retVal, $pos, $len);
2348  }  }
2349    
2350  =head3 AddToListMap  =head3 OpenDir
2351    
2352  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>      my @files = OpenDir($dirName, $filtered, $flag);
2353    
2354  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Open a directory and return all the file names. This function essentially performs
2355  is created for the key. Otherwise, the new value is pushed onto the list.  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2356    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2357    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2358    filtered out of the return list. If the directory does not open and I<$flag> is not
2359    set, an exception is thrown. So, for example,
2360    
2361  =over 4      my @files = OpenDir("/Volumes/fig/contigs", 1);
2362    
2363  =item hash  is effectively the same as
2364    
2365  Reference to the target hash.      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2366        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2367    
2368  =item key  Similarly, the following code
2369    
2370  Key for which the value is to be added.      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2371    
2372  =item value1, value2, ... valueN  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2373    automatically returns an empty list if the directory fails to open.
2374    
2375  List of values to add to the key's value list.  =over 4
2376    
2377  =back  =item dirName
2378    
2379  =cut  Name of the directory to open.
2380    
2381  sub AddToListMap {  =item filtered
     # Get the parameters.  
     my ($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;  
     }  
 }  
2382    
2383  =head3 DebugMode  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2384    from the list, else FALSE.
2385    
2386  C<< if (Tracer::DebugMode) { ...code... } >>  =item flag
2387    
2388  Return TRUE if debug mode has been turned on, else abort.  TRUE if a failure to open is okay, else FALSE
2389    
2390  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.  
2391    
2392  =cut  =cut
2393    #: Return Type @;
2394  sub DebugMode {  sub OpenDir {
2395        # Get the parameters.
2396        my ($dirName, $filtered, $flag) = @_;
2397      # Declare the return variable.      # Declare the return variable.
2398      my $retVal = 0;      my @retVal = ();
2399      # Check the debug configuration.      # Open the directory.
2400      my $password = CGI::cookie("DebugMode");      if (opendir(my $dirHandle, $dirName)) {
2401      my $encrypted = Digest::MD5::md5_hex($password);          # The directory opened successfully. Get the appropriate list according to the
2402      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {          # strictures of the filter parameter.
2403          $retVal = 1;          if ($filtered) {
2404                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2405      } else {      } else {
2406          # Here debug mode is off, so we generate an error.              @retVal = readdir $dirHandle;
         Confess("Cannot use this facility without logging in.");  
2407      }      }
2408      # Return the determination indicator.      } elsif (! $flag) {
2409      return $retVal;          # Here the directory would not open and it's considered an error.
2410            Confess("Could not open directory $dirName.");
2411        }
2412        # Return the result.
2413        return @retVal;
2414  }  }
2415    
 =head3 Strip  
2416    
2417  C<< my $string = Tracer::Strip($line); >>  =head3 Insure
2418    
2419  Strip all line terminators off a string. This is necessary when dealing with files      Insure($dirName, $chmod);
2420  that may have been transferred back and forth several times among different  
2421  operating environments.  Insure a directory is present.
2422    
2423  =over 4  =over 4
2424    
2425  =item line  =item dirName
2426    
2427  Line of text to be stripped.  Name of the directory to check. If it does not exist, it will be created.
2428    
2429  =item RETURN  =item chmod (optional)
2430    
2431  The same line of text with all the line-ending characters chopped from the end.  Security privileges to be given to the directory if it is created.
2432    
2433  =back  =back
2434    
2435  =cut  =cut
2436    
2437  sub Strip {  sub Insure {
2438      # Get a copy of the parameter string.      my ($dirName, $chmod) = @_;
2439      my ($string) = @_;      if (! -d $dirName) {
2440      my $retVal = (defined $string ? $string : "");          Trace("Creating $dirName directory.") if T(2);
2441      # Strip the line terminator characters.          eval {
2442      $retVal =~ s/(\r|\n)+$//g;              mkpath $dirName;
2443      # Return the result.              # If we have permissions specified, set them here.
2444      return $retVal;              if (defined($chmod)) {
2445                    chmod $chmod, $dirName;
2446                }
2447            };
2448            if ($@) {
2449                Confess("Error creating $dirName: $@");
2450            }
2451        }
2452  }  }
2453    
2454  =head3 Pad  =head3 ChDir
2455    
2456  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      ChDir($dirName);
2457    
2458  Pad a string to a specified length. The pad character will be a  Change to the specified directory.
 space, and the padding will be on the right side unless specified  
 in the third parameter.  
2459    
2460  =over 4  =over 4
2461    
2462  =item string  =item dirName
   
 String to be padded.  
   
 =item len  
   
 Desired length of the padded string.  
   
 =item left (optional)  
   
 TRUE if the string is to be left-padded; otherwise it will be padded on the right.  
   
 =item padChar (optional)  
   
 Character to use for padding. The default is a space.  
   
 =item RETURN  
2463    
2464  Returns a copy of the original string with the pad character added to the  Name of the directory to which we want to change.
 specified end so that it achieves the desired length.  
2465    
2466  =back  =back
2467    
2468  =cut  =cut
2469    
2470  sub Pad {  sub ChDir {
2471      # Get the parameters.      my ($dirName) = @_;
2472      my ($string, $len, $left, $padChar) = @_;      if (! -d $dirName) {
2473      # Compute the padding character.          Confess("Cannot change to directory $dirName: no such directory.");
     if (! defined $padChar) {  
         $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;  
2474          } else {          } else {
2475              $retVal .= $pad;          Trace("Changing to directory $dirName.") if T(File => 4);
2476            my $okFlag = chdir $dirName;
2477            if (! $okFlag) {
2478                Confess("Error switching to directory $dirName.");
2479          }          }
2480      }      }
     # Return the result.  
     return $retVal;  
2481  }  }
2482    
2483  =head3 EOF  =head3 SetPermissions
2484    
2485  This is a constant that is lexically greater than any useful string.      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2486    
2487  =cut  Set the permissions for a directory and all the files and folders inside it.
2488    In addition, the group ownership will be changed to the specified value.
2489    
2490  sub EOF {  This method is more vulnerable than most to permission and compatability
2491      return "\xFF\xFF\xFF\xFF\xFF";  problems, so it does internal error recovery.
 }  
2492    
2493  =head3 TICK  =over 4
2494    
2495  C<< my @results = TICK($commandString); >>  =item dirName
2496    
2497  Perform a back-tick operation on a command. If this is a Windows environment, any leading  Name of the directory to process.
 dot-slash (C<./> will be removed. So, for example, if you were doing  
2498    
2499      `./protein.cgi`  =item group
2500    
2501  from inside a CGI script, it would work fine in Unix, but would issue an error message  Name of the group to be assigned.
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
2502    
2503      TICK("./protein.cgi")  =item mask
2504    
2505  it will work correctly in both environments.  Permission mask. Bits that are C<1> in this mask will be ORed into the
2506    permission bits of any file or directory that does not already have them
2507    set to 1.
2508    
2509  =over 4  =item otherMasks
2510    
2511  =item commandString  Map of search patterns to permission masks. If a directory name matches
2512    one of the patterns, that directory and all its members and subdirectories
2513    will be assigned the new pattern. For example, the following would
2514    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2515    
2516  The command string to pass to the system.      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2517    
2518  =item RETURN  The list is ordered, so the following would use 0777 for C<tmp1> and
2519    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2520    
2521  Returns the standard output from the specified command, as a list.      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2522                                                       '^tmp' => 0666);
2523    
2524    Note that the pattern matches are all case-insensitive, and only directory
2525    names are matched, not file names.
2526    
2527  =back  =back
2528    
2529  =cut  =cut
2530  #: Return Type @;  
2531  sub TICK {  sub SetPermissions {
2532      # Get the parameters.      # Get the parameters.
2533      my ($commandString) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2534      # Chop off the dot-slash if this is Windows.      # Set up for error recovery.
2535      if ($FIG_Config::win_mode) {      eval {
2536          $commandString =~ s!^\./!!;          # Switch to the specified directory.
2537            ChDir($dirName);
2538            # Get the group ID.
2539            my $gid = getgrnam($group);
2540            # Get the mask for tracing.
2541            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2542            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2543            my $fixCount = 0;
2544            my $lookCount = 0;
2545            # @dirs will be a stack of directories to be processed.
2546            my @dirs = (getcwd());
2547            while (scalar(@dirs) > 0) {
2548                # Get the current directory.
2549                my $dir = pop @dirs;
2550                # Check for a match to one of the specified directory names. To do
2551                # that, we need to pull the individual part of the name off of the
2552                # whole path.
2553                my $simpleName = $dir;
2554                if ($dir =~ m!/([^/]+)$!) {
2555                    $simpleName = $1;
2556                }
2557                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2558                # Search for a match.
2559                my $match = 0;
2560                my $i;
2561                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2562                    my $pattern = $otherMasks[$i];
2563                    if ($simpleName =~ /$pattern/i) {
2564                        $match = 1;
2565                    }
2566                }
2567                # Check for a match. Note we use $i-1 because the loop added 2
2568                # before terminating due to the match.
2569                if ($match && $otherMasks[$i-1] != $mask) {
2570                    # This directory matches one of the incoming patterns, and it's
2571                    # a different mask, so we process it recursively with that mask.
2572                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2573                } else {
2574                    # Here we can process normally. Get all of the non-hidden members.
2575                    my @submems = OpenDir($dir, 1);
2576                    for my $submem (@submems) {
2577                        # Get the full name.
2578                        my $thisMem = "$dir/$submem";
2579                        Trace("Checking member $thisMem.") if T(4);
2580                        $lookCount++;
2581                        if ($lookCount % 1000 == 0) {
2582                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2583                        }
2584                        # Fix the group.
2585                        chown -1, $gid, $thisMem;
2586                        # Insure this member is not a symlink.
2587                        if (! -l $thisMem) {
2588                            # Get its info.
2589                            my $fileInfo = stat $thisMem;
2590                            # Only proceed if we got the info. Otherwise, it's a hard link
2591                            # and we want to skip it anyway.
2592                            if ($fileInfo) {
2593                                my $fileMode = $fileInfo->mode;
2594                                if (($fileMode & $mask) != $mask) {
2595                                    # Fix this member.
2596                                    $fileMode |= $mask;
2597                                    chmod $fileMode, $thisMem;
2598                                    $fixCount++;
2599                                }
2600                                # If it's a subdirectory, stack it.
2601                                if (-d $thisMem) {
2602                                    push @dirs, $thisMem;
2603                                }
2604                            }
2605                        }
2606                    }
2607                }
2608            }
2609            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2610        };
2611        # Check for an error.
2612        if ($@) {
2613            Confess("SetPermissions error: $@");
2614      }      }
     # Activate the command and return the result.  
     return `$commandString`;  
2615  }  }
2616    
2617  =head3 ScriptSetup  =head3 GetLine
   
 C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  
   
 Perform standard tracing and debugging setup for scripts. The value returned is  
 the CGI object followed by a pre-built variable hash.  
2618    
2619  The C<Trace> form parameter is used to determine whether or not tracing is active and      my @data = Tracer::GetLine($handle);
 which trace modules (other than C<Tracer> itself) should be turned on. Specifying  
 the C<CGI> trace module will trace parameter and environment information. Parameters are  
 traced at level 3 and environment variables at level 4. To trace to a file instead of to  
 the web page, set C<TF> to 1. At the end of the script, the client should call  
 L</ScriptFinish> to output the web page.  
2620    
2621  In some situations, it is not practical to invoke tracing via form parameters. For this  Read a line of data from a tab-delimited file.
 situation, you can turn on emergency tracing from the debugging control panel.  
 Tracing will then be turned on automatically for all programs that use the L</ETracing>  
 method, which includes every program that uses this method or L</StandardSetup>.  
2622    
2623  =over 4  =over 4
2624    
2625  =item noTrace (optional)  =item handle
2626    
2627  If specified, tracing will be suppressed. This is useful if the script wants to set up  Open file handle from which to read.
 tracing manually.  
2628    
2629  =item RETURN  =item RETURN
2630    
2631  Returns a two-element list consisting of a CGI query object and a variable hash for  Returns a list of the fields in the record read. The fields are presumed to be
2632  the output page.  tab-delimited. If we are at the end of the file, then an empty list will be
2633    returned. If an empty line is read, a single list item consisting of a null
2634    string will be returned.
2635    
2636  =back  =back
2637    
2638  =cut  =cut
2639    
2640  sub ScriptSetup {  sub GetLine {
2641      # Get the parameters.      # Get the parameters.
2642      my ($noTrace) = @_;      my ($handle) = @_;
2643      # Get the CGI query object.      # Declare the return variable.
2644      my $cgi = CGI->new();      my @retVal = ();
2645      # Set up tracing if it's not suppressed.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2646      ETracing($cgi) unless $noTrace;      # Read from the file.
2647      # Create the variable hash.      my $line = <$handle>;
2648      my $varHash = { results => '' };      # Only proceed if we found something.
2649      # Return the query object and variable hash.      if (defined $line) {
2650      return ($cgi, $varHash);          # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2651            # upload control and have a nonstandard EOL combination.
2652            $line =~ s/(\r|\n)+$//;
2653            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2654            if (T(File => 4)) {
2655                my $escapedLine = $line;
2656                $escapedLine =~ s/\n/\\n/g;
2657                $escapedLine =~ s/\r/\\r/g;
2658                $escapedLine =~ s/\t/\\t/g;
2659                Trace("Line read: -->$escapedLine<--");
2660  }  }
2661            # If the line is empty, return a single empty string; otherwise, parse
2662  =head3 ETracing          # it into fields.
2663            if ($line eq "") {
2664  C<< ETracing($parameter); >>              push @retVal, "";
   
 Set up emergency tracing. Emergency tracing is tracing that is turned  
 on automatically for any program that calls this method. The emergency  
 tracing parameters are stored in a a file identified by a tracing key.  
 If this method is called with a CGI object, then the tracing key is  
 taken from a cookie. If it is called with no parameters, then the tracing  
 key is taken from an environment variable. If it is called with a string,  
 the tracing key is that string.  
   
 =over 4  
   
 =item parameter  
   
 A parameter from which the tracing key is computed. If it is a scalar,  
 that scalar is used as the tracing key. If it is a CGI object, the  
 tracing key is taken from the C<IP> cookie. If it is omitted, the  
 tracing key is taken from the C<TRACING> environment variable. If it  
 is a CGI object and emergency tracing is not on, the C<Trace> and  
 C<TF> parameters will be used to determine the type of tracing.  
   
 =back  
   
 =cut  
   
 sub ETracing {  
     # Get the parameter.  
     my ($parameter) = @_;  
     # Check for CGI mode.  
     my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);  
     # Default to no tracing except errors.  
     my ($tracing, $dest) = ("0", "WARN");  
     # Check for emergency tracing.  
     my $tkey = EmergencyKey($parameter);  
     my $emergencyFile = EmergencyFileName($tkey);  
     if (-e $emergencyFile) {  
         # We have the file. Read in the data.  
         my @tracing = GetFile($emergencyFile);  
         # Pull off the time limit.  
         my $expire = shift @tracing;  
         # Convert it to seconds.  
         $expire *= 3600;  
         # Check the file data.  
         my $stat = stat($emergencyFile);  
         my ($now) = gettimeofday;  
         if ($now - $stat->mtime > $expire) {  
             # Delete the expired file.  
             unlink $emergencyFile;  
2665          } else {          } else {
2666              # Emergency tracing is on. Pull off the destination and              push @retVal, split /\t/,$line;
             # the trace level;  
             $dest = shift @tracing;  
             my $level = shift @tracing;  
             # Convert the destination to a real tracing destination.  
             # temp directory.  
             $dest = EmergencyTracingDest($tkey, $dest);  
             # Insure Tracer is specified.  
             my %moduleHash = map { $_ => 1 } @tracing;  
             $moduleHash{Tracer} = 1;  
             # Set the trace parameter.  
             $tracing = join(" ", $level, sort keys %moduleHash);  
         }  
     } elsif (defined $cgi) {  
         # There's no emergency tracing, but we have a CGI object, so check  
         # for tracing from the form parameters.  
         if ($cgi->param('Trace')) {  
             # Here the user has requested tracing via a form.  
             $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");  
             $tracing = $cgi->param('Trace') . " Tracer";  
         }  
2667      }      }
2668      # Setup the tracing we've determined from all the stuff above.      } else {
2669      TSetup($tracing, $dest);          # Trace the reason the read failed.
2670      # If we're a web script, trace the parameter and environment data.          Trace("End of file: $!") if T(File => 3);
     if (defined $cgi) {  
         TraceParms($cgi);  
2671      }      }
2672        # Return the result.
2673        return @retVal;
2674  }  }
2675    
2676  =head3 EmergencyFileName  =head3 PutLine
2677    
2678  C<< my $fileName = Tracer::EmergencyFileName($tkey); >>      Tracer::PutLine($handle, \@fields, $eol);
2679    
2680  Return the emergency tracing file name. This is the file that specifies  Write a line of data to a tab-delimited file. The specified field values will be
2681  the tracing information.  output in tab-separated form, with a trailing new-line.
2682    
2683  =over 4  =over 4
2684    
2685  =item tkey  =item handle
2686    
2687  Tracing key for the current program.  Output file handle.
2688    
2689  =item RETURN  =item fields
2690    
2691  Returns the name of the file to contain the emergency tracing information.  List of field values.
2692    
2693    =item eol (optional)
2694    
2695    End-of-line character (default is "\n").
2696    
2697  =back  =back
2698    
2699  =cut  =cut
2700    
2701  sub EmergencyFileName {  sub PutLine {
2702      # Get the parameters.      # Get the parameters.
2703      my ($tkey) = @_;      my ($handle, $fields, $eol) = @_;
2704      # Compute the emergency tracing file name.      # Write the data.
2705      return "$FIG_Config::temp/Emergency$tkey.txt";      print $handle join("\t", @{$fields}) . ($eol || "\n");
2706  }  }
2707    
 =head3 EmergencyFileTarget  
   
 C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>  
2708    
2709  Return the emergency tracing target file name. This is the file that receives  =head3 PrintLine
 the tracing output for file-based tracing.  
2710    
2711  =over 4      Tracer::PrintLine($line);
2712    
2713  =item tkey  Print a line of text with a trailing new-line.
2714    
2715  Tracing key for the current program.  =over 4
2716    
2717  =item RETURN  =item line
2718    
2719  Returns the name of the file to contain the trace output.  Line of text to print.
2720    
2721  =back  =back
2722    
2723  =cut  =cut
2724    
2725  sub EmergencyFileTarget {  sub PrintLine {
2726      # Get the parameters.      # Get the parameters.
2727      my ($tkey) = @_;      my ($line) = @_;
2728      # Compute the emergency tracing file name.      # Print the line.
2729      return "$FIG_Config::temp/trace$tkey.log";      print "$line\n";
2730  }  }
2731    
 =head3 EmergencyTracingDest  
2732    
2733  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>  =head2 Other Useful Methods
2734    
2735  This method converts an emergency tracing destination to a real  =head3 ParseParm
 tracing destination. The main difference is that if the  
 destination is C<FILE> or C<APPEND>, we convert it to file  
 output.  
2736    
2737  =over 4      my $listValue = Tracer::ParseParm($string);
2738    
2739  =item tkey  Convert a parameter into a list reference. If the parameter is undefined,
2740    an undefined value will be returned. Otherwise, it will be parsed as a
2741    comma-separated list of values.
2742    
2743  Tracing key for this environment.  =over 4
2744    
2745  =item myDest  =item string
2746    
2747  Destination from the emergency tracing file.  Incoming string.
2748    
2749  =item RETURN  =item RETURN
2750    
2751  Returns a destination that can be passed into L</TSetup>.  Returns a reference to a list of values, or C<undef> if the incoming value
2752    was undefined.
2753    
2754  =back  =back
2755    
2756  =cut  =cut
2757    
2758  sub EmergencyTracingDest {  sub ParseParm {
2759      # Get the parameters.      # Get the parameters.
2760      my ($tkey, $myDest) = @_;      my ($string) = @_;
2761      # Declare the return variable.      # Declare the return variable.
2762      my $retVal;      my $retVal;
2763      # Process according to the destination value.      # Check for data.
2764      if ($myDest eq 'FILE') {      if (defined $string) {
2765          $retVal = ">" . EmergencyFileTarget($tkey);          # We have some, so split it into a list.
2766      } elsif ($myDest eq 'APPEND') {          $retVal = [ split /\s*,\s*/, $string];
         $retVal = ">>" . EmergencyFileTarget($tkey);  
     } else {  
         $retVal = $myDest;  
2767      }      }
2768      # Return the result.      # Return the result.
2769      return $retVal;      return $retVal;
2770  }  }
2771    
2772  =head3 Emergency  =head3 Now
2773    
2774  C<< Emergency($key, $hours, $dest, $level, @modules); >>      my $string = Tracer::Now();
2775    
2776  Turn on emergency tracing. This method can only be invoked over the web and is  Return a displayable time stamp containing the local time. Whatever format this
2777  should not be called if debug mode is off. The caller specifies the duration of the  method produces must be parseable by L</ParseDate>.
2778  emergency in hours, the desired tracing destination, the trace level,  
2779  and a list of the trace modules to activate. For the length of the duration, when a  =cut
2780  program in an environment with the specified tracing key active invokes a Sprout  
2781  CGI script, tracing will be turned on automatically. See L</TSetup> for more  sub Now {
2782  about tracing setup and L</ETracing> for more about emergency tracing.      return DisplayTime(time);
2783    }
2784    
2785    =head3 DisplayTime
2786    
2787        my $string = Tracer::DisplayTime($time);
2788    
2789    Convert a time value to a displayable time stamp. Whatever format this
2790    method produces must be parseable by L</ParseDate>.
2791    
2792  =over 4  =over 4
2793    
2794  =item tkey  =item time
2795    
2796  The tracing key. This is used to identify the control file and the trace file.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2797    
2798  =item hours  =item RETURN
2799    
2800  Number of hours to keep emergency tracing alive.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2801    
2802  =item dest  =back
2803    
2804  Tracing destination. If no path information is specified for a file  =cut
 destination, it is put in the FIG temporary directory.  
2805    
2806  =item level  sub DisplayTime {
2807        my ($time) = @_;
2808        my $retVal = "(n/a)";
2809        if (defined $time) {
2810            my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2811            $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2812                      _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2813        }
2814        return $retVal;
2815    }
2816    
2817  Tracing level. A higher level means more trace messages.  # Pad a number to 2 digits.
2818    sub _p2 {
2819        my ($value) = @_;
2820        $value = "0$value" if ($value < 10);
2821        return $value;
2822    }
2823    
2824  =item modules  =head3 Escape
2825    
2826  A list of the tracing modules to activate.      my $codedString = Tracer::Escape($realString);
2827    
2828    Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2829    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2830    result is to reverse the effect of L</UnEscape>.
2831    
2832    =over 4
2833    
2834    =item realString
2835    
2836    String to escape.
2837    
2838    =item RETURN
2839    
2840    Escaped equivalent of the real string.
2841    
2842  =back  =back
2843    
2844  =cut  =cut
2845    
2846  sub Emergency {  sub Escape {
2847      # Get the parameters.      # Get the parameter.
2848      my ($tkey, $hours, $dest, $level, @modules) = @_;      my ($realString) = @_;
2849      # Create the emergency file.      # Initialize the return variable.
2850      my $specFile = EmergencyFileName($tkey);      my $retVal = "";
2851      my $outHandle = Open(undef, ">$specFile");      # Loop through the parameter string, looking for sequences to escape.
2852      print $outHandle join("\n", $hours, $dest, $level, @modules, "");      while (length $realString > 0) {
2853            # Look for the first sequence to escape.
2854            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2855                # Here we found it. The text preceding the sequence is in $1. The sequence
2856                # itself is in $2. First, move the clear text to the return variable.
2857                $retVal .= $1;
2858                # Strip the processed section off the real string.
2859                $realString = substr $realString, (length $2) + (length $1);
2860                # Get the matched character.
2861                my $char = $2;
2862                # If we have a CR, we are done.
2863                if ($char ne "\r") {
2864                    # It's not a CR, so encode the escape sequence.
2865                    $char =~ tr/\t\n/tn/;
2866                    $retVal .= "\\" . $char;
2867                }
2868            } else {
2869                # Here there are no more escape sequences. The rest of the string is
2870                # transferred unmodified.
2871                $retVal .= $realString;
2872                $realString = "";
2873            }
2874        }
2875        # Return the result.
2876        return $retVal;
2877  }  }
2878    
2879  =head3 EmergencyKey  =head3 UnEscape
2880    
2881  C<< my $tkey = EmergencyKey($parameter); >>      my $realString = Tracer::UnEscape($codedString);
2882    
2883  Return the Key to be used for emergency tracing. This could be an IP address,  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2884   a session ID, or a user name, depending on the environment.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2885    be deleted.
2886    
2887  =over 4  =over 4
2888    
2889  =item parameter  =item codedString
2890    
2891  Parameter defining the method for finding the tracing key. If it is a scalar,  String to un-escape.
 then it is presumed to be the tracing key itself. If it is a CGI object, then  
 the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is  
 taken from the C<TRACING> environment variable.  
2892    
2893  =item RETURN  =item RETURN
2894    
2895  Returns the key to be used for labels in emergency tracing.  Returns a copy of the original string with the escape sequences converted to their actual
2896    values.
2897    
2898  =back  =back
2899    
2900  =cut  =cut
2901    
2902  sub EmergencyKey {  sub UnEscape {
2903      # Get the parameters.      # Get the parameter.
2904      my ($parameter) = @_;      my ($codedString) = @_;
2905      # Declare the return variable.      # Initialize the return variable.
2906      my $retVal;      my $retVal = "";
2907      # Determine the parameter type.      # Only proceed if the incoming string is nonempty.
2908      if (! defined $parameter) {      if (defined $codedString) {
2909          # Here we're supposed to check the environment.          # Loop through the parameter string, looking for escape sequences. We can't do
2910          $retVal = $ENV{TRACING};          # translating because it causes problems with the escaped slash. ("\\t" becomes
2911            # "\<tab>" no matter what we do.)
2912            while (length $codedString > 0) {
2913                # Look for the first escape sequence.
2914                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2915                    # Here we found it. The text preceding the sequence is in $1. The sequence
2916                    # itself is in $2. First, move the clear text to the return variable.
2917                    $retVal .= $1;
2918                    $codedString = substr $codedString, (2 + length $1);
2919                    # Get the escape value.
2920                    my $char = $2;
2921                    # If we have a "\r", we are done.
2922                    if ($char ne 'r') {
2923                        # Here it's not an 'r', so we convert it.
2924                        $char =~ tr/\\tn/\\\t\n/;
2925                        $retVal .= $char;
2926                    }
2927      } else {      } else {
2928          my $ptype = ref $parameter;                  # Here there are no more escape sequences. The rest of the string is
2929          if ($ptype eq 'CGI') {                  # transferred unmodified.
2930              # Here we were invoked from a web page. Look for a cookie.                  $retVal .= $codedString;
2931              $retVal = $parameter->cookie('IP');                  $codedString = "";
         } elsif (! $ptype) {  
             # Here the key was passed in.  
             $retVal = $parameter;  
2932          }          }
2933      }      }
     # If no luck finding a key, use the PID.  
     if (! defined $retVal) {  
         $retVal = $$;  
2934      }      }
2935      # Return the result.      # Return the result.
2936      return $retVal;      return $retVal;
2937  }  }
2938    
2939    =head3 Percent
2940    
2941  =head3 TraceParms      my $percent = Tracer::Percent($number, $base);
   
 C<< Tracer::TraceParms($cgi); >>  
2942    
2943  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Returns the percent of the base represented by the given number. If the base
2944  at level CGI => 4.  is zero, returns zero.
2945    
2946  =over 4  =over 4
2947    
2948  =item cgi  =item number
2949    
2950  CGI query object containing the parameters to trace.  Percent numerator.
2951    
2952    =item base
2953    
2954    Percent base.
2955    
2956    =item RETURN
2957    
2958    Returns the percentage of the base represented by the numerator.
2959    
2960  =back  =back
2961    
2962  =cut  =cut
2963    
2964  sub TraceParms {  sub Percent {
2965      # Get the parameters.      # Get the parameters.
2966      my ($cgi) = @_;      my ($number, $base) = @_;
2967      if (T(CGI => 3)) {      # Declare the return variable.
2968          # Here we want to trace the parameter data.      my $retVal = 0;
2969          my @names = $cgi->param;      # Compute the percent.
2970          for my $parmName (sort @names) {      if ($base != 0) {
2971              # Note we skip the Trace parameters, which are for our use only.          $retVal = $number * 100 / $base;
             if ($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}");  
         }  
2972      }      }
2973        # Return the result.
2974        return $retVal;
2975  }  }
2976    
2977  =head3 ScriptFinish  =head3 Constrain
2978    
2979  C<< ScriptFinish($webData, $varHash); >>      my $constrained = Constrain($value, $min, $max);
2980    
2981  Output a web page at the end of a script. Either the string to be output or the  Modify a numeric value to bring it to a point in between a maximum and a minimum.
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
2982    
2983  A typical standard script would loook like the following.  =over 4
2984    
2985      BEGIN {  =item value
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
2986    
2987      my ($cgi, $varHash) = ScriptSetup();  Value to constrain.
     eval {  
         # ... get data from $cgi, put it in $varHash ...  
     };  
     if ($@) {  
         Trace("Script Error: $@") if T(0);  
     }  
     ScriptFinish("Html/MyTemplate.html", $varHash);  
2988    
2989  The idea here is that even if the script fails, you'll see trace messages and  =item min (optional)
 useful output.  
2990    
2991  =over 4  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
2992    
2993  =item webData  =item max (optional)
2994    
2995  A string containing either the full web page to be written to the output or the  Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
2996    
2997  =item varHash (optional)  =item RETURN
2998    
2999  If specified, then a reference to a hash mapping variable names for a template  Returns the incoming value, constrained according to the other parameters.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3000    
3001  =back  =back
3002    
3003  =cut  =cut
3004    
3005  sub ScriptFinish {  sub Constrain {
3006      # Get the parameters.      # Get the parameters.
3007      my ($webData, $varHash) = @_;      my ($value, $min, $max) = @_;
3008      # Check for a template file situation.      # Declare the return variable.
3009      my $outputString;      my $retVal = $value;
3010      if (defined $varHash) {      # Apply the minimum constraint.
3011          # Here we have a template file. We need to determine the template type.      if (defined $min && $retVal < $min) {
3012          my $template;          $retVal = $min;
3013          if ($FIG_Config::template_url && $webData =~ /\.php$/) {      }
3014              $template = "$FIG_Config::template_url/$webData";      # Apply the maximum constraint.
3015          } else {      if (defined $max && $retVal > $max) {
3016              $template = "<<$webData";          $retVal = $max;
         }  
         $outputString = PageBuilder::Build($template, $varHash, "Html");  
     } else {  
         # Here the user gave us a raw string.  
         $outputString = $webData;  
     }  
     # Check for trace messages.  
     if ($Destination ne "NONE" && $TraceLevel > 0) {  
         # We have trace messages, so we want to put them at the end of the body. This  
         # is either at the end of the whole string or at the beginning of the BODY  
         # end-tag.  
         my $pos = length $outputString;  
         if ($outputString =~ m#</body>#gi) {  
             $pos = (pos $outputString) - 7;  
         }  
         # If the trace messages were queued, we unroll them. Otherwise, we display the  
         # destination.  
         my $traceHtml;  
         if ($Destination eq "QUEUE") {  
             $traceHtml = QTrace('Html');  
         } elsif ($Destination =~ /^>>(.+)$/) {  
             # Here the tracing output it to a file. We code it as a hyperlink so the user  
             # can copy the file name into the clipboard easily.  
             my $actualDest = $1;  
             $traceHtml = "<p>Tracing output to $actualDest.</p>\n";  
         } else {  
             # Here we have one of the special destinations.  
             $traceHtml = "<P>Tracing output type is $Destination.</p>\n";  
         }  
         substr $outputString, $pos, 0, $traceHtml;  
3017      }      }
3018      # Write the output string.      # Return the result.
3019      print $outputString;      return $retVal;
3020  }  }
3021    
3022  =head3 Insure  =head3 Min
3023    
3024  C<< Insure($dirName); >>      my $min = Min($value1, $value2, ... $valueN);
3025    
3026  Insure a directory is present.  Return the minimum argument. The arguments are treated as numbers.
3027    
3028  =over 4  =over 4
3029    
3030  =item dirName  =item $value1, $value2, ... $valueN
   
 Name of the directory to check. If it does not exist, it will be created.  
   
 =back  
   
 =cut  
   
 sub Insure {  
     my ($dirName) = @_;  
     if (! -d $dirName) {  
         Trace("Creating $dirName directory.") if T(File => 2);  
         eval { mkpath $dirName; };  
         if ($@) {  
             Confess("Error creating $dirName: $@");  
         }  
     }  
 }  
   
 =head3 ChDir  
   
 C<< ChDir($dirName); >>  
   
 Change to the specified directory.  
3031    
3032  =over 4  List of numbers to compare.
3033    
3034  =item dirName  =item RETURN
3035    
3036  Name of the directory to which we want to change.  Returns the lowest number in the list.
3037    
3038  =back  =back
3039    
3040  =cut  =cut
3041    
3042  sub ChDir {  sub Min {
3043      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
3044      if (! -d $dirName) {      my ($retVal, @values) = @_;
3045          Confess("Cannot change to directory $dirName: no such directory.");      # Loop through the remaining parameters, looking for the lowest.
3046      } else {      for my $value (@values) {
3047          Trace("Changing to directory $dirName.") if T(File => 4);          if ($value < $retVal) {
3048          my $okFlag = chdir $dirName;              $retVal = $value;
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
         }  
3049      }      }
3050  }  }
3051        # Return the minimum found.
3052        return $retVal;
3053    }
3054    
3055  =head3 SendSMS  =head3 Max
   
 C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>  
   
 Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  
 user name, password, and API ID for the relevant account in the hash reference variable  
 I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For  
 example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID  
 is C<2561022>, then the FIG_Config file must contain  
   
     $phone =  { user => 'BruceTheHumanPet',  
                 password => 'silly',  
                 api_id => '2561022' };  
3056    
3057  The original purpose of this method was to insure Bruce would be notified immediately when the      my $max = Max($value1, $value2, ... $valueN);
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3058    
3059  The message ID will be returned if successful, and C<undef> if an error occurs.  Return the maximum argument. The arguments are treated as numbers.
3060    
3061  =over 4  =over 4
3062    
3063  =item phoneNumber  =item $value1, $value2, ... $valueN
   
 Phone number to receive the message, in international format. A United States phone number  
 would be prefixed by "1". A British phone number would be prefixed by "44".  
   
 =item msg  
3064    
3065  Message to send to the specified phone.  List of numbers to compare.
3066    
3067  =item RETURN  =item RETURN
3068    
3069  Returns the message ID if successful, and C<undef> if the message could not be sent.  Returns the highest number in the list.
3070    
3071  =back  =back
3072    
3073  =cut  =cut
3074    
3075  sub SendSMS {  sub Max {
3076      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3077      my ($phoneNumber, $msg) = @_;      my ($retVal, @values) = @_;
3078      # Declare the return variable. If we do not change it, C<undef> will be returned.      # Loop through the remaining parameters, looking for the highest.
3079      my $retVal;      for my $value (@values) {
3080      # Only proceed if we have phone support.          if ($value > $retVal) {
3081      if (! defined $FIG_Config::phone) {              $retVal = $value;
         Trace("Phone support not present in FIG_Config.") if T(1);  
     } else {  
         # Get the phone data.  
         my $parms = $FIG_Config::phone;  
         # Get the Clickatell URL.  
         my $url = "http://api.clickatell.com/http/";  
         # Create the user agent.  
         my $ua = LWP::UserAgent->new;  
         # Request a Clickatell session.  
         my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},  
                                      password => $parms->{password},  
                                      api_id => $parms->{api_id},  
                                      to => $phoneNumber,  
                                      text => $msg});  
         # Check for an error.  
         if (! $resp->is_success) {  
             Trace("Alert failed.") if T(1);  
         } else {  
             # Get the message ID.  
             my $rstring = $resp->content;  
             if ($rstring =~ /^ID:\s+(.*)$/) {  
                 $retVal = $1;  
             } else {  
                 Trace("Phone attempt failed with $rstring") if T(1);  
             }  
3082          }          }
3083      }      }
3084      # Return the result.      # Return the maximum found.
3085      return $retVal;      return $retVal;
3086  }  }
3087    
3088  =head3 CommaFormat  =head3 Strip
3089    
3090  C<< my $formatted = Tracer::CommaFormat($number); >>      my $string = Tracer::Strip($line);
3091    
3092  Insert commas into a number.  Strip all line terminators off a string. This is necessary when dealing with files
3093    that may have been transferred back and forth several times among different
3094    operating environments.
3095    
3096  =over 4  =over 4
3097    
3098  =item number  =item line
3099    
3100  A sequence of digits.  Line of text to be stripped.
3101    
3102  =item RETURN  =item RETURN
3103    
3104  Returns the same digits with commas strategically inserted.  The same line of text with all the line-ending characters chopped from the end.
3105    
3106  =back  =back
3107    
3108  =cut  =cut
3109    
3110  sub CommaFormat {  sub Strip {
3111      # Get the parameters.      # Get a copy of the parameter string.
3112      my ($number) = @_;      my ($string) = @_;
3113      # Pad the length up to a multiple of three.      my $retVal = (defined $string ? $string : "");
3114      my $padded = "$number";      # Strip the line terminator characters.
3115      $padded = " " . $padded while length($padded) % 3 != 0;      $retVal =~ s/(\r|\n)+$//g;
     # This is a fancy PERL trick. The parentheses in the SPLIT pattern  
     # cause the delimiters to be included in the output stream. The  
     # GREP removes the empty strings in between the delimiters.  
     my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));  
     # Clean out the spaces.  
     $retVal =~ s/ //g;  
3116      # Return the result.      # Return the result.
3117      return $retVal;      return $retVal;
3118  }  }
 =head3 SetPermissions  
3119    
3120  C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  =head3 Pad
3121    
3122  Set the permissions for a directory and all the files and folders inside it.      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
 In addition, the group ownership will be changed to the specified value.  
3123    
3124  This method is more vulnerable than most to permission and compatability  Pad a string to a specified length. The pad character will be a
3125  problems, so it does internal error recovery.  space, and the padding will be on the right side unless specified
3126    in the third parameter.
3127    
3128  =over 4  =over 4
3129    
3130  =item dirName  =item string
   
 Name of the directory to process.  
   
 =item group  
3131    
3132  Name of the group to be assigned.  String to be padded.
3133    
3134  =item mask  =item len
3135    
3136  Permission mask. Bits that are C<1> in this mask will be ORed into the  Desired length of the padded string.
 permission bits of any file or directory that does not already have them  
 set to 1.  
3137    
3138  =item otherMasks  =item left (optional)
3139    
3140  Map of search patterns to permission masks. If a directory name matches  TRUE if the string is to be left-padded; otherwise it will be padded on the right.
 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>.  
3141    
3142      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  =item padChar (optional)
3143    
3144  The list is ordered, so the following would use 0777 for C<tmp1> and  Character to use for padding. The default is a space.
 0666 for C<tmp>, C<tmp2>, or C<tmp3>.  
3145    
3146      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  =item RETURN
                                                    '^tmp' => 0666);  
3147    
3148  Note that the pattern matches are all case-insensitive, and only directory  Returns a copy of the original string with the pad character added to the
3149  names are matched, not file names.  specified end so that it achieves the desired length.
3150    
3151  =back  =back
3152    
3153  =cut  =cut
3154    
3155  sub SetPermissions {  sub Pad {
3156      # Get the parameters.      # Get the parameters.
3157      my ($dirName, $group, $mask, @otherMasks) = @_;      my ($string, $len, $left, $padChar) = @_;
3158      # Set up for error recovery.      # Compute the padding character.
3159      eval {      if (! defined $padChar) {
3160          # Switch to the specified directory.          $padChar = " ";
         ChDir($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(File => 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(File => 4);  
             # Search for a match.  
             my $match = 0;  
             my $i;  
             for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {  
                 my $pattern = $otherMasks[$i];  
                 if ($simpleName =~ /$pattern/i) {  
                     $match = 1;  
                 }  
3161              }              }
3162              # Check for a match. Note we use $i-1 because the loop added 2      # Compute the number of spaces needed.
3163              # before terminating due to the match.      my $needed = $len - length $string;
3164              if ($match && $otherMasks[$i-1] != $mask) {      # Copy the string into the return variable.
3165                  # This directory matches one of the incoming patterns, and it's      my $retVal = $string;
3166                  # a different mask, so we process it recursively with that mask.      # Only proceed if padding is needed.
3167                  SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);      if ($needed > 0) {
3168            # Create the pad string.
3169            my $pad = $padChar x $needed;
3170            # Affix it to the return value.
3171            if ($left) {
3172                $retVal = $pad . $retVal;
3173              } else {              } else {
3174                  # Here we can process normally. Get all of the non-hidden members.              $retVal .= $pad;
                 my @submems = OpenDir($dir, 1);  
                 for my $submem (@submems) {  
                     # Get the full name.  
                     my $thisMem = "$dir/$submem";  
                     Trace("Checking member $thisMem.") if T(4);  
                     $lookCount++;  
                     if ($lookCount % 1000 == 0) {  
                         Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);  
                     }  
                     # Fix the group.  
                     chown -1, $gid, $thisMem;  
                     # Insure this member is not a symlink.  
                     if (! -l $thisMem) {  
                         # Get its info.  
                         my $fileInfo = stat $thisMem;  
                         # Only proceed if we got the info. Otherwise, it's a hard link  
                         # and we want to skip it anyway.  
                         if ($fileInfo) {  
                             my $fileMode = $fileInfo->mode;  
                             if (($fileMode & $mask) != $mask) {  
                                 # Fix this member.  
                                 $fileMode |= $mask;  
                                 chmod $fileMode, $thisMem;  
                                 $fixCount++;  
                             }  
                             # If it's a subdirectory, stack it.  
                             if (-d $thisMem) {  
                                 push @dirs, $thisMem;  
                             }  
3175                          }                          }
3176                      }                      }
3177        # Return the result.
3178        return $retVal;
3179                  }                  }
3180    
3181    =head3 EOF
3182    
3183    This is a constant that is lexically greater than any useful string.
3184    
3185    =cut
3186    
3187    sub EOF {
3188        return "\xFF\xFF\xFF\xFF\xFF";
3189              }              }
3190    
3191    =head3 TICK
3192    
3193        my @results = TICK($commandString);
3194    
3195    Perform a back-tick operation on a command. If this is a Windows environment, any leading
3196    dot-slash (C<./> will be removed. So, for example, if you were doing
3197    
3198        `./protein.cgi`
3199    
3200    from inside a CGI script, it would work fine in Unix, but would issue an error message
3201    in Windows complaining that C<'.'> is not a valid command. If instead you code
3202    
3203        TICK("./protein.cgi")
3204    
3205    it will work correctly in both environments.
3206    
3207    =over 4
3208    
3209    =item commandString
3210    
3211    The command string to pass to the system.
3212    
3213    =item RETURN
3214    
3215    Returns the standard output from the specified command, as a list.
3216    
3217    =back
3218    
3219    =cut
3220    #: Return Type @;
3221    sub TICK {
3222        # Get the parameters.
3223        my ($commandString) = @_;
3224        # Chop off the dot-slash if this is Windows.
3225        if ($FIG_Config::win_mode) {
3226            $commandString =~ s!^\./!!;
3227          }          }
3228          Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);      # Activate the command and return the result.
3229      };      return `$commandString`;
     # Check for an error.  
     if ($@) {  
         Confess("SetPermissions error: $@");  
3230      }      }
3231    
3232    
3233    =head3 CommaFormat
3234    
3235        my $formatted = Tracer::CommaFormat($number);
3236    
3237    Insert commas into a number.
3238    
3239    =over 4
3240    
3241    =item number
3242    
3243    A sequence of digits.
3244    
3245    =item RETURN
3246    
3247    Returns the same digits with commas strategically inserted.
3248    
3249    =back
3250    
3251    =cut
3252    
3253    sub CommaFormat {
3254        # Get the parameters.
3255        my ($number) = @_;
3256        # Pad the length up to a multiple of three.
3257        my $padded = "$number";
3258        $padded = " " . $padded while length($padded) % 3 != 0;
3259        # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3260        # cause the delimiters to be included in the output stream. The
3261        # GREP removes the empty strings in between the delimiters.
3262        my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3263        # Clean out the spaces.
3264        $retVal =~ s/ //g;
3265        # Return the result.
3266        return $retVal;
3267  }  }
3268    
3269    
3270  =head3 CompareLists  =head3 CompareLists
3271    
3272  C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3273    
3274  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
3275  are presumed to be sorted alphabetically by the value in the $keyIndex column.  are presumed to be sorted alphabetically by the value in the $keyIndex column.
# Line 2941  Line 3334 
3334      return ($inserted, $deleted);      return ($inserted, $deleted);
3335  }  }
3336    
3337  =head3 GetLine  =head3 Cmp
3338    
3339  C<< my @data = Tracer::GetLine($handle); >>      my $cmp = Tracer::Cmp($a, $b);
3340    
3341  Read a line of data from a tab-delimited file.  This method performs a universal sort comparison. Each value coming in is
3342    separated into a leading text part and a trailing number part. The text
3343    part is string compared, and if both parts are equal, then the number
3344    parts are compared numerically. A stream of just numbers or a stream of
3345    just s