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revision 1.73, Tue Oct 3 12:04:50 2006 UTC revision 1.102, Thu May 8 22:52:30 2008 UTC
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1  #  # -*- perl -*-
2    ########################################################################
3  # Copyright (c) 2003-2006 University of Chicago and Fellowship  # Copyright (c) 2003-2006 University of Chicago and Fellowship
4  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
5  #  #
# Line 13  Line 14 
14  # at info@ci.uchicago.edu or the Fellowship for Interpretation of  # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15  # Genomes at veronika@thefig.info or download a copy from  # Genomes at veronika@thefig.info or download a copy from
16  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
17  #  ########################################################################
18    
19  package Tracer;  package Tracer;
20    
21      require Exporter;      require Exporter;
22      @ISA = ('Exporter');      @ISA = ('Exporter');
23      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn);
24      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
25      use strict;      use strict;
26      use Carp qw(longmess croak);      use Carp qw(longmess croak carp);
27      use CGI;      use CGI;
28      use Cwd;      use Cwd;
29      use FIG_Config;      use FIG_Config;
# Line 34  Line 35 
35      use LWP::UserAgent;      use LWP::UserAgent;
36      use Time::HiRes 'gettimeofday';      use Time::HiRes 'gettimeofday';
37      use URI::Escape;      use URI::Escape;
38        use Time::Local;
39        use POSIX qw(strftime);
40        use Time::Zone;
41    
42    
43  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
44    
# Line 158  Line 163 
163    
164  Sometimes, you need a way for tracing to happen automatically without putting parameters  Sometimes, you need a way for tracing to happen automatically without putting parameters
165  in a form or on the command line. Emergency tracing does this. You invoke emergency tracing  in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
166  from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.  from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
167  Emergency tracing requires you specify a tracing key. For command-line tools, the key is  that you specify a tracing key. For command-line tools, the key is
168  taken from the C<TRACING> environment variable. For web services, the key is taken from  taken from the C<TRACING> environment variable. For web services, the key is taken from
169  a cookie. Either way, the key tells the tracing facility who you are, so that you control  a cookie. Either way, the key tells the tracing facility who you are, so that you control
170  the tracing in your environment without stepping on other users.  the tracing in your environment without stepping on other users.
# Line 182  Line 187 
187    
188  The web script will look for the tracing key in the cookies, and the command-line  The web script will look for the tracing key in the cookies, and the command-line
189  script will look for it in the C<TRACING> environment variable. If you are  script will look for it in the C<TRACING> environment variable. If you are
190  using the L</StandardScript> or L</StandardSetup> methods, emergency tracing  using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
191  will be configured automatically.  will be configured automatically.
192    
 =head3 Debugging Control Panel  
   
 The debugging control panel provides several tools to assist in development of  
 SEED and Sprout software. You access the debugging control panel from the URL  
 C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,  
 for example, the panel access point for the development NMPDR system is  
 C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to  
 find out what the password is. From this page, you can also specify a tracing  
 key. If you don't specify a key, one will be generated for you.  
   
 =head4 Emergency Tracing Form  
   
 At the bottom of the debugging control panel is a form that allows you to  
 specify a trace level and tracing categories. Special and common categories  
 are listed with check boxes. You can hold your mouse over a check box to see  
 what its category does. In general, however, a category name is the same as  
 the name of the package in which the trace message occurs.  
   
 Additional categories can be entered in an input box, delimited by spaces or commas.  
   
 The B<Activate> button turns on Emergency tracing at the level you specify with the  
 specified categories active. The B<Terminate> button turns tracing off. The  
 B<Show File> button displays the current contents of the trace file. The tracing  
 form at the bottom of the control panel is designed for emergency tracing, so it  
 will only affect programs that call L</ETracing>, L</StandardScript>,  
 or L</StandardSetup>.  
   
 =head4 Script Form  
   
 The top form of the debugging control panel allows you to enter a tiny script and  
 have the output generated in a formatted table. Certain object variables are  
 predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),  
 and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.  
   
 The last line of the script must be a scalar, but it can be a reference to a hash,  
 a list, a list of lists, and various other combinations. If you select the appropriate  
 data type in the dropdown box, the output will be formatted accordingly. The form  
 also has controls for specifying tracing. These controls override any emergency  
 tracing in effect.  
   
 =head4 Database Query Forms  
   
 The forms between the script form and the emergency tracing form allow you to  
 make queries against the database. The FIG query form allows simple queries against  
 a single FIG table. The Sprout query form uses the B<GetAll> method to do a  
 multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>  
 package, and it takes five parameters.  
   
     GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);  
   
 Each of the five parameters corresponds to a text box on the query form:  
   
 =over 4  
   
 =item Objects  
   
 Comma-separated list containing the names of the entity and relationship objects to be retrieved.  
   
 =item Filter  
   
 WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  
 be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form  
 B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a  
 field, I<objectName> is the name of the entity or relationship object containing the field, and  
 I<number> is the 1-based position of the object in the object list. Any parameters  
 specified in the filter clause should be specified in the B<Params> field.  
 The fields in a filter clause can come from primary entity relations,  
 relationship relations, or secondary entity relations; however, all of the  
 entities and relationships involved must be included in the list of object names.  
   
 =item Params  
   
 List of the parameters to be substituted in for the parameters marks in the filter clause. This  
 is a comma-separated list without any quoting or escaping.  
   
 =item fields  
   
 Comma-separated list of the fields to be returned in each element of the list returned. Fields  
 are specified in the same manner as in the filter clause.  
   
 =item count  
   
 Maximum number of records to return. If omitted or 0, all available records will be returned.  
   
 =back  
   
 B<GetAll> automatically joins together the entities and relationships listed in the object  
 names. This simplifies the coding of the filter clause, but it means that some queries are  
 not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation  
 that has yet to be addressed.  
   
193  =cut  =cut
194    
195  # Declare the configuration variables.  # Declare the configuration variables.
196    
197  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
198  my $TeeFlag = 0;            # TRUE if output is going to a file and to the  my $TeeFlag = 0;            # TRUE if output is going to a file and to the
199                              # standard output                              # standard output
200  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
201                              # hash of active category names                              # hash of active category names
202    my @LevelNames = qw(error warn notice info detail);
203  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
204                              # messages                              # messages
205  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
206  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
207    my $LastLevel = 0;          # level of the last test call
208  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
209  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
210    my $SavedCGI;               # CGI object passed to ETracing
211    umask 2;                    # Fix the damn umask so everything is group-writable.
212    
213  =head2 Public Methods  =head2 Tracing Methods
214    
215    =head3 Setups
216    
217        my $count = Tracer::Setups();
218    
219    Return the number of times L</TSetup> has been called.
220    
221    This method allows for the creation of conditional tracing setups where, for example, we
222    may want to set up tracing if nobody else has done it before us.
223    
224    =cut
225    
226    sub Setups {
227        return $SetupCount;
228    }
229    
230  =head3 TSetup  =head3 TSetup
231    
232  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
233    
234  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
235  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 346  Line 279 
279          }          }
280      }      }
281      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
282      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
283      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
284        # the standard output (tee mode).
285      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
286          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
287              $TeeFlag = 1;              $TeeFlag = 1;
288              $target = substr($target, 1);              $target = substr($target, 1);
289          }          }
290          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
291                # We need to initialize the file (which clears it).
292              open TRACEFILE, $target;              open TRACEFILE, $target;
293              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
294              close TRACEFILE;              close TRACEFILE;
295                # Set to append mode now that the file has been cleared.
296              $Destination = ">$target";              $Destination = ">$target";
297          } else {          } else {
298              $Destination = $target;              $Destination = $target;
# Line 368  Line 304 
304      $SetupCount++;      $SetupCount++;
305  }  }
306    
307  =head3 StandardSetup  =head3 SetLevel
308    
309  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
310    
311  This method performs standard command-line parsing and tracing setup. The return  Modify the trace level. A higher trace level will cause more messages to appear.
 values are a hash of the command-line options and a list of the positional  
 parameters. Tracing is automatically set up and the command-line options are  
 validated.  
312    
313  This is a complex method that does a lot of grunt work. The parameters can  =over 4
 be more easily understood, however, once they are examined individually.  
314    
315  The I<categories> parameter is the most obtuse. It is a reference to a list of  =item newLevel
 special-purpose tracing categories. Most tracing categories are PERL package  
 names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,  
 B<ERDB>, and B<SproutLoad> packages, you would specify the categories  
316    
317      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
318    
319  This would cause trace messages in the specified three packages to appear in  =back
 the output. There are two special tracing categories that are automatically  
 handled by this method. In other words, if you used L</TSetup> you would need  
 to include these categories manually, but if you use this method they are turned  
 on automatically.  
320    
321  =over 4  =cut
322    
323  =item SQL  sub SetLevel {
324        $TraceLevel = $_[0];
325    }
326    
327  Traces SQL commands and activity.  =head3 ParseDate
328    
329  =item Tracer      my $time = Tracer::ParseDate($dateString);
330    
331  Traces error messages and call stacks.  Convert a date into a PERL time number. This method expects a date-like string
332    and parses it into a number. The string must be vaguely date-like or it will
333    return an undefined value. Our requirement is that a month and day be
334    present and that three pieces of the date string (time of day, month and day,
335    year) be separated by likely delimiters, such as spaces, commas, and such-like.
336    
337  =back  If a time of day is present, it must be in military time with two digits for
338    everything but the hour.
339    
340  C<SQL> is only turned on if the C<-sql> option is specified in the command line.  The year must be exactly four digits.
 The trace level is specified using the C<-trace> command-line option. For example,  
 the following command line for C<TransactFeatures> turns on SQL tracing and runs  
 all tracing at level 3.  
341    
342      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  Additional stuff can be in the string. We presume it's time zones or weekdays or something
343    equally innocuous. This means, however, that a sufficiently long sentence with date-like
344    parts in it may be interpreted as a date. Hopefully this will not be a problem.
345    
346  Standard tracing is output to the standard output and echoed to the file  It should be guaranteed that this method will parse the output of the L</Now> function.
 C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the  
 process ID. You can also specify the C<user> parameter to put a user ID  
 instead of a process ID in the trace file name. So, for example  
347    
348  The default trace level is 2. To get all messages, specify a trace level of 4.  The parameters are as follows.
 For a genome-by-genome update, use 3.  
349    
350      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  =over 4
351    
352  would send the trace output to C<traceBruce.log> in the temporary directory.  =item dateString
353    
354  The I<options> parameter is a reference to a hash containing the command-line  The date string to convert.
 options, their default values, and an explanation of what they mean. Command-line  
 options may be in the form of switches or keywords. In the case of a switch, the  
 option value is 1 if it is specified and 0 if it is not specified. In the case  
 of a keyword, the value is separated from the option name by an equal sign. You  
 can see this last in the command-line example above.  
355    
356  You can specify a different default trace level by setting C<$options->{trace}>  =item RETURN
 prior to calling this method.  
357    
358  An example at this point would help. Consider, for example, the command-line utility  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
359  C<TransactFeatures>. It accepts a list of positional parameters plus the options  the date string is invalid. A valid date string must contain a month and day.
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
360    
361      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  =back
                         { safe => [0, "use database transactions"],  
                           noAlias => [0, "do not expect aliases in CHANGE transactions"],  
                           start => [' ', "start with this genome"],  
                           tblFiles => [0, "output TBL files containing the corrected IDs"] },  
                         "command transactionDirectory IDfile",  
                       @ARGV);  
362    
363    =cut
364    
365  The call to C<ParseCommand> specifies the default values for the options and  # Universal month conversion table.
366  stores the actual options in a hash that is returned as C<$options>. The  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
367  positional parameters are returned in C<@parameters>.                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
368                                Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
369                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
370                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
371                                Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
372                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
373                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
374                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
375                                Oct =>  9, October  =>   9, '10' =>  9,
376                                Nov => 10, November =>  10, '11' => 10,
377                                Dec => 11, December =>  11, '12' => 11
378                            };
379    
380  The following is a sample command line for C<TransactFeatures>.  sub ParseDate {
381        # Get the parameters.
382        my ($dateString) = @_;
383        # Declare the return variable.
384        my $retVal;
385        # Find the month and day of month. There are two ways that can happen. We check for the
386        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
387        # won't be fooled into thinking the month is Sunday.
388        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
389            my ($mon, $mday) = (MONTHS->{$1}, $2);
390            # Insist that the month and day are valid.
391            if (defined($mon) && $2 >= 1 && $2 <= 31) {
392                # Find the time.
393                my ($hour, $min, $sec) = (0, 0, 0);
394                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
395                    ($hour, $min, $sec) = ($1, $2, $3);
396                }
397                # Find the year.
398                my $year;
399                if ($dateString =~ /\b(\d{4})\b/) {
400                    $year = $1;
401                } else {
402                    # Get the default year, which is this one. Note we must convert it to
403                    # the four-digit value expected by "timelocal".
404                    (undef, undef, undef, undef, undef, $year) = localtime();
405                    $year += 1900;
406                }
407                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
408            }
409        }
410        # Return the result.
411        return $retVal;
412    }
413    
414      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  =head3 LogErrors
415    
416  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional      Tracer::LogErrors($fileName);
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
417    
418      { trace => 2, sql => 0, safe => 0,  Route the standard error output to a log file.
       noAlias => 1, start => ' ', tblFiles => 0 }  
419    
420  Use of C<StandardSetup> in this way provides a simple way of performing  =over 4
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
421    
422  If the C<background> option is specified on the command line, then the  =item fileName
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
423    
424      -user=Bruce -background  Name of the file to receive the error output.
425    
426  then the trace output would go to C<traceBruce.log>, the standard output to  =back
 C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to  
 simplify starting a command in the background.  
427    
428  The user name is also used as the tracing key for L</Emergency Tracing>.  =cut
 Specifying a value of C<E> for the trace level causes emergency tracing to  
 be used instead of custom tracing. If the user name is not specified,  
 the tracing key is taken from the C<Tracing> environment variable. If there  
 is no value for that variable, the tracing key will be computed from the PID.  
429    
430  Finally, if the special option C<-h> is specified, the option names will  sub LogErrors {
431  be traced at level 0 and the program will exit without processing.      # Get the file name.
432  This provides a limited help capability. For example, if the user enters      my ($fileName) = @_;
433        # Open the file as the standard error output.
434        open STDERR, '>', $fileName;
435    }
436    
437      TransactFeatures -h  =head3 Trace
438    
439  he would see the following output.      Trace($message);
440    
441      TransactFeatures [options] command transactionDirectory IDfile  Write a trace message to the target location specified in L</TSetup>. If there has not been
442          -trace    tracing level (default E)  any prior call to B<TSetup>.
         -sql      trace SQL commands  
         -safe     use database transactions  
         -noAlias  do not expect aliases in CHANGE transactions  
         -start    start with this genome  
         -tblFiles output TBL files containing the corrected IDs  
443    
444  The caller has the option of modifying the tracing scheme by placing a value  =over 4
 for C<trace> in the incoming options hash. The default value can be overridden,  
 or the tracing to the standard output can be turned off by suffixing a minus  
 sign to the trace level. So, for example,  
445    
446      { trace => [0, "tracing level (default 0)"],  =item message
        ...  
447    
448  would set the default trace level to 0 instead of E, while  Message to write.
449    
450      { trace => ["2-", "tracing level (default 2)"],  =back
        ...  
451    
452  would set the default to 2, but trace only to the log file, not to the  =cut
 standard output.  
453    
454  The parameters to this method are as follows.  sub Trace {
455        # Get the parameters.
456        my ($message) = @_;
457        # Strip off any line terminators at the end of the message. We will add
458        # new-line stuff ourselves.
459        my $stripped = Strip($message);
460        # Compute the caller information.
461        my ($callPackage, $callFile, $callLine) = caller();
462        my $callFileTitle = basename($callFile);
463        # Check the caller.
464        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
465        # Get the timestamp.
466        my $timeStamp = Now();
467        # Build the prefix.
468        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
469        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
470        # Format the message.
471        my $formatted = "$prefix $stripped";
472        # Process according to the destination.
473        if ($Destination eq "TEXT") {
474            # Write the message to the standard output.
475            print "$formatted\n";
476        } elsif ($Destination eq "ERROR") {
477            # Write the message to the error output. Here, we want our prefix fields.
478            print STDERR "$formatted\n";
479        } elsif ($Destination eq "WARN") {
480            # Emit the message to the standard error output. It is presumed that the
481            # error logger will add its own prefix fields, the notable exception being
482            # the caller info.
483            print STDERR "$callerInfo$stripped\n";
484        } elsif ($Destination eq "QUEUE") {
485            # Push the message into the queue.
486            push @Queue, "$formatted";
487        } elsif ($Destination eq "HTML") {
488            # Convert the message to HTML and write it to the standard output.
489            my $escapedMessage = CGI::escapeHTML($stripped);
490            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
491        } elsif ($Destination =~ m/^>>/) {
492            # Write the trace message to an output file.
493            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
494            print TRACING "$formatted\n";
495            close TRACING;
496            # If the Tee flag is on, echo it to the standard output.
497            if ($TeeFlag) {
498                print "$formatted\n";
499            }
500        }
501    }
502    
503  =over 4  =head3 T
504    
505  =item categories      my $switch = T($category, $traceLevel);
506    
507  Reference to a list of tracing category names. These should be names of      or
 packages whose internal workings will need to be debugged to get the  
 command working.  
508    
509  =item options      my $switch = T($traceLevel);
510    
511  Reference to a hash containing the legal options for the current command mapped  Return TRUE if the trace level is at or above a specified value and the specified category
512  to their default values and descriptions. The user can override the defaults  is active, else FALSE. If no category is specified, the caller's package name is used.
 by specifying the options as command-line switches prefixed by a hyphen.  
 Tracing-related options may be added to this hash. If the C<-h> option is  
 specified on the command line, the option descriptions will be used to  
 explain the options. To turn off tracing to the standard output, add a  
 minus sign to the value for C<trace> (see above).  
513    
514  =item parmHelp  =over 4
515    
516  A string that vaguely describes the positional parameters. This is used  =item category
 if the user specifies the C<-h> option.  
517    
518  =item argv  Category to which the message belongs. If not specified, the caller's package name is
519    used.
520    
521  List of command line parameters, including the option switches, which must  =item traceLevel
522  precede the positional parameters and be prefixed by a hyphen.  
523    Relevant tracing level.
524    
525  =item RETURN  =item RETURN
526    
527  Returns a list. The first element of the list is the reference to a hash that  TRUE if a message at the specified trace level would appear in the trace, else FALSE.
 maps the command-line option switches to their values. These will either be the  
 default values or overrides specified on the command line. The remaining  
 elements of the list are the position parameters, in order.  
528    
529  =back  =back
530    
531  =cut  =cut
532    
533  sub StandardSetup {  sub T {
534        # Declare the return variable.
535        my $retVal = 0;
536        # Only proceed if tracing is turned on.
537        if ($Destination ne "NONE") {
538      # Get the parameters.      # Get the parameters.
539      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
540      # Get the default tracing key.          if (!defined $traceLevel) {
541      my $tkey = EmergencyKey();              # Here we have no category, so we need to get the calling package.
542      # Add the tracing options.              # The calling package is normally the first parameter. If it is
543      if (! exists $options->{trace}) {              # omitted, the first parameter will be the tracelevel. So, the
544          $options->{trace} = ['E', "tracing level (E for emergency tracing)"];              # first thing we do is shift the so-called category into the
545      }              # $traceLevel variable where it belongs.
546      $options->{sql} = [0, "turn on SQL tracing"];              $traceLevel = $category;
547      $options->{h} = [0, "display command-line options"];              my ($package, $fileName, $line) = caller;
548      $options->{user} = [$tkey, "tracing key"];              # If there is no calling package, we default to "main".
549      $options->{background} = [0, "spool standard and error output"];              if (!$package) {
550      # Create a parsing hash from the options hash. The parsing hash                  $category = "main";
     # contains the default values rather than the default value  
     # and the description. While we're at it, we'll memorize the  
     # length of the longest option name.  
     my $longestName = 0;  
     my %parseOptions = ();  
     for my $key (keys %{$options}) {  
         if (length $key > $longestName) {  
             $longestName = length $key;  
         }  
         $parseOptions{$key} = $options->{$key}->[0];  
     }  
     # Parse the command line.  
     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);  
     # Get the logfile suffix.  
     my $suffix = $retOptions->{user};  
     # Check for background mode.  
     if ($retOptions->{background}) {  
         my $outFileName = "$FIG_Config::temp/out$suffix.log";  
         my $errFileName = "$FIG_Config::temp/err$suffix.log";  
         open STDOUT, ">$outFileName";  
         open STDERR, ">$errFileName";  
     }  
     # Now we want to set up tracing. First, we need to know if the user  
     # wants emergency tracing.  
     if ($retOptions->{trace} eq 'E') {  
         ETracing($retOptions->{user});  
     } else {  
         # Here the tracing is controlled from the command line.  
         my @cats = @{$categories};  
         if ($retOptions->{sql}) {  
             push @cats, "SQL";  
         }  
         # Add the default categories.  
         push @cats, "Tracer";  
         # Next, we create the category string by joining the categories.  
         my $cats = join(" ", @cats);  
         # Check to determine whether or not the caller wants to turn off tracing  
         # to the standard output.  
         my $traceLevel = $retOptions->{trace};  
         my $textOKFlag = 1;  
         if ($traceLevel =~ /^(.)-/) {  
             $traceLevel = $1;  
             $textOKFlag = 0;  
         }  
         # Now we set up the trace mode.  
         my $traceMode;  
         # Verify that we can open a file in the FIG temporary directory.  
         my $traceFileName = "$FIG_Config::temp/trace$suffix.log";  
         if (open TESTTRACE, ">$traceFileName") {  
             # Here we can trace to a file.  
             $traceMode = ">$traceFileName";  
             if ($textOKFlag) {  
                 # Echo to standard output if the text-OK flag is set.  
                 $traceMode = "+$traceMode";  
             }  
             # Close the test file.  
             close TESTTRACE;  
         } else {  
             # Here we can't trace to a file. We trace to the standard output if it's  
             # okay, and the error log otherwise.  
             if ($textOKFlag) {  
                 $traceMode = "TEXT";  
551              } else {              } else {
552                  $traceMode = "WARN";                  my @cats = split /::/, $package;
553              }                  $category = $cats[$#cats];
         }  
         # Now set up the tracing.  
         TSetup("$traceLevel $cats", $traceMode);  
554      }      }
     # Check for the "h" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($retOptions->{h}) {  
         $0 =~ m#[/\\](\w+)(\.pl)?$#i;  
         print "$1 [options] $parmHelp\n";  
         for my $key (sort keys %{$options}) {  
             my $name = Pad($key, $longestName, 0, ' ');  
             my $desc = $options->{$key}->[1];  
             if ($options->{$key}->[0]) {  
                 $desc .= " (default " . $options->{$key}->[0] . ")";  
555              }              }
556              print "  $name $desc\n";          # Save the category name and level.
557            $LastCategory = $category;
558            $LastLevel = $traceLevel;
559            # Convert it to lower case before we hash it.
560            $category = lc $category;
561            # Validate the trace level.
562            if (ref $traceLevel) {
563                Confess("Bad trace level.");
564            } elsif (ref $TraceLevel) {
565                Confess("Bad trace config.");
566          }          }
567          exit(0);          # Make the check. Note that level 0 shows even if the category is turned off.
568            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
569      }      }
570      # Return the parsed parameters.      # Return the computed result.
571      return ($retOptions, @retParameters);      return $retVal;
572  }  }
573    
574  =head3 Setups  =head3 QTrace
   
 C<< my $count = Tracer::Setups(); >>  
   
 Return the number of times L</TSetup> has been called.  
   
 This method allows for the creation of conditional tracing setups where, for example, we  
 may want to set up tracing if nobody else has done it before us.  
   
 =cut  
575    
576  sub Setups {      my $data = QTrace($format);
     return $SetupCount;  
 }  
577    
578  =head3 Open  Return the queued trace data in the specified format.
579    
580  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  =over 4
581    
582  Open a file.  =item format
583    
584  The I<$fileSpec> is essentially the second argument of the PERL C<open>  C<html> to format the data as an HTML list, C<text> to format it as straight text.
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
585    
586      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =back
587    
588  would open for output appended to the specified file, and  =cut
589    
590      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  sub QTrace {
591        # Get the parameter.
592        my ($format) = @_;
593        # Create the return variable.
594        my $retVal = "";
595        # Only proceed if there is an actual queue.
596        if (@Queue) {
597            # Process according to the format.
598            if ($format =~ m/^HTML$/i) {
599                # Convert the queue into an HTML list.
600                $retVal = "<ul>\n";
601                for my $line (@Queue) {
602                    my $escapedLine = CGI::escapeHTML($line);
603                    $retVal .= "<li>$escapedLine</li>\n";
604                }
605                $retVal .= "</ul>\n";
606            } elsif ($format =~ m/^TEXT$/i) {
607                # Convert the queue into a list of text lines.
608                $retVal = join("\n", @Queue) . "\n";
609            }
610            # Clear the queue.
611            @Queue = ();
612        }
613        # Return the formatted list.
614        return $retVal;
615    }
616    
617  would open a pipe that sorts the records written and removes duplicates. Note  =head3 Confess
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
618    
619      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");      Confess($message);
620    
621  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  Trace the call stack and abort the program with the specified message. When used with
622  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
623  failed open will throw an exception and the third parameter will be used to construct  So, for example
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
624    
625      Could not open "/usr/spool/news/twitlog"      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
626    
627  Note that the mode characters are automatically cleaned from the file name.  Will abort the program with a stack trace if the value of C<$recNum> is negative.
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
628    
629      Could not open "/usr/spool/news/twitlog": file not found.  =over 4
630    
631  In some versions of PERL the only error message we get is a number, which  =item message
 corresponds to the C++ C<errno> value.  
632    
633      Could not open "/usr/spool/news/twitlog": 6.  Message to include in the trace.
634    
635  =over 4  =back
636    
637  =item fileHandle  =cut
638    
639  File handle. If this parameter is C<undef>, a file handle will be generated  sub Confess {
640  and returned as the value of this method.      # Get the parameters.
641        my ($message) = @_;
642        # Set up the category and level.
643        $LastCategory = "(confess)";
644        $LastLevel = 0;
645        if (! defined($FIG_Config::no_tool_hdr)) {
646            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
647            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
648            # Only proceed if the tool header file is actually present.
649            if (-f $toolHeaderFile) {
650                my $fh;
651                if (open $fh, "<$toolHeaderFile") {
652                    my @lines = <$fh>;
653                    Trace("Tool header has " . scalar(@lines) . " lines.");
654                }
655            }
656        }
657        # Trace the call stack.
658        Cluck($message);
659        # Abort the program.
660        croak(">>> $message");
661    }
662    
663  =item fileSpec  =head3 Warn
664    
665  File name and mode, as per the PERL C<open> function.      Warn($message);
666    
667  =item message (optional)  This method traces an important message. If an RSS feed is configured
668    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
669    then the message will be echoed to the feed. In general, a tracing
670    destination of C<WARN> indicates that the caller is running as a web
671    service in a production environment; however, this is not a requirement.
672    
673    The L</Cluck> method calls this one for its final message. Since
674    L</Confess> calls L</Cluck>, this means that any error which is caught
675    and confessed will put something in the feed. This insures that someone
676    will be alerted relatively quickly when a failure occurs.
677    
678  Error message to use if the open fails. If omitted, a standard error message  =over 4
 will be generated. In either case, the error information from the file system  
 is appended to the message. To specify a conditional open that does not throw  
 an error if it fails, use C<0>.  
679    
680  =item RETURN  =item message
681    
682  Returns the name of the file handle assigned to the file, or C<undef> if the  Message to be traced.
 open failed.  
683    
684  =back  =back
685    
686  =cut  =cut
687    
688  sub Open {  sub Warn {
689      # Get the parameters.      # Get the parameters.
690      my ($fileHandle, $fileSpec, $message) = @_;      my ($message) = @_;
691      # Attempt to open the file.      # Trace the message.
692      my $rv = open $fileHandle, $fileSpec;      Trace($message);
693      # If the open failed, generate an error message.      # Check for debug mode.
694      if (! $rv) {      my $debugMode = (exists $Categories{feed} && $TraceLevel > 0);
695          # Save the system error message.      # An error here would be disastrous. Note, however, that we aren't too worried
696          my $sysMessage = $!;      # about losing events. The error log is always available for the occasions where
697          # See if we need a default message.      # we mess up. Note that if debug mode is specified, we do this stuff even in a
698          if (!$message) {      # test environment.
699              # Clean any obvious mode characters and leading spaces from the      eval {
700              # filename.          # Do we need to put this in the RSS feed?
701              my ($fileName) = FindNamePart($fileSpec);          if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $debugMode)) {
702              $message = "Could not open \"$fileName\"";              # Yes. We now need to compute the date, the link, and the title.
703                # First, the date, in a very specific format.
704                my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
705                    (tz_local_offset() / 30);
706                Trace("Generating RSS feed. Date = $date.") if $debugMode;
707                # Environment data goes in here. We start with the date.
708                my $environment = "$date.  ";
709                # If we need to recap the message (because it's too long to be a title), we'll
710                # put it in here.
711                my $recap;
712                # Copy the message and remove excess space.
713                my $title = $message;
714                $title =~ s/\s+/ /gs;
715                # If it's too long, we have to split it up.
716                if (length $title > 60) {
717                    # Put the full message in the environment string.
718                    $recap = $title;
719                    # Excerpt it as the title.
720                    $title = substr($title, 0, 50) . "...";
721                }
722                # If we have a CGI object, then this is a web error. Otherwise, it's
723                # command-line.
724                if (defined $SavedCGI) {
725                    # We're in a web service. The environment is the user's IP, and the link
726                    # is the URL that got us here.
727                    my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
728                    $environment .= "Event Reported at IP address $key.";
729                    my $url = $SavedCGI->url(-full => 1, -query => 1);
730                    # We need the user agent string and (if available) the referrer.
731                    # The referrer will be the link.
732                    $environment .= "User Agent $ENV{HTTP_USER_AGENT}";
733                    if ($ENV{HTTP_REFERER}) {
734                        my $link = $ENV{HTTP_REFERER};
735                        $environment .= " referred from <a href=\"$link\">$link</a>.";
736                    } else {
737                        $environment .= " referrer unknown.";
738                    }
739                    # Close off the sentence with the original link.
740                    $environment .= " URL of error is <a href=\"$url\">$url</a>.";
741                } else {
742                    # No CGI object, so we're a command-line tool. Use the tracing
743                    # key and the PID as the user identifier, and add the command.
744                    my $key = EmergencyKey();
745                    $environment .= "Event Reported by $key Process $$. Command $ENV{_}.";
746                }
747                # Build a GUID. We use the current time, the title, and the process ID,
748                # then digest the result.
749                my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
750                # Finally, the description. This is a stack trace plus various environmental stuff.
751                my $stackTrace = "";
752                my @trace = LongMess();
753                # Only proceed if we got something back.
754                if (scalar(@trace) > 0) {
755                    $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
756                    $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
757                }
758                # We got the stack trace. Now it's time to put it all together.
759                # We have a goofy thing here in that we need to HTML-escape some sections of the description
760                # twice. They will be escaped once here, and then once when written by XML::Simple. They are
761                # unescaped once when processed by the RSS reader, and stuff in the description is treated as
762                # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
763                # our <br>s and <pre>s are used to format the description.
764                $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
765                my $description = "$recap$environment  $stackTrace";
766                Trace("Unescaped description is:\n$description") if $debugMode;
767                # Okay, we have all the pieces. Create a hash of the new event.
768                my $newItem = { title => $title,
769                                description => $description,
770                                category => $LastCategory,
771                                pubDate => $date,
772                                guid => $guid,
773                               };
774                # We need XML capability for this.
775                require XML::Simple;
776                # The RSS document goes in here.
777                my $rss;
778                # Get the name of the RSS file. It's in the FIG temporary directory.
779                my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
780                # Does it exist?
781                if (-s $fileName) {
782                    # Slurp it in.
783                    $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
784                } else {
785                    my $size = -s $fileName;
786                    # Create an empty channel.
787                    $rss = {
788                        channel => {
789                            title => 'NMPDR Warning Feed',
790                            link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
791                            description => "Important messages regarding the status of the NMPDR.",
792                            generator => "NMPDR Trace Facility",
793                            docs => "http://blogs.law.harvard.edu/tech/rss",
794                            item => []
795                        },
796                    };
797          }          }
798          # Terminate with an error using the supplied message and the              # Get the channel object.
799          # error message from the file system.              my $channel = $rss->{channel};
800          Confess("$message: $!");              # Update the last-build date.
801                $channel->{lastBuildDate} = $date;
802                # Get the item array.
803                my $items = $channel->{item};
804                # Insure it has only 100 entries.
805                while (scalar @{$items} > 100) {
806                    pop @{$items};
807                }
808                # Add our new item at the front.
809                unshift @{$items}, $newItem;
810                # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
811                # the requirements for those.
812                my $xml = XML::Simple::XMLout($rss, NoAttr => 1, RootName => undef, XmlDecl => '');
813                # Here we put in the root and declaration. The problem is that the root has to have the version attribute
814                # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
815                $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
816                # We don't use Open here because we can't afford an error.
817                if (open XMLOUT, ">$fileName") {
818                    print XMLOUT $xml;
819                    close XMLOUT;
820                }
821            }
822        };
823        # We only worry about problems in debug mode. The loss of an error message is an annoyance, not a
824        # crisis.
825        if ($@ && $debugMode) {
826            my $error = $@;
827            Trace("Feed Error: $error");
828      }      }
     # Return the file handle.  
     return $fileHandle;  
829  }  }
830    
831  =head3 FindNamePart  =head3 Assert
   
 C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>  
832    
833  Extract the portion of a file specification that contains the file name.      Assert($condition1, $condition2, ... $conditionN);
834    
835  A file specification is the string passed to an C<open> call. It specifies the file  Return TRUE if all the conditions are true. This method can be used in conjunction with
836  mode and name. In a truly complex situation, it can specify a pipe sequence. This  the OR operator and the L</Confess> method as a debugging assert.
837  method assumes that the file name is whatever follows the first angle bracket  So, for example
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
838    
839      >>/usr/fig/myfile.txt      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
840    
841  If the method cannot find a file name using its normal methods, it will return the  Will abort the program with a stack trace if the value of C<$recNum> is negative.
 whole incoming string.  
842    
843  =over 4  =cut
844    sub Assert {
845        my $retVal = 1;
846        LOOP: for my $condition (@_) {
847            if (! $condition) {
848                $retVal = 0;
849                last LOOP;
850            }
851        }
852        return $retVal;
853    }
854    
855  =item fileSpec  =head3 Cluck
856    
857  File specification string from which the file name is to be extracted.      Cluck($message);
858    
859  =item RETURN  Trace the call stack. Note that for best results, you should qualify the call with a
860    trace condition. For example,
861    
862  Returns a three-element list. The first element contains the file name portion of      Cluck("Starting record parse.") if T(3);
863  the specified string, or the whole string if a file name cannot be found via normal  
864  methods. The second element contains the start position of the file name portion and  will only trace the stack if the trace level for the package is 3 or more.
865  the third element contains the length.  
866    =over 4
867    
868    =item message
869    
870    Message to include in the trace.
871    
872  =back  =back
873    
874  =cut  =cut
875  #: Return Type $;  
876  sub FindNamePart {  sub Cluck {
877      # Get the parameters.      # Get the parameters.
878      my ($fileSpec) = @_;      my ($message) = @_;
879      # Default to the whole input string.      # Trace what's happening.
880      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);      Trace("Stack trace for event: $message");
881      # Parse out the file name if we can.      # Get the stack trace.
882      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {      my @trace = LongMess();
883          $retVal = $2;      # Convert the trace to a series of messages.
884          $len = length $retVal;      for my $line (@trace) {
885          $pos = (length $fileSpec) - (length $3) - $len;          # Replace the tab at the beginning with spaces.
886            $line =~ s/^\t/    /;
887            # Trace the line.
888            Trace($line);
889      }      }
890      # Return the result.      # Issue a warning. This displays the event message and inserts it into the RSS error feed.
891      return ($retVal, $pos, $len);      Warn($message);
892  }  }
893    
894  =head3 OpenDir  =head3 LongMess
895    
896  C<< my @files = OpenDir($dirName, $filtered, $flag); >>      my @lines = Tracer::LongMess();
897    
898  Open a directory and return all the file names. This function essentially performs  Return a stack trace with all tracing methods removed. The return will be in the form of a list
899  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  of message strings.
 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  
 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be  
 filtered out of the return list. If the directory does not open and I<$flag> is not  
 set, an exception is thrown. So, for example,  
900    
901      my @files = OpenDir("/Volumes/fig/contigs", 1);  =cut
902    
903  is effectively the same as  sub LongMess {
904        # Declare the return variable.
905        my @retVal = ();
906        my $confession = longmess("");
907        for my $line (split /\s*\n/, $confession) {
908            unless ($line =~ /Tracer\.pm/) {
909                # Here we have a line worth keeping. Push it onto the result list.
910                push @retVal, $line;
911            }
912        }
913        # Return the result.
914        return @retVal;
915    }
916    
917      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  =head3 ScriptSetup (deprecated)
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
918    
919  Similarly, the following code      my ($cgi, $varHash) = ScriptSetup($noTrace);
920    
921      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  Perform standard tracing and debugging setup for scripts. The value returned is
922    the CGI object followed by a pre-built variable hash. At the end of the script,
923    the client should call L</ScriptFinish> to output the web page.
924    
925  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  This method calls L</ETracing> to configure tracing, which allows the tracing
926  automatically returns an empty list if the directory fails to open.  to be configured via the emergency tracing form on the debugging control panel.
927    Tracing will then be turned on automatically for all programs that use the L</ETracing>
928    method, which includes every program that uses this method or L</StandardSetup>.
929    
930  =over 4  =over 4
931    
932  =item dirName  =item noTrace (optional)
933    
934  Name of the directory to open.  If specified, tracing will be suppressed. This is useful if the script wants to set up
935    tracing manually.
936    
937  =item filtered  =item RETURN
938    
939  TRUE if files whose names begin with a period (C<.>) should be automatically removed  Returns a two-element list consisting of a CGI query object and a variable hash for
940  from the list, else FALSE.  the output page.
941    
942  =item flag  =back
943    
944  TRUE if a failure to open is okay, else FALSE  =cut
945    
946    sub ScriptSetup {
947        # Get the parameters.
948        my ($noTrace) = @_;
949        # Get the CGI query object.
950        my $cgi = CGI->new();
951        # Set up tracing if it's not suppressed.
952        ETracing($cgi) unless $noTrace;
953        # Create the variable hash.
954        my $varHash = { results => '' };
955        # Return the query object and variable hash.
956        return ($cgi, $varHash);
957    }
958    
959    =head3 ETracing
960    
961        ETracing($parameter);
962    
963    Set up emergency tracing. Emergency tracing is tracing that is turned
964    on automatically for any program that calls this method. The emergency
965    tracing parameters are stored in a a file identified by a tracing key.
966    If this method is called with a CGI object, then the tracing key is
967    taken from a cookie. If it is called with no parameters, then the tracing
968    key is taken from an environment variable. If it is called with a string,
969    the tracing key is that string.
970    
971    =over 4
972    
973    =item parameter
974    
975    A parameter from which the tracing key is computed. If it is a scalar,
976    that scalar is used as the tracing key. If it is a CGI object, the
977    tracing key is taken from the C<IP> cookie. If it is omitted, the
978    tracing key is taken from the C<TRACING> environment variable. If it
979    is a CGI object and emergency tracing is not on, the C<Trace> and
980    C<TF> parameters will be used to determine the type of tracing.
981    
982  =back  =back
983    
984  =cut  =cut
985  #: Return Type @;  
986  sub OpenDir {  sub ETracing {
987      # Get the parameters.      # Get the parameter.
988      my ($dirName, $filtered, $flag) = @_;      my ($parameter) = @_;
989      # Declare the return variable.      # Check for CGI mode.
990      my @retVal = ();      if (defined $parameter && ref $parameter eq 'CGI') {
991      # Open the directory.          $SavedCGI = $parameter;
     if (opendir(my $dirHandle, $dirName)) {  
         # The directory opened successfully. Get the appropriate list according to the  
         # strictures of the filter parameter.  
         if ($filtered) {  
             @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;  
992          } else {          } else {
993              @retVal = readdir $dirHandle;          $SavedCGI = undef;
994        }
995        # Default to no tracing except errors.
996        my ($tracing, $dest) = ("0", "WARN");
997        # Check for emergency tracing.
998        my $tkey = EmergencyKey($parameter);
999        my $emergencyFile = EmergencyFileName($tkey);
1000        if (-e $emergencyFile) {
1001            # We have the file. Read in the data.
1002            my @tracing = GetFile($emergencyFile);
1003            # Pull off the time limit.
1004            my $expire = shift @tracing;
1005            # Convert it to seconds.
1006            $expire *= 3600;
1007            # Check the file data.
1008            my $stat = stat($emergencyFile);
1009            my ($now) = gettimeofday;
1010            if ($now - $stat->mtime > $expire) {
1011                # Delete the expired file.
1012                unlink $emergencyFile;
1013            } else {
1014                # Emergency tracing is on. Pull off the destination and
1015                # the trace level;
1016                $dest = shift @tracing;
1017                my $level = shift @tracing;
1018                # Convert the destination to a real tracing destination.
1019                # temp directory.
1020                $dest = EmergencyTracingDest($tkey, $dest);
1021                # Insure Tracer is specified.
1022                my %moduleHash = map { $_ => 1 } @tracing;
1023                $moduleHash{Tracer} = 1;
1024                # Set the trace parameter.
1025                $tracing = join(" ", $level, sort keys %moduleHash);
1026            }
1027        } elsif (defined $SavedCGI) {
1028            # There's no emergency tracing, but we have a CGI object, so check
1029            # for tracing from the form parameters.
1030            if ($SavedCGI->param('Trace')) {
1031                # Here the user has requested tracing via a form.
1032                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1033                $tracing = $SavedCGI->param('Trace') . " Tracer";
1034            }
1035        }
1036        # Setup the tracing we've determined from all the stuff above.
1037        TSetup($tracing, $dest);
1038        # Check to see if we're a web script.
1039        if (defined $SavedCGI) {
1040            # Yes we are. Trace the form and environment data.
1041            TraceParms($SavedCGI);
1042            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1043            # emitted by the script in its raw form.
1044            if (T(Raw => 3)) {
1045                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1046          }          }
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
1047      }      }
     # Return the result.  
     return @retVal;  
1048  }  }
1049    
1050  =head3 SetLevel  =head3 EmergencyFileName
1051    
1052  C<< Tracer::SetLevel($newLevel); >>      my $fileName = Tracer::EmergencyFileName($tkey);
1053    
1054  Modify the trace level. A higher trace level will cause more messages to appear.  Return the emergency tracing file name. This is the file that specifies
1055    the tracing information.
1056    
1057  =over 4  =over 4
1058    
1059  =item newLevel  =item tkey
1060    
1061  Proposed new trace level.  Tracing key for the current program.
1062    
1063    =item RETURN
1064    
1065    Returns the name of the file to contain the emergency tracing information.
1066    
1067  =back  =back
1068    
1069  =cut  =cut
1070    
1071  sub SetLevel {  sub EmergencyFileName {
1072      $TraceLevel = $_[0];      # Get the parameters.
1073        my ($tkey) = @_;
1074        # Compute the emergency tracing file name.
1075        return "$FIG_Config::temp/Emergency$tkey.txt";
1076  }  }
1077    
1078  =head3 Now  =head3 EmergencyFileTarget
1079    
1080  C<< my $string = Tracer::Now(); >>      my $fileName = Tracer::EmergencyFileTarget($tkey);
1081    
1082  Return a displayable time stamp containing the local time.  Return the emergency tracing target file name. This is the file that receives
1083    the tracing output for file-based tracing.
1084    
1085    =over 4
1086    
1087    =item tkey
1088    
1089    Tracing key for the current program.
1090    
1091    =item RETURN
1092    
1093    Returns the name of the file to contain the trace output.
1094    
1095    =back
1096    
1097  =cut  =cut
1098    
1099  sub Now {  sub EmergencyFileTarget {
1100      my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);      # Get the parameters.
1101      my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .      my ($tkey) = @_;
1102                   _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);      # Compute the emergency tracing file name.
1103      return $retVal;      return "$FIG_Config::temp/trace$tkey.log";
1104    }
1105    
1106    =head3 EmergencyTracingDest
1107    
1108        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1109    
1110    This method converts an emergency tracing destination to a real
1111    tracing destination. The main difference is that if the
1112    destination is C<FILE> or C<APPEND>, we convert it to file
1113    output. If the destination is C<DUAL>, we convert it to file
1114    and standard output.
1115    
1116    =over 4
1117    
1118    =item tkey
1119    
1120    Tracing key for this environment.
1121    
1122    =item myDest
1123    
1124    Destination from the emergency tracing file.
1125    
1126    =item RETURN
1127    
1128    Returns a destination that can be passed into L</TSetup>.
1129    
1130    =back
1131    
1132    =cut
1133    
1134    sub EmergencyTracingDest {
1135        # Get the parameters.
1136        my ($tkey, $myDest) = @_;
1137        # Declare the return variable.
1138        my $retVal = $myDest;
1139        # Process according to the destination value.
1140        if ($myDest eq 'FILE') {
1141            $retVal = ">" . EmergencyFileTarget($tkey);
1142        } elsif ($myDest eq 'APPEND') {
1143            $retVal = ">>" . EmergencyFileTarget($tkey);
1144        } elsif ($myDest eq 'DUAL') {
1145            $retVal = "+>" . EmergencyFileTarget($tkey);
1146        } elsif ($myDest eq 'WARN') {
1147            $retVal = "WARN";
1148        }
1149        # Return the result.
1150        return $retVal;
1151    }
1152    
1153    =head3 Emergency
1154    
1155        Emergency($key, $hours, $dest, $level, @modules);
1156    
1157    Turn on emergency tracing. This method is normally invoked over the web from
1158    a debugging console, but it can also be called by the C<trace.pl> script.
1159    The caller specifies the duration of the emergency in hours, the desired tracing
1160    destination, the trace level, and a list of the trace modules to activate.
1161    For the length of the duration, when a program in an environment with the
1162    specified tracing key active invokes a Sprout CGI script, tracing will be
1163    turned on automatically. See L</TSetup> for more about tracing setup and
1164    L</ETracing> for more about emergency tracing.
1165    
1166    =over 4
1167    
1168    =item tkey
1169    
1170    The tracing key. This is used to identify the control file and the trace file.
1171    
1172    =item hours
1173    
1174    Number of hours to keep emergency tracing alive.
1175    
1176    =item dest
1177    
1178    Tracing destination. If no path information is specified for a file
1179    destination, it is put in the FIG temporary directory.
1180    
1181    =item level
1182    
1183    Tracing level. A higher level means more trace messages.
1184    
1185    =item modules
1186    
1187    A list of the tracing modules to activate.
1188    
1189    =back
1190    
1191    =cut
1192    
1193    sub Emergency {
1194        # Get the parameters.
1195        my ($tkey, $hours, $dest, $level, @modules) = @_;
1196        # Create the emergency file.
1197        my $specFile = EmergencyFileName($tkey);
1198        my $outHandle = Open(undef, ">$specFile");
1199        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1200    }
1201    
1202    =head3 EmergencyKey
1203    
1204        my $tkey = EmergencyKey($parameter);
1205    
1206    Return the Key to be used for emergency tracing. This could be an IP address,
1207     a session ID, or a user name, depending on the environment.
1208    
1209    =over 4
1210    
1211    =item parameter
1212    
1213    Parameter defining the method for finding the tracing key. If it is a scalar,
1214    then it is presumed to be the tracing key itself. If it is a CGI object, then
1215    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1216    taken from the C<TRACING> environment variable.
1217    
1218    =item RETURN
1219    
1220    Returns the key to be used for labels in emergency tracing.
1221    
1222    =back
1223    
1224    =cut
1225    
1226    sub EmergencyKey {
1227        # Get the parameters.
1228        my ($parameter) = @_;
1229        # Declare the return variable.
1230        my $retVal;
1231        # Determine the parameter type.
1232        if (! defined $parameter) {
1233            # Here we're supposed to check the environment. If that fails, we
1234            # get the effective login ID.
1235            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1236        } else {
1237            my $ptype = ref $parameter;
1238            if ($ptype eq 'CGI') {
1239                # Here we were invoked from a web page. Look for a cookie.
1240                $retVal = $parameter->cookie('IP');
1241            } elsif (! $ptype) {
1242                # Here the key was passed in.
1243                $retVal = $parameter;
1244            }
1245        }
1246        # If no luck finding a key, use the PID.
1247        if (! defined $retVal) {
1248            $retVal = $$;
1249        }
1250        # Return the result.
1251        return $retVal;
1252    }
1253    
1254    
1255    =head3 TraceParms
1256    
1257        Tracer::TraceParms($cgi);
1258    
1259    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1260    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1261    
1262    =over 4
1263    
1264    =item cgi
1265    
1266    CGI query object containing the parameters to trace.
1267    
1268    =back
1269    
1270    =cut
1271    
1272    sub TraceParms {
1273        # Get the parameters.
1274        my ($cgi) = @_;
1275        if (T(CGI => 2)) {
1276            # Here we trace the GET-style URL for the script.
1277            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1278        }
1279        if (T(CGI => 3)) {
1280            # Here we want to trace the parameter data.
1281            my @names = $cgi->param;
1282            for my $parmName (sort @names) {
1283                # Note we skip the Trace parameters, which are for our use only.
1284                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1285                    my @values = $cgi->param($parmName);
1286                    Trace("[CGI] $parmName = " . join(", ", @values));
1287                }
1288            }
1289            # Display the request method.
1290            my $method = $cgi->request_method();
1291            Trace("Method: $method");
1292        }
1293        if (T(CGI => 4)) {
1294            # Here we want the environment data too.
1295            for my $envName (sort keys %ENV) {
1296                Trace("[ENV] $envName = $ENV{$envName}");
1297            }
1298        }
1299    }
1300    
1301    =head3 TraceImages
1302    
1303        Tracer::TraceImages($htmlString);
1304    
1305    Trace information about all of an html document's images. The tracing
1306    will be for type "IMG" at level 3. The image's source string
1307    will be displayed. This is generally either the URL of the image or
1308    raw data for the image itself. If the source is too long, only the first 300
1309    characters will be shown at trace level 3. The entire source will be shown,
1310    however, at trace level 4. This method is not very smart, and might catch
1311    Javascript code, but it is still useful when debugging the arcane
1312    behavior of images in multiple browser environments.
1313    
1314    =over 4
1315    
1316    =item htmlString
1317    
1318    HTML text for an outgoing web page.
1319    
1320    =back
1321    
1322    =cut
1323    
1324    sub TraceImages {
1325        # Only proceed if we're at the proper trace level.
1326        if (T(IMG => 3)) {
1327            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1328            # into a variable called "$htmlString". This is because we expect html strings to be
1329            # long, and don't want to copy them any more than we have to.
1330            Trace(length($_[0]) . " characters in web page.");
1331            # Loop through the HTML, culling image tags.
1332            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1333                # Extract the source string and determine whether or not it's too long.
1334                my $srcString = $1;
1335                my $pos = pos($_[0]) - length($srcString);
1336                my $excess = length($srcString) - 300;
1337                # We'll put the display string in here.
1338                my $srcDisplay = $srcString;
1339                # If it's a data string, split it at the comma.
1340                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1341                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1342                # a long string, however, we only show the first 300 characters.
1343                if ($excess > 0 && ! T(IMG => 4)) {
1344                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1345                }
1346                # Output the trace message.
1347                Trace("Image tag at position $pos:\n$srcDisplay");
1348            }
1349        }
1350    }
1351    
1352    
1353    =head3 ScriptFinish (deprecated)
1354    
1355        ScriptFinish($webData, $varHash);
1356    
1357    Output a web page at the end of a script. Either the string to be output or the
1358    name of a template file can be specified. If the second parameter is omitted,
1359    it is assumed we have a string to be output; otherwise, it is assumed we have the
1360    name of a template file. The template should have the variable C<DebugData>
1361    specified in any form that invokes a standard script. If debugging mode is turned
1362    on, a form field will be put in that allows the user to enter tracing data.
1363    Trace messages will be placed immediately before the terminal C<BODY> tag in
1364    the output, formatted as a list.
1365    
1366    A typical standard script would loook like the following.
1367    
1368        BEGIN {
1369            # Print the HTML header.
1370            print "CONTENT-TYPE: text/html\n\n";
1371        }
1372        use Tracer;
1373        use CGI;
1374        use FIG;
1375        # ... more uses ...
1376    
1377        my ($cgi, $varHash) = ScriptSetup();
1378        eval {
1379            # ... get data from $cgi, put it in $varHash ...
1380        };
1381        if ($@) {
1382            Trace("Script Error: $@") if T(0);
1383        }
1384        ScriptFinish("Html/MyTemplate.html", $varHash);
1385    
1386    The idea here is that even if the script fails, you'll see trace messages and
1387    useful output.
1388    
1389    =over 4
1390    
1391    =item webData
1392    
1393    A string containing either the full web page to be written to the output or the
1394    name of a template file from which the page is to be constructed. If the name
1395    of a template file is specified, then the second parameter must be present;
1396    otherwise, it must be absent.
1397    
1398    =item varHash (optional)
1399    
1400    If specified, then a reference to a hash mapping variable names for a template
1401    to their values. The template file will be read into memory, and variable markers
1402    will be replaced by data in this hash reference.
1403    
1404    =back
1405    
1406    =cut
1407    
1408    sub ScriptFinish {
1409        # Get the parameters.
1410        my ($webData, $varHash) = @_;
1411        # Check for a template file situation.
1412        my $outputString;
1413        if (defined $varHash) {
1414            # Here we have a template file. We need to determine the template type.
1415            my $template;
1416            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1417                $template = "$FIG_Config::template_url/$webData";
1418            } else {
1419                $template = "<<$webData";
1420            }
1421            $outputString = PageBuilder::Build($template, $varHash, "Html");
1422        } else {
1423            # Here the user gave us a raw string.
1424            $outputString = $webData;
1425        }
1426        # Check for trace messages.
1427        if ($Destination ne "NONE" && $TraceLevel > 0) {
1428            # We have trace messages, so we want to put them at the end of the body. This
1429            # is either at the end of the whole string or at the beginning of the BODY
1430            # end-tag.
1431            my $pos = length $outputString;
1432            if ($outputString =~ m#</body>#gi) {
1433                $pos = (pos $outputString) - 7;
1434            }
1435            # If the trace messages were queued, we unroll them. Otherwise, we display the
1436            # destination.
1437            my $traceHtml;
1438            if ($Destination eq "QUEUE") {
1439                $traceHtml = QTrace('Html');
1440            } elsif ($Destination =~ /^>>(.+)$/) {
1441                # Here the tracing output it to a file. We code it as a hyperlink so the user
1442                # can copy the file name into the clipboard easily.
1443                my $actualDest = $1;
1444                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1445            } else {
1446                # Here we have one of the special destinations.
1447                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1448            }
1449            substr $outputString, $pos, 0, $traceHtml;
1450        }
1451        # Write the output string.
1452        print $outputString;
1453    }
1454    
1455    =head2 Command-Line Utility Methods
1456    
1457    =head3 SendSMS
1458    
1459        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1460    
1461    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1462    user name, password, and API ID for the relevant account in the hash reference variable
1463    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1464    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1465    is C<2561022>, then the FIG_Config file must contain
1466    
1467        $phone =  { user => 'BruceTheHumanPet',
1468                    password => 'silly',
1469                    api_id => '2561022' };
1470    
1471    The original purpose of this method was to insure Bruce would be notified immediately when the
1472    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1473    when you call this method.
1474    
1475    The message ID will be returned if successful, and C<undef> if an error occurs.
1476    
1477    =over 4
1478    
1479    =item phoneNumber
1480    
1481    Phone number to receive the message, in international format. A United States phone number
1482    would be prefixed by "1". A British phone number would be prefixed by "44".
1483    
1484    =item msg
1485    
1486    Message to send to the specified phone.
1487    
1488    =item RETURN
1489    
1490    Returns the message ID if successful, and C<undef> if the message could not be sent.
1491    
1492    =back
1493    
1494    =cut
1495    
1496    sub SendSMS {
1497        # Get the parameters.
1498        my ($phoneNumber, $msg) = @_;
1499        # Declare the return variable. If we do not change it, C<undef> will be returned.
1500        my $retVal;
1501        # Only proceed if we have phone support.
1502        if (! defined $FIG_Config::phone) {
1503            Trace("Phone support not present in FIG_Config.") if T(1);
1504        } else {
1505            # Get the phone data.
1506            my $parms = $FIG_Config::phone;
1507            # Get the Clickatell URL.
1508            my $url = "http://api.clickatell.com/http/";
1509            # Create the user agent.
1510            my $ua = LWP::UserAgent->new;
1511            # Request a Clickatell session.
1512            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1513                                         password => $parms->{password},
1514                                         api_id => $parms->{api_id},
1515                                         to => $phoneNumber,
1516                                         text => $msg});
1517            # Check for an error.
1518            if (! $resp->is_success) {
1519                Trace("Alert failed.") if T(1);
1520            } else {
1521                # Get the message ID.
1522                my $rstring = $resp->content;
1523                if ($rstring =~ /^ID:\s+(.*)$/) {
1524                    $retVal = $1;
1525                } else {
1526                    Trace("Phone attempt failed with $rstring") if T(1);
1527                }
1528            }
1529        }
1530        # Return the result.
1531        return $retVal;
1532    }
1533    
1534    =head3 StandardSetup
1535    
1536        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1537    
1538    This method performs standard command-line parsing and tracing setup. The return
1539    values are a hash of the command-line options and a list of the positional
1540    parameters. Tracing is automatically set up and the command-line options are
1541    validated.
1542    
1543    This is a complex method that does a lot of grunt work. The parameters can
1544    be more easily understood, however, once they are examined individually.
1545    
1546    The I<categories> parameter is the most obtuse. It is a reference to a list of
1547    special-purpose tracing categories. Most tracing categories are PERL package
1548    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1549    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1550    
1551        ["Sprout", "SproutLoad", "ERDB"]
1552    
1553    This would cause trace messages in the specified three packages to appear in
1554    the output. There are two special tracing categories that are automatically
1555    handled by this method. In other words, if you used L</TSetup> you would need
1556    to include these categories manually, but if you use this method they are turned
1557    on automatically.
1558    
1559    =over 4
1560    
1561    =item SQL
1562    
1563    Traces SQL commands and activity.
1564    
1565    =item Tracer
1566    
1567    Traces error messages and call stacks.
1568    
1569    =back
1570    
1571    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1572    The trace level is specified using the C<-trace> command-line option. For example,
1573    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1574    all tracing at level 3.
1575    
1576        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1577    
1578    Standard tracing is output to the standard output and echoed to the file
1579    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1580    process ID. You can also specify the C<user> parameter to put a user ID
1581    instead of a process ID in the trace file name. So, for example
1582    
1583    The default trace level is 2. To get all messages, specify a trace level of 4.
1584    For a genome-by-genome update, use 3.
1585    
1586        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1587    
1588    would send the trace output to C<traceBruce.log> in the temporary directory.
1589    
1590    The I<options> parameter is a reference to a hash containing the command-line
1591    options, their default values, and an explanation of what they mean. Command-line
1592    options may be in the form of switches or keywords. In the case of a switch, the
1593    option value is 1 if it is specified and 0 if it is not specified. In the case
1594    of a keyword, the value is separated from the option name by an equal sign. You
1595    can see this last in the command-line example above.
1596    
1597    You can specify a different default trace level by setting C<$options->{trace}>
1598    prior to calling this method.
1599    
1600    An example at this point would help. Consider, for example, the command-line utility
1601    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1602    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1603    the following code.
1604    
1605        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1606                            { safe => [0, "use database transactions"],
1607                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1608                              start => [' ', "start with this genome"],
1609                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1610                            "<command> <transactionDirectory> <IDfile>",
1611                          @ARGV);
1612    
1613    
1614    The call to C<ParseCommand> specifies the default values for the options and
1615    stores the actual options in a hash that is returned as C<$options>. The
1616    positional parameters are returned in C<@parameters>.
1617    
1618    The following is a sample command line for C<TransactFeatures>.
1619    
1620        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1621    
1622    Single and double hyphens are equivalent. So, you could also code the
1623    above command as
1624    
1625        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1626    
1627    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1628    parameters, and would find themselves in I<@parameters> after executing the
1629    above code fragment. The tracing would be set to level 2, and the categories
1630    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1631    and C<DocUtils> was included because it came in within the first parameter
1632    to this method. The I<$options> hash would be
1633    
1634        { trace => 2, sql => 0, safe => 0,
1635          noAlias => 1, start => ' ', tblFiles => 0 }
1636    
1637    Use of C<StandardSetup> in this way provides a simple way of performing
1638    standard tracing setup and command-line parsing. Note that the caller is
1639    not even aware of the command-line switches C<-trace> and C<-sql>, which
1640    are used by this method to control the tracing. If additional tracing features
1641    need to be added in the future, they can be processed by this method without
1642    upsetting the command-line utilities.
1643    
1644    If the C<background> option is specified on the command line, then the
1645    standard and error outputs will be directed to files in the temporary
1646    directory, using the same suffix as the trace file. So, if the command
1647    line specified
1648    
1649        -user=Bruce -background
1650    
1651    then the trace output would go to C<traceBruce.log>, the standard output to
1652    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1653    simplify starting a command in the background.
1654    
1655    The user name is also used as the tracing key for L</Emergency Tracing>.
1656    Specifying a value of C<E> for the trace level causes emergency tracing to
1657    be used instead of custom tracing. If the user name is not specified,
1658    the tracing key is taken from the C<Tracing> environment variable. If there
1659    is no value for that variable, the tracing key will be computed from the PID.
1660    
1661    Finally, if the special option C<-help> is specified, the option
1662    names will be traced at level 0 and the program will exit without processing.
1663    This provides a limited help capability. For example, if the user enters
1664    
1665        TransactFeatures -help
1666    
1667    he would see the following output.
1668    
1669        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1670            -trace    tracing level (default E)
1671            -sql      trace SQL commands
1672            -safe     use database transactions
1673            -noAlias  do not expect aliases in CHANGE transactions
1674            -start    start with this genome
1675            -tblFiles output TBL files containing the corrected IDs
1676    
1677    The caller has the option of modifying the tracing scheme by placing a value
1678    for C<trace> in the incoming options hash. The default value can be overridden,
1679    or the tracing to the standard output can be turned off by suffixing a minus
1680    sign to the trace level. So, for example,
1681    
1682        { trace => [0, "tracing level (default 0)"],
1683           ...
1684    
1685    would set the default trace level to 0 instead of E, while
1686    
1687        { trace => ["2-", "tracing level (default 2)"],
1688           ...
1689    
1690    would set the default to 2, but trace only to the log file, not to the
1691    standard output.
1692    
1693    The parameters to this method are as follows.
1694    
1695    =over 4
1696    
1697    =item categories
1698    
1699    Reference to a list of tracing category names. These should be names of
1700    packages whose internal workings will need to be debugged to get the
1701    command working.
1702    
1703    =item options
1704    
1705    Reference to a hash containing the legal options for the current command mapped
1706    to their default values and descriptions. The user can override the defaults
1707    by specifying the options as command-line switches prefixed by a hyphen.
1708    Tracing-related options may be added to this hash. If the C<-h> option is
1709    specified on the command line, the option descriptions will be used to
1710    explain the options. To turn off tracing to the standard output, add a
1711    minus sign to the value for C<trace> (see above).
1712    
1713    =item parmHelp
1714    
1715    A string that vaguely describes the positional parameters. This is used
1716    if the user specifies the C<-h> option.
1717    
1718    =item argv
1719    
1720    List of command line parameters, including the option switches, which must
1721    precede the positional parameters and be prefixed by a hyphen.
1722    
1723    =item RETURN
1724    
1725    Returns a list. The first element of the list is the reference to a hash that
1726    maps the command-line option switches to their values. These will either be the
1727    default values or overrides specified on the command line. The remaining
1728    elements of the list are the position parameters, in order.
1729    
1730    =back
1731    
1732    =cut
1733    
1734    sub StandardSetup {
1735        # Get the parameters.
1736        my ($categories, $options, $parmHelp, @argv) = @_;
1737        # Get the default tracing key.
1738        my $tkey = EmergencyKey();
1739        # Add the tracing options.
1740        if (! exists $options->{trace}) {
1741            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1742        }
1743        $options->{sql} = [0, "turn on SQL tracing"];
1744        $options->{help} = [0, "display command-line options"];
1745        $options->{user} = [$tkey, "tracing key"];
1746        $options->{background} = [0, "spool standard and error output"];
1747        # Create a parsing hash from the options hash. The parsing hash
1748        # contains the default values rather than the default value
1749        # and the description. While we're at it, we'll memorize the
1750        # length of the longest option name.
1751        my $longestName = 0;
1752        my %parseOptions = ();
1753        for my $key (keys %{$options}) {
1754            if (length $key > $longestName) {
1755                $longestName = length $key;
1756            }
1757            $parseOptions{$key} = $options->{$key}->[0];
1758        }
1759        # Parse the command line.
1760        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1761        # Get the logfile suffix.
1762        my $suffix = $retOptions->{user};
1763        # Check for background mode.
1764        if ($retOptions->{background}) {
1765            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1766            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1767            open STDOUT, ">$outFileName";
1768            open STDERR, ">$errFileName";
1769            # Check for phone support. If we have phone support and a phone number,
1770            # we want to turn it on.
1771            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1772                $retOptions->{phone} = $ENV{PHONE};
1773            }
1774        }
1775        # Now we want to set up tracing. First, we need to know if the user
1776        # wants emergency tracing.
1777        if ($retOptions->{trace} eq 'E') {
1778            ETracing($retOptions->{user});
1779        } else {
1780            # Here the tracing is controlled from the command line.
1781            my @cats = @{$categories};
1782            if ($retOptions->{sql}) {
1783                push @cats, "SQL";
1784            }
1785            # Add the default categories.
1786            push @cats, "Tracer";
1787            # Next, we create the category string by joining the categories.
1788            my $cats = join(" ", @cats);
1789            # Check to determine whether or not the caller wants to turn off tracing
1790            # to the standard output.
1791            my $traceLevel = $retOptions->{trace};
1792            my $textOKFlag = 1;
1793            if ($traceLevel =~ /^(.)-/) {
1794                $traceLevel = $1;
1795                $textOKFlag = 0;
1796            }
1797            # Now we set up the trace mode.
1798            my $traceMode;
1799            # Verify that we can open a file in the FIG temporary directory.
1800            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1801            if (open TESTTRACE, ">$traceFileName") {
1802                # Here we can trace to a file.
1803                $traceMode = ">$traceFileName";
1804                if ($textOKFlag) {
1805                    # Echo to standard output if the text-OK flag is set.
1806                    $traceMode = "+$traceMode";
1807                }
1808                # Close the test file.
1809                close TESTTRACE;
1810            } else {
1811                # Here we can't trace to a file. Complain about this.
1812                warn "Could not open trace file $traceFileName: $!\n";
1813                # We trace to the standard output if it's
1814                # okay, and the error log otherwise.
1815                if ($textOKFlag) {
1816                    $traceMode = "TEXT";
1817                } else {
1818                    $traceMode = "WARN";
1819                }
1820            }
1821            # Now set up the tracing.
1822            TSetup("$traceLevel $cats", $traceMode);
1823        }
1824        # Check for the "help" option. If it is specified, dump the command-line
1825        # options and exit the program.
1826        if ($retOptions->{help}) {
1827            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1828            print "$1 [options] $parmHelp\n";
1829            for my $key (sort keys %{$options}) {
1830                my $name = Pad($key, $longestName, 0, ' ');
1831                my $desc = $options->{$key}->[1];
1832                if ($options->{$key}->[0]) {
1833                    $desc .= " (default " . $options->{$key}->[0] . ")";
1834  }  }
1835                print "  $name $desc\n";
 # Pad a number to 2 digits.  
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
1836  }  }
1837            exit(0);
1838  =head3 LogErrors      }
1839        # Trace the options, if applicable.
1840  C<< Tracer::LogErrors($fileName); >>      if (T(3)) {
1841            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1842  Route the standard error output to a log file.          Trace("Selected options: " . join(", ", sort @parms) . ".");
1843        }
1844  =over 4      # Return the parsed parameters.
1845        return ($retOptions, @retParameters);
 =item fileName  
   
 Name of the file to receive the error output.  
   
 =back  
   
 =cut  
   
 sub LogErrors {  
     # Get the file name.  
     my ($fileName) = @_;  
     # Open the file as the standard error output.  
     open STDERR, '>', $fileName;  
1846  }  }
1847    
1848  =head3 ReadOptions  =head3 ReadOptions
1849    
1850  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1851    
1852  Read a set of options from a file. Each option is encoded in a line of text that has the  Read a set of options from a file. Each option is encoded in a line of text that has the
1853  format  format
# Line 1017  Line 1908 
1908    
1909  =head3 GetOptions  =head3 GetOptions
1910    
1911  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1912    
1913  Merge a specified set of options into a table of defaults. This method takes two hash references  Merge a specified set of options into a table of defaults. This method takes two hash references
1914  as input and uses the data from the second to update the first. If the second does not exist,  as input and uses the data from the second to update the first. If the second does not exist,
# Line 1026  Line 1917 
1917    
1918  Consider the following example.  Consider the following example.
1919    
1920  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1921    
1922  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1923  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 1034  Line 1925 
1925  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1926  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1927    
1928  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1929    
1930  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1931    
# Line 1078  Line 1969 
1969    
1970  =head3 MergeOptions  =head3 MergeOptions
1971    
1972  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
1973    
1974  Merge default values into a hash table. This method looks at the key-value pairs in the  Merge default values into a hash table. This method looks at the key-value pairs in the
1975  second (default) hash, and if a matching key is not found in the first hash, the default  second (default) hash, and if a matching key is not found in the first hash, the default
# Line 1110  Line 2001 
2001      }      }
2002  }  }
2003    
 =head3 Trace  
   
 C<< Trace($message); >>  
   
 Write a trace message to the target location specified in L</TSetup>. If there has not been  
 any prior call to B<TSetup>.  
   
 =over 4  
   
 =item message  
   
 Message to write.  
   
 =back  
   
 =cut  
   
 sub Trace {  
     # Get the parameters.  
     my ($message) = @_;  
     # Get the timestamp.  
     my $timeStamp = Now();  
     # Format the message. Note we strip off any line terminators at the end.  
     my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);  
     # Process according to the destination.  
     if ($Destination eq "TEXT") {  
         # Write the message to the standard output.  
         print "$formatted\n";  
     } elsif ($Destination eq "ERROR") {  
         # Write the message to the error output.  
         print STDERR "$formatted\n";  
     } elsif ($Destination eq "QUEUE") {  
         # Push the message into the queue.  
         push @Queue, "$formatted";  
     } elsif ($Destination eq "HTML") {  
         # Convert the message to HTML and write it to the standard output.  
         my $escapedMessage = CGI::escapeHTML($message);  
         print "<p>$formatted</p>\n";  
     } elsif ($Destination eq "WARN") {  
        # Emit the message as a warning.  
        warn $message;  
     } elsif ($Destination =~ m/^>>/) {  
         # Write the trace message to an output file.  
         (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";  
         print TRACING "$formatted\n";  
         close TRACING;  
         # If the Tee flag is on, echo it to the standard output.  
         if ($TeeFlag) {  
             print "$formatted\n";  
         }  
     }  
 }  
   
 =head3 T  
   
 C<< my $switch = T($category, $traceLevel); >>  
   
     or  
   
 C<< my $switch = T($traceLevel); >>  
   
 Return TRUE if the trace level is at or above a specified value and the specified category  
 is active, else FALSE. If no category is specified, the caller's package name is used.  
   
 =over 4  
   
 =item category  
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
   
 Relevant tracing level.  
   
 =item RETURN  
   
 TRUE if a message at the specified trace level would appear in the trace, else FALSE.  
   
 =back  
   
 =cut  
   
 sub T {  
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
         # Get the parameters.  
         my ($category, $traceLevel) = @_;  
         if (!defined $traceLevel) {  
             # Here we have no category, so we need to get the calling package.  
             # The calling package is normally the first parameter. If it is  
             # omitted, the first parameter will be the tracelevel. So, the  
             # first thing we do is shift the so-called category into the  
             # $traceLevel variable where it belongs.  
             $traceLevel = $category;  
             my ($package, $fileName, $line) = caller;  
             # If there is no calling package, we default to "main".  
             if (!$package) {  
                 $category = "main";  
             } else {  
                 $category = $package;  
             }  
         }  
         # Save the category name.  
         $LastCategory = $category;  
         # Convert it to lower case before we hash it.  
         $category = lc $category;  
         # Use the category and tracelevel to compute the result.  
         if (ref $traceLevel) {  
             Confess("Bad trace level.");  
         } elsif (ref $TraceLevel) {  
             Confess("Bad trace config.");  
         }  
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
     }  
     # Return the computed result.  
     return $retVal;  
 }  
   
2004  =head3 ParseCommand  =head3 ParseCommand
2005    
2006  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2007    
2008  Parse a command line consisting of a list of parameters. The initial parameters may be option  Parse a command line consisting of a list of parameters. The initial parameters may be option
2009  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2010  off and merged into a table of default options. The remainder of the command line is  off and merged into a table of default options. The remainder of the command line is
2011  returned as a list of positional arguments. For example, consider the following invocation.  returned as a list of positional arguments. For example, consider the following invocation.
2012    
2013  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2014    
2015  In this case, the list @words will be treated as a command line. There are two options available,  In this case, the list @words will be treated as a command line and there are two options available,
2016  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
2017    
2018  C<< -logFile=error.log apple orange rutabaga >>      -logFile=error.log apple orange rutabaga
2019    
2020  then at the end of the invocation, C<$options> will be  then at the end of the invocation, C<$options> will be
2021    
2022  C<< { errors => 0, logFile => 'error.log' } >>      { errors => 0, logFile => 'error.log' }
2023    
2024  and C<@arguments> will contain  and C<@arguments> will contain
2025    
2026  C<< apple orange rutabaga >>      apple orange rutabaga
2027    
2028  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2029  support for quote characters.  support for quote characters. Options can be specified with single or double hyphens.
2030    
2031  =over 4  =over 4
2032    
# Line 1281  Line 2051 
2051      my ($optionTable, @inputList) = @_;      my ($optionTable, @inputList) = @_;
2052      # Process any options in the input list.      # Process any options in the input list.
2053      my %overrides = ();      my %overrides = ();
2054      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2055          # Get the current option.          # Get the current option.
2056          my $arg = shift @inputList;          my $arg = shift @inputList;
2057          # Pull out the option name.          # Pull out the option name.
2058          $arg =~ /^-([^=]*)/g;          $arg =~ /^--?([^=]*)/g;
2059          my $name = $1;          my $name = $1;
2060          # Check for an option value.          # Check for an option value.
2061          if ($arg =~ /\G=(.*)$/g) {          if ($arg =~ /\G=(.*)$/g) {
# Line 1307  Line 2077 
2077      return ($optionTable, @retVal);      return ($optionTable, @retVal);
2078  }  }
2079    
 =head3 Escape  
2080    
2081  C<< my $codedString = Tracer::Escape($realString); >>  =head2 File Utility Methods
2082    
2083  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  =head3 GetFile
2084  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
2085  result is to reverse the effect of L</UnEscape>.      my @fileContents = Tracer::GetFile($fileName);
2086    
2087        or
2088    
2089        my $fileContents = Tracer::GetFile($fileName);
2090    
2091    Return the entire contents of a file. In list context, line-ends are removed and
2092    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2093    
2094  =over 4  =over 4
2095    
2096  =item realString  =item fileName
2097    
2098  String to escape.  Name of the file to read.
2099    
2100  =item RETURN  =item RETURN
2101    
2102  Escaped equivalent of the real string.  In a list context, returns the entire file as a list with the line terminators removed.
2103    In a scalar context, returns the entire file as a string. If an error occurs opening
2104    the file, an empty list will be returned.
2105    
2106  =back  =back
2107    
2108  =cut  =cut
2109    
2110  sub Escape {  sub GetFile {
2111      # Get the parameter.      # Get the parameters.
2112      my ($realString) = @_;      my ($fileName) = @_;
2113      # Initialize the return variable.      # Declare the return variable.
2114      my $retVal = "";      my @retVal = ();
2115      # Loop through the parameter string, looking for sequences to escape.      # Open the file for input.
2116      while (length $realString > 0) {      my $handle = Open(undef, "<$fileName");
2117          # Look for the first sequence to escape.      # Read the whole file into the return variable, stripping off any terminator
2118          if ($realString =~ /^(.*?)([\n\t\r\\])/) {      # characters.
2119              # Here we found it. The text preceding the sequence is in $1. The sequence      my $lineCount = 0;
2120              # itself is in $2. First, move the clear text to the return variable.      while (my $line = <$handle>) {
2121              $retVal .= $1;          $lineCount++;
2122              # Strip the processed section off the real string.          $line = Strip($line);
2123              $realString = substr $realString, (length $2) + (length $1);          push @retVal, $line;
             # Get the matched character.  
             my $char = $2;  
             # If we have a CR, we are done.  
             if ($char ne "\r") {  
                 # It's not a CR, so encode the escape sequence.  
                 $char =~ tr/\t\n/tn/;  
                 $retVal .= "\\" . $char;  
2124              }              }
2125        # Close it.
2126        close $handle;
2127        my $actualLines = @retVal;
2128        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2129        # Return the file's contents in the desired format.
2130        if (wantarray) {
2131            return @retVal;
2132          } else {          } else {
2133              # Here there are no more escape sequences. The rest of the string is          return join "\n", @retVal;
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
         }  
2134      }      }
     # Return the result.  
     return $retVal;  
2135  }  }
2136    
2137  =head3 UnEscape  =head3 PutFile
   
 C<< my $realString = Tracer::UnEscape($codedString); >>  
   
 Replace escape sequences with their actual equivalents. C<\t> will be replaced by  
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
   
 =over 4  
   
 =item codedString  
   
 String to un-escape.  
   
 =item RETURN  
   
 Returns a copy of the original string with the escape sequences converted to their actual  
 values.  
2138    
2139  =back      Tracer::PutFile($fileName, \@lines);
2140    
2141  =cut  Write out a file from a list of lines of text.
2142    
2143  sub UnEscape {  =over 4
2144      # Get the parameter.  
2145      my ($codedString) = @_;  =item fileName
2146      # Initialize the return variable.  
2147      my $retVal = "";  Name of the output file.
2148      # Only proceed if the incoming string is nonempty.  
2149      if (defined $codedString) {  =item lines
2150          # Loop through the parameter string, looking for escape sequences. We can't do  
2151          # translating because it causes problems with the escaped slash. ("\\t" becomes  Reference to a list of text lines. The lines will be written to the file in order, with trailing
2152          # "\<tab>" no matter what we do.)  new-line characters. Alternatively, may be a string, in which case the string will be written without
2153          while (length $codedString > 0) {  modification.
2154              # Look for the first escape sequence.  
2155              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {  =back
2156                  # Here we found it. The text preceding the sequence is in $1. The sequence  
2157                  # itself is in $2. First, move the clear text to the return variable.  =cut
2158                  $retVal .= $1;  
2159                  $codedString = substr $codedString, (2 + length $1);  sub PutFile {
2160                  # Get the escape value.      # Get the parameters.
2161                  my $char = $2;      my ($fileName, $lines) = @_;
2162                  # If we have a "\r", we are done.      # Open the output file.
2163                  if ($char ne 'r') {      my $handle = Open(undef, ">$fileName");
2164                      # Here it's not an 'r', so we convert it.      # Count the lines written.
2165                      $char =~ tr/\\tn/\\\t\n/;      if (ref $lines ne 'ARRAY') {
2166                      $retVal .= $char;          # Here we have a scalar, so we write it raw.
2167                  }          print $handle $lines;
2168            Trace("Scalar put to file $fileName.") if T(File => 3);
2169              } else {              } else {
2170                  # Here there are no more escape sequences. The rest of the string is          # Write the lines one at a time.
2171                  # transferred unmodified.          my $count = 0;
2172                  $retVal .= $codedString;          for my $line (@{$lines}) {
2173                  $codedString = "";              print $handle "$line\n";
2174              }              $count++;
2175          }          }
2176            Trace("$count lines put to file $fileName.") if T(File => 3);
2177      }      }
2178      # Return the result.      # Close the output file.
2179      return $retVal;      close $handle;
2180  }  }
2181    
2182  =head3 ParseRecord  =head3 ParseRecord
2183    
2184  C<< my @fields = Tracer::ParseRecord($line); >>      my @fields = Tracer::ParseRecord($line);
2185    
2186  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2187  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
# Line 1469  Line 2226 
2226    
2227  =head3 Merge  =head3 Merge
2228    
2229  C<< my @mergedList = Tracer::Merge(@inputList); >>      my @mergedList = Tracer::Merge(@inputList);
2230    
2231  Sort a list of strings and remove duplicates.  Sort a list of strings and remove duplicates.
2232    
# Line 1515  Line 2272 
2272      return @inputList;      return @inputList;
2273  }  }
2274    
2275  =head3 Percent  =head3 Open
   
 C<< my $percent = Tracer::Percent($number, $base); >>  
   
 Returns the percent of the base represented by the given number. If the base  
 is zero, returns zero.  
   
 =over 4  
2276    
2277  =item number      my $handle = Open($fileHandle, $fileSpec, $message);
2278    
2279  Percent numerator.  Open a file.
2280    
2281  =item base  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2282    function. The mode is specified using Unix-like shell information. So, for
2283    example,
2284    
2285  Percent base.      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2286    
2287  =item RETURN  would open for output appended to the specified file, and
2288    
2289  Returns the percentage of the base represented by the numerator.      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2290    
2291  =back  would open a pipe that sorts the records written and removes duplicates. Note
2292    the use of file handle syntax in the Open call. To use anonymous file handles,
2293    code as follows.
2294    
2295  =cut      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2296    
2297  sub Percent {  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2298      # Get the parameters.  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2299      my ($number, $base) = @_;  failed open will throw an exception and the third parameter will be used to construct
2300      # Declare the return variable.  an error message. If the parameter is omitted, a standard message is constructed
2301      my $retVal = 0;  using the file spec.
     # Compute the percent.  
     if ($base != 0) {  
         $retVal = $number * 100 / $base;  
     }  
     # Return the result.  
     return $retVal;  
 }  
2302    
2303  =head3 GetFile      Could not open "/usr/spool/news/twitlog"
2304    
2305  C<< my @fileContents = Tracer::GetFile($fileName); >>  Note that the mode characters are automatically cleaned from the file name.
2306    The actual error message from the file system will be captured and appended to the
2307    message in any case.
2308    
2309      or      Could not open "/usr/spool/news/twitlog": file not found.
2310    
2311  C<< my $fileContents = Tracer::GetFile($fileName); >>  In some versions of PERL the only error message we get is a number, which
2312    corresponds to the C++ C<errno> value.
2313    
2314  Return the entire contents of a file. In list context, line-ends are removed and      Could not open "/usr/spool/news/twitlog": 6.
 each line is a list element. In scalar context, line-ends are replaced by C<\n>.  
2315    
2316  =over 4  =over 4
2317    
2318  =item fileName  =item fileHandle
   
 Name of the file to read.  
   
 =item RETURN  
   
 In a list context, returns the entire file as a list with the line terminators removed.  
 In a scalar context, returns the entire file as a string. If an error occurs opening  
 the file, an empty list will be returned.  
   
 =back  
   
 =cut  
   
 sub GetFile {  
     # Get the parameters.  
     my ($fileName) = @_;  
     # Declare the return variable.  
     my @retVal = ();  
     # Open the file for input.  
     my $handle = Open(undef, "<$fileName");  
     # Read the whole file into the return variable, stripping off any terminator  
     # characters.  
     my $lineCount = 0;  
     while (my $line = <$handle>) {  
         $lineCount++;  
         $line = Strip($line);  
         push @retVal, $line;  
     }  
     # Close it.  
     close $handle;  
     my $actualLines = @retVal;  
     # Return the file's contents in the desired format.  
     if (wantarray) {  
         return @retVal;  
     } else {  
         return join "\n", @retVal;  
     }  
 }  
   
 =head3 PutFile  
2319    
2320  C<< Tracer::PutFile($fileName, \@lines); >>  File handle. If this parameter is C<undef>, a file handle will be generated
2321    and returned as the value of this method.
2322    
2323  Write out a file from a list of lines of text.  =item fileSpec
2324    
2325  =over 4  File name and mode, as per the PERL C<open> function.
2326    
2327  =item fileName  =item message (optional)
2328    
2329  Name of the output file.  Error message to use if the open fails. If omitted, a standard error message
2330    will be generated. In either case, the error information from the file system
2331    is appended to the message. To specify a conditional open that does not throw
2332    an error if it fails, use C<0>.
2333    
2334  =item lines  =item RETURN
2335    
2336  Reference to a list of text lines. The lines will be written to the file in order, with trailing  Returns the name of the file handle assigned to the file, or C<undef> if the
2337  new-line characters. Alternatively, may be a string, in which case the string will be written without  open failed.
 modification.  
2338    
2339  =back  =back
2340    
2341  =cut  =cut
2342    
2343  sub PutFile {  sub Open {
2344      # Get the parameters.      # Get the parameters.
2345      my ($fileName, $lines) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2346      # Open the output file.      # Attempt to open the file.
2347      my $handle = Open(undef, ">$fileName");      my $rv = open $fileHandle, $fileSpec;
2348      if (ref $lines ne 'ARRAY') {      # If the open failed, generate an error message.
2349          # Here we have a scalar, so we write it raw.      if (! $rv) {
2350          print $handle $lines;          # Save the system error message.
2351      } else {          my $sysMessage = $!;
2352          # Write the lines one at a time.          # See if we need a default message.
2353          for my $line (@{$lines}) {          if (!$message) {
2354              print $handle "$line\n";              # Clean any obvious mode characters and leading spaces from the
2355                # filename.
2356                my ($fileName) = FindNamePart($fileSpec);
2357                $message = "Could not open \"$fileName\"";
2358          }          }
2359            # Terminate with an error using the supplied message and the
2360            # error message from the file system.
2361            Confess("$message: $!");
2362      }      }
2363      # Close the output file.      # Return the file handle.
2364      close $handle;      return $fileHandle;
2365  }  }
2366    
2367  =head3 QTrace  =head3 FindNamePart
   
 C<< my $data = QTrace($format); >>  
   
 Return the queued trace data in the specified format.  
   
 =over 4  
   
 =item format  
   
 C<html> to format the data as an HTML list, C<text> to format it as straight text.  
   
 =back  
2368    
2369  =cut      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2370    
2371  sub QTrace {  Extract the portion of a file specification that contains the file name.
     # Get the parameter.  
     my ($format) = @_;  
     # Create the return variable.  
     my $retVal = "";  
     # Only proceed if there is an actual queue.  
     if (@Queue) {  
         # Process according to the format.  
         if ($format =~ m/^HTML$/i) {  
             # Convert the queue into an HTML list.  
             $retVal = "<ul>\n";  
             for my $line (@Queue) {  
                 my $escapedLine = CGI::escapeHTML($line);  
                 $retVal .= "<li>$escapedLine</li>\n";  
             }  
             $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
             # Convert the queue into a list of text lines.  
             $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
     }  
     # Return the formatted list.  
     return $retVal;  
 }  
2372    
2373  =head3 Confess  A file specification is the string passed to an C<open> call. It specifies the file
2374    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2375    method assumes that the file name is whatever follows the first angle bracket
2376    sequence.  So, for example, in the following strings the file name is
2377    C</usr/fig/myfile.txt>.
2378    
2379  C<< Confess($message); >>      >>/usr/fig/myfile.txt
2380        </usr/fig/myfile.txt
2381        | sort -u > /usr/fig/myfile.txt
2382    
2383  Trace the call stack and abort the program with the specified message. When used with  If the method cannot find a file name using its normal methods, it will return the
2384  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  whole incoming string.
 So, for example  
2385    
2386  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
2387    
2388  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item fileSpec
2389    
2390  =over 4  File specification string from which the file name is to be extracted.
2391    
2392  =item message  =item RETURN
2393    
2394  Message to include in the trace.  Returns a three-element list. The first element contains the file name portion of
2395    the specified string, or the whole string if a file name cannot be found via normal
2396    methods. The second element contains the start position of the file name portion and
2397    the third element contains the length.
2398    
2399  =back  =back
2400    
2401  =cut  =cut
2402    #: Return Type $;
2403  sub Confess {  sub FindNamePart {
2404      # Get the parameters.      # Get the parameters.
2405      my ($message) = @_;      my ($fileSpec) = @_;
2406      # Trace the call stack.      # Default to the whole input string.
2407      Cluck($message);      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2408      # Abort the program.      # Parse out the file name if we can.
2409      croak(">>> $message");      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2410            $retVal = $2;
2411            $len = length $retVal;
2412            $pos = (length $fileSpec) - (length $3) - $len;
2413        }
2414        # Return the result.
2415        return ($retVal, $pos, $len);
2416  }  }
2417    
2418  =head3 Assert  =head3 OpenDir
2419    
2420  C<< Assert($condition1, $condition2, ... $conditionN); >>      my @files = OpenDir($dirName, $filtered, $flag);
2421    
2422  Return TRUE if all the conditions are true. This method can be used in conjunction with  Open a directory and return all the file names. This function essentially performs
2423  the OR operator and the L</Confess> method as a debugging assert.  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2424  So, for example  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2425    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2426    filtered out of the return list. If the directory does not open and I<$flag> is not
2427    set, an exception is thrown. So, for example,
2428    
2429  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      my @files = OpenDir("/Volumes/fig/contigs", 1);
2430    
2431  Will abort the program with a stack trace if the value of C<$recNum> is negative.  is effectively the same as
2432    
2433  =cut      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2434  sub Assert {      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
2435    
2436  =head3 Cluck  Similarly, the following code
2437    
2438  C<< Cluck($message); >>      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2439    
2440  Trace the call stack. Note that for best results, you should qualify the call with a  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2441  trace condition. For example,  automatically returns an empty list if the directory fails to open.
2442    
2443  C<< Cluck("Starting record parse.") if T(3); >>  =over 4
2444    
2445  will only trace the stack if the trace level for the package is 3 or more.  =item dirName
2446    
2447  =over 4  Name of the directory to open.
2448    
2449  =item message  =item filtered
2450    
2451  Message to include in the trace.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2452    from the list, else FALSE.
2453    
2454    =item flag
2455    
2456    TRUE if a failure to open is okay, else FALSE
2457    
2458  =back  =back
2459    
2460  =cut  =cut
2461    #: Return Type @;
2462  sub Cluck {  sub OpenDir {
2463      # Get the parameters.      # Get the parameters.
2464      my ($message) = @_;      my ($dirName, $filtered, $flag) = @_;
2465      # Trace what's happening.      # Declare the return variable.
2466      Trace("Stack trace for event: $message");      my @retVal = ();
2467      my $confession = longmess($message);      # Open the directory.
2468      # Convert the confession to a series of trace messages. Note we skip any      if (opendir(my $dirHandle, $dirName)) {
2469      # messages relating to calls into Tracer.          # The directory opened successfully. Get the appropriate list according to the
2470      for my $line (split /\s*\n/, $confession) {          # strictures of the filter parameter.
2471          Trace($line) if ($line !~ /Tracer\.pm/);          if ($filtered) {
2472                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2473            } else {
2474                @retVal = readdir $dirHandle;
2475            }
2476        } elsif (! $flag) {
2477            # Here the directory would not open and it's considered an error.
2478            Confess("Could not open directory $dirName.");
2479      }      }
2480        # Return the result.
2481        return @retVal;
2482  }  }
2483    
 =head3 Min  
2484    
2485  C<< my $min = Min($value1, $value2, ... $valueN); >>  =head3 Insure
2486    
2487        Insure($dirName, $chmod);
2488    
2489  Return the minimum argument. The arguments are treated as numbers.  Insure a directory is present.
2490    
2491  =over 4  =over 4
2492    
2493  =item $value1, $value2, ... $valueN  =item dirName
2494    
2495  List of numbers to compare.  Name of the directory to check. If it does not exist, it will be created.
2496    
2497  =item RETURN  =item chmod (optional)
2498    
2499  Returns the lowest number in the list.  Security privileges to be given to the directory if it is created.
2500    
2501  =back  =back
2502    
2503  =cut  =cut
2504    
2505  sub Min {  sub Insure {
2506      # Get the parameters. Note that we prime the return value with the first parameter.      my ($dirName, $chmod) = @_;
2507      my ($retVal, @values) = @_;      if (! -d $dirName) {
2508      # Loop through the remaining parameters, looking for the lowest.          Trace("Creating $dirName directory.") if T(2);
2509      for my $value (@values) {          eval {
2510          if ($value < $retVal) {              mkpath $dirName;
2511              $retVal = $value;              # If we have permissions specified, set them here.
2512                if (defined($chmod)) {
2513                    chmod $chmod, $dirName;
2514                }
2515            };
2516            if ($@) {
2517                Confess("Error creating $dirName: $@");
2518          }          }
2519      }      }
     # Return the minimum found.  
     return $retVal;  
2520  }  }
2521    
2522  =head3 Max  =head3 ChDir
2523    
2524  C<< my $max = Max($value1, $value2, ... $valueN); >>      ChDir($dirName);
2525    
2526  Return the maximum argument. The arguments are treated as numbers.  Change to the specified directory.
2527    
2528  =over 4  =over 4
2529    
2530  =item $value1, $value2, ... $valueN  =item dirName
   
 List of numbers to compare.  
   
 =item RETURN  
2531    
2532  Returns the highest number in the list.  Name of the directory to which we want to change.
2533    
2534  =back  =back
2535    
2536  =cut  =cut
2537    
2538  sub Max {  sub ChDir {
2539      # Get the parameters. Note that we prime the return value with the first parameter.      my ($dirName) = @_;
2540      my ($retVal, @values) = @_;      if (! -d $dirName) {
2541      # Loop through the remaining parameters, looking for the highest.          Confess("Cannot change to directory $dirName: no such directory.");
2542      for my $value (@values) {      } else {
2543          if ($value > $retVal) {          Trace("Changing to directory $dirName.") if T(File => 4);
2544              $retVal = $value;          my $okFlag = chdir $dirName;
2545            if (! $okFlag) {
2546                Confess("Error switching to directory $dirName.");
2547          }          }
2548      }      }
     # Return the maximum found.  
     return $retVal;  
2549  }  }
2550    
2551  =head3 AddToListMap  =head3 SetPermissions
2552    
2553        Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2554    
2555  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>  Set the permissions for a directory and all the files and folders inside it.
2556    In addition, the group ownership will be changed to the specified value.
2557    
2558  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  This method is more vulnerable than most to permission and compatability
2559  is created for the key. Otherwise, the new value is pushed onto the list.  problems, so it does internal error recovery.
2560    
2561  =over 4  =over 4
2562    
2563  =item hash  =item dirName
2564    
2565  Reference to the target hash.  Name of the directory to process.
2566    
2567  =item key  =item group
2568    
2569  Key for which the value is to be added.  Name of the group to be assigned.
2570    
2571  =item value1, value2, ... valueN  =item mask
2572    
2573  List of values to add to the key's value list.  Permission mask. Bits that are C<1> in this mask will be ORed into the
2574    permission bits of any file or directory that does not already have them
2575    set to 1.
2576    
2577  =back  =item otherMasks
2578    
2579  =cut  Map of search patterns to permission masks. If a directory name matches
2580    one of the patterns, that directory and all its members and subdirectories
2581    will be assigned the new pattern. For example, the following would
2582    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2583    
2584  sub AddToListMap {      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
     # Get the parameters.  
     my ($hash, $key, @values) = @_;  
     # Process according to whether or not the key already has a value.  
     if (! exists $hash->{$key}) {  
         $hash->{$key} = [@values];  
     } else {  
         push @{$hash->{$key}}, @values;  
     }  
 }  
2585    
2586  =head3 DebugMode  The list is ordered, so the following would use 0777 for C<tmp1> and
2587    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2588    
2589  C<< if (Tracer::DebugMode) { ...code... } >>      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2590                                                       '^tmp' => 0666);
2591    
2592  Return TRUE if debug mode has been turned on, else abort.  Note that the pattern matches are all case-insensitive, and only directory
2593    names are matched, not file names.
2594    
2595  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.  
2596    
2597  =cut  =cut
2598    
2599  sub DebugMode {  sub SetPermissions {
2600      # Declare the return variable.      # Get the parameters.
2601      my $retVal = 0;      my ($dirName, $group, $mask, @otherMasks) = @_;
2602      # Check the debug configuration.      # Set up for error recovery.
2603      my $password = CGI::cookie("DebugMode");      eval {
2604      my $encrypted = Digest::MD5::md5_hex($password);          # Switch to the specified directory.
2605      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {          ChDir($dirName);
2606          $retVal = 1;          # Get the group ID.
2607            my $gid = getgrnam($group);
2608            # Get the mask for tracing.
2609            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2610            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2611            my $fixCount = 0;
2612            my $lookCount = 0;
2613            # @dirs will be a stack of directories to be processed.
2614            my @dirs = (getcwd());
2615            while (scalar(@dirs) > 0) {
2616                # Get the current directory.
2617                my $dir = pop @dirs;
2618                # Check for a match to one of the specified directory names. To do
2619                # that, we need to pull the individual part of the name off of the
2620                # whole path.
2621                my $simpleName = $dir;
2622                if ($dir =~ m!/([^/]+)$!) {
2623                    $simpleName = $1;
2624                }
2625                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2626                # Search for a match.
2627                my $match = 0;
2628                my $i;
2629                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2630                    my $pattern = $otherMasks[$i];
2631                    if ($simpleName =~ /$pattern/i) {
2632                        $match = 1;
2633                    }
2634                }
2635                # Check for a match. Note we use $i-1 because the loop added 2
2636                # before terminating due to the match.
2637                if ($match && $otherMasks[$i-1] != $mask) {
2638                    # This directory matches one of the incoming patterns, and it's
2639                    # a different mask, so we process it recursively with that mask.
2640                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2641      } else {      } else {
2642          # Here debug mode is off, so we generate an error.                  # Here we can process normally. Get all of the non-hidden members.
2643          Confess("Cannot use this facility without logging in.");                  my @submems = OpenDir($dir, 1);
2644                    for my $submem (@submems) {
2645                        # Get the full name.
2646                        my $thisMem = "$dir/$submem";
2647                        Trace("Checking member $thisMem.") if T(4);
2648                        $lookCount++;
2649                        if ($lookCount % 1000 == 0) {
2650                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2651                        }
2652                        # Fix the group.
2653                        chown -1, $gid, $thisMem;
2654                        # Insure this member is not a symlink.
2655                        if (! -l $thisMem) {
2656                            # Get its info.
2657                            my $fileInfo = stat $thisMem;
2658                            # Only proceed if we got the info. Otherwise, it's a hard link
2659                            # and we want to skip it anyway.
2660                            if ($fileInfo) {
2661                                my $fileMode = $fileInfo->mode;
2662                                if (($fileMode & $mask) != $mask) {
2663                                    # Fix this member.
2664                                    $fileMode |= $mask;
2665                                    chmod $fileMode, $thisMem;
2666                                    $fixCount++;
2667                                }
2668                                # If it's a subdirectory, stack it.
2669                                if (-d $thisMem) {
2670                                    push @dirs, $thisMem;
2671                                }
2672                            }
2673                        }
2674                    }
2675                }
2676            }
2677            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2678        };
2679        # Check for an error.
2680        if ($@) {
2681            Confess("SetPermissions error: $@");
2682      }      }
     # Return the determination indicator.  
     return $retVal;  
2683  }  }
2684    
2685  =head3 Strip  =head3 GetLine
2686    
2687  C<< my $string = Tracer::Strip($line); >>      my @data = Tracer::GetLine($handle);
2688    
2689  Strip all line terminators off a string. This is necessary when dealing with files  Read a line of data from a tab-delimited file.
 that may have been transferred back and forth several times among different  
 operating environments.  
2690    
2691  =over 4  =over 4
2692    
2693  =item line  =item handle
2694    
2695  Line of text to be stripped.  Open file handle from which to read.
2696    
2697  =item RETURN  =item RETURN
2698    
2699  The same line of text with all the line-ending characters chopped from the end.  Returns a list of the fields in the record read. The fields are presumed to be
2700    tab-delimited. If we are at the end of the file, then an empty list will be
2701    returned. If an empty line is read, a single list item consisting of a null
2702    string will be returned.
2703    
2704  =back  =back
2705    
2706  =cut  =cut
2707    
2708  sub Strip {  sub GetLine {
2709      # Get a copy of the parameter string.      # Get the parameters.
2710      my ($string) = @_;      my ($handle) = @_;
2711      my $retVal = (defined $string ? $string : "");      # Declare the return variable.
2712      # Strip the line terminator characters.      my @retVal = ();
2713      $retVal =~ s/(\r|\n)+$//g;      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2714        # Read from the file.
2715        my $line = <$handle>;
2716        # Only proceed if we found something.
2717        if (defined $line) {
2718            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2719            # upload control and have a nonstandard EOL combination.
2720            $line =~ s/(\r|\n)+$//;
2721            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2722            if (T(File => 4)) {
2723                my $escapedLine = $line;
2724                $escapedLine =~ s/\n/\\n/g;
2725                $escapedLine =~ s/\r/\\r/g;
2726                $escapedLine =~ s/\t/\\t/g;
2727                Trace("Line read: -->$escapedLine<--");
2728            }
2729            # If the line is empty, return a single empty string; otherwise, parse
2730            # it into fields.
2731            if ($line eq "") {
2732                push @retVal, "";
2733            } else {
2734                push @retVal, split /\t/,$line;
2735            }
2736        } else {
2737            # Trace the reason the read failed.
2738            Trace("End of file: $!") if T(File => 3);
2739        }
2740      # Return the result.      # Return the result.
2741      return $retVal;      return @retVal;
2742  }  }
2743    
2744  =head3 Pad  =head3 PutLine
2745    
2746  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      Tracer::PutLine($handle, \@fields, $eol);
2747    
2748  Pad a string to a specified length. The pad character will be a  Write a line of data to a tab-delimited file. The specified field values will be
2749  space, and the padding will be on the right side unless specified  output in tab-separated form, with a trailing new-line.
 in the third parameter.  
2750    
2751  =over 4  =over 4
2752    
2753  =item string  =item handle
   
 String to be padded.  
   
 =item len  
   
 Desired length of the padded string.  
   
 =item left (optional)  
2754    
2755  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  Output file handle.
2756    
2757  =item padChar (optional)  =item fields
2758    
2759  Character to use for padding. The default is a space.  List of field values.
2760    
2761  =item RETURN  =item eol (optional)
2762    
2763  Returns a copy of the original string with the pad character added to the  End-of-line character (default is "\n").
 specified end so that it achieves the desired length.  
2764    
2765  =back  =back
2766    
2767  =cut  =cut
2768    
2769  sub Pad {  sub PutLine {
2770      # Get the parameters.      # Get the parameters.
2771      my ($string, $len, $left, $padChar) = @_;      my ($handle, $fields, $eol) = @_;
2772      # Compute the padding character.      # Write the data.
2773      if (! defined $padChar) {      print $handle join("\t", @{$fields}) . ($eol || "\n");
         $padChar = " ";  
     }  
     # Compute the number of spaces needed.  
     my $needed = $len - length $string;  
     # Copy the string into the return variable.  
     my $retVal = $string;  
     # Only proceed if padding is needed.  
     if ($needed > 0) {  
         # Create the pad string.  
         my $pad = $padChar x $needed;  
         # Affix it to the return value.  
         if ($left) {  
             $retVal = $pad . $retVal;  
         } else {  
             $retVal .= $pad;  
         }  
     }  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 EOF  
   
 This is a constant that is lexically greater than any useful string.  
   
 =cut  
   
 sub EOF {  
     return "\xFF\xFF\xFF\xFF\xFF";  
2774  }  }
2775    
 =head3 TICK  
   
 C<< my @results = TICK($commandString); >>  
2776    
2777  Perform a back-tick operation on a command. If this is a Windows environment, any leading  =head3 PrintLine
 dot-slash (C<./> will be removed. So, for example, if you were doing  
   
     `./protein.cgi`  
2778    
2779  from inside a CGI script, it would work fine in Unix, but would issue an error message      Tracer::PrintLine($line);
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
   
     TICK("./protein.cgi")  
2780    
2781  it will work correctly in both environments.  Print a line of text with a trailing new-line.
2782    
2783  =over 4  =over 4
2784    
2785  =item commandString  =item line
   
 The command string to pass to the system.  
   
 =item RETURN  
2786    
2787  Returns the standard output from the specified command, as a list.  Line of text to print.
2788    
2789  =back  =back
2790    
2791  =cut  =cut
2792  #: Return Type @;  
2793  sub TICK {  sub PrintLine {
2794      # Get the parameters.      # Get the parameters.
2795      my ($commandString) = @_;      my ($line) = @_;
2796      # Chop off the dot-slash if this is Windows.      # Print the line.
2797      if ($FIG_Config::win_mode) {      print "$line\n";
         $commandString =~ s!^\./!!;  
     }  
     # Activate the command and return the result.  
     return `$commandString`;  
2798  }  }
2799    
 =head3 ScriptSetup  
2800    
2801  C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  =head2 Other Useful Methods
2802    
2803  Perform standard tracing and debugging setup for scripts. The value returned is  =head3 ParseParm
 the CGI object followed by a pre-built variable hash.  
2804    
2805  The C<Trace> form parameter is used to determine whether or not tracing is active and      my $listValue = Tracer::ParseParm($string);
 which trace modules (other than C<Tracer> itself) should be turned on. Specifying  
 the C<CGI> trace module will trace parameter and environment information. Parameters are  
 traced at level 3 and environment variables at level 4. To trace to a file instead of to  
 the web page, set C<TF> to 1. At the end of the script, the client should call  
 L</ScriptFinish> to output the web page.  
2806    
2807  In some situations, it is not practical to invoke tracing via form parameters. For this  Convert a parameter into a list reference. If the parameter is undefined,
2808  situation, you can turn on emergency tracing from the debugging control panel.  an undefined value will be returned. Otherwise, it will be parsed as a
2809  Tracing will then be turned on automatically for all programs that use the L</ETracing>  comma-separated list of values.
 method, which includes every program that uses this method or L</StandardSetup>.  
2810    
2811  =over 4  =over 4
2812    
2813  =item noTrace (optional)  =item string
2814    
2815  If specified, tracing will be suppressed. This is useful if the script wants to set up  Incoming string.
 tracing manually.  
2816    
2817  =item RETURN  =item RETURN
2818    
2819  Returns a two-element list consisting of a CGI query object and a variable hash for  Returns a reference to a list of values, or C<undef> if the incoming value
2820  the output page.  was undefined.
2821    
2822  =back  =back
2823    
2824  =cut  =cut
2825    
2826  sub ScriptSetup {  sub ParseParm {
2827      # Get the parameters.      # Get the parameters.
2828      my ($noTrace) = @_;      my ($string) = @_;
2829      # Get the CGI query object.      # Declare the return variable.
2830      my $cgi = CGI->new();      my $retVal;
2831      # Set up tracing if it's not suppressed.      # Check for data.
2832      ETracing($cgi) unless $noTrace;      if (defined $string) {
2833      # Create the variable hash.          # We have some, so split it into a list.
2834      my $varHash = { results => '' };          $retVal = [ split /\s*,\s*/, $string];
     # Return the query object and variable hash.  
     return ($cgi, $varHash);  
 }  
   
 =head3 ETracing  
   
 C<< ETracing($parameter); >>  
   
 Set up emergency tracing. Emergency tracing is tracing that is turned  
 on automatically for any program that calls this method. The emergency  
 tracing parameters are stored in a a file identified by a tracing key.  
 If this method is called with a CGI object, then the tracing key is  
 taken from a cookie. If it is called with no parameters, then the tracing  
 key is taken from an environment variable. If it is called with a string,  
 the tracing key is that string.  
   
 =over 4  
   
 =item parameter  
   
 A parameter from which the tracing key is computed. If it is a scalar,  
 that scalar is used as the tracing key. If it is a CGI object, the  
 tracing key is taken from the C<IP> cookie. If it is omitted, the  
 tracing key is taken from the C<TRACING> environment variable. If it  
 is a CGI object and emergency tracing is not on, the C<Trace> and  
 C<TF> parameters will be used to determine the type of tracing.  
   
 =back  
   
 =cut  
   
 sub ETracing {  
     # Get the parameter.  
     my ($parameter) = @_;  
     # Check for CGI mode.  
     my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);  
     # Default to no tracing except errors.  
     my ($tracing, $dest) = ("0", "WARN");  
     # Check for emergency tracing.  
     my $tkey = EmergencyKey($parameter);  
     my $emergencyFile = EmergencyFileName($tkey);  
     if (-e $emergencyFile) {  
         # We have the file. Read in the data.  
         my @tracing = GetFile($emergencyFile);  
         # Pull off the time limit.  
         my $expire = shift @tracing;  
         # Convert it to seconds.  
         $expire *= 3600;  
         # Check the file data.  
         my $stat = stat($emergencyFile);  
         my ($now) = gettimeofday;  
         if ($now - $stat->mtime > $expire) {  
             # Delete the expired file.  
             unlink $emergencyFile;  
         } else {  
             # Emergency tracing is on. Pull off the destination and  
             # the trace level;  
             $dest = shift @tracing;  
             my $level = shift @tracing;  
             # Convert the destination to a real tracing destination.  
             # temp directory.  
             $dest = EmergencyTracingDest($tkey, $dest);  
             # Insure Tracer is specified.  
             my %moduleHash = map { $_ => 1 } @tracing;  
             $moduleHash{Tracer} = 1;  
             # Set the trace parameter.  
             $tracing = join(" ", $level, sort keys %moduleHash);  
         }  
     } elsif (defined $cgi) {  
         # There's no emergency tracing, but we have a CGI object, so check  
         # for tracing from the form parameters.  
         if ($cgi->param('Trace')) {  
             # Here the user has requested tracing via a form.  
             $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");  
             $tracing = $cgi->param('Trace') . " Tracer";  
         }  
     }  
     # Setup the tracing we've determined from all the stuff above.  
     TSetup($tracing, $dest);  
     # If we're a web script, trace the parameter and environment data.  
     if (defined $cgi) {  
         TraceParms($cgi);  
2835      }      }
2836        # Return the result.
2837        return $retVal;
2838  }  }
2839    
2840  =head3 EmergencyFileName  =head3 Now
   
 C<< my $fileName = Tracer::EmergencyFileName($tkey); >>  
   
 Return the emergency tracing file name. This is the file that specifies  
 the tracing information.  
   
 =over 4  
   
 =item tkey  
   
 Tracing key for the current program.  
   
 =item RETURN  
2841    
2842  Returns the name of the file to contain the emergency tracing information.      my $string = Tracer::Now();
2843    
2844  =back  Return a displayable time stamp containing the local time. Whatever format this
2845    method produces must be parseable by L</ParseDate>.
2846    
2847  =cut  =cut
2848    
2849  sub EmergencyFileName {  sub Now {
2850      # Get the parameters.      return DisplayTime(time);
     my ($tkey) = @_;  
     # Compute the emergency tracing file name.  
     return "$FIG_Config::temp/Emergency$tkey.txt";  
2851  }  }
2852    
2853  =head3 EmergencyFileTarget  =head3 DisplayTime
2854    
2855  C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>      my $string = Tracer::DisplayTime($time);
2856    
2857  Return the emergency tracing target file name. This is the file that receives  Convert a time value to a displayable time stamp. Whatever format this
2858  the tracing output for file-based tracing.  method produces must be parseable by L</ParseDate>.
2859    
2860  =over 4  =over 4
2861    
2862  =item tkey  =item time
2863    
2864  Tracing key for the current program.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2865    
2866  =item RETURN  =item RETURN
2867    
2868  Returns the name of the file to contain the trace output.  Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2869    
2870  =back  =back
2871    
2872  =cut  =cut
2873    
2874  sub EmergencyFileTarget {  sub DisplayTime {
2875      # Get the parameters.      my ($time) = @_;
2876      my ($tkey) = @_;      my $retVal = "(n/a)";
2877      # Compute the emergency tracing file name.      if (defined $time) {
2878      return "$FIG_Config::temp/trace$tkey.log";          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2879            $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2880                      _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2881        }
2882        return $retVal;
2883  }  }
2884    
2885  =head3 EmergencyTracingDest  # Pad a number to 2 digits.
2886    sub _p2 {
2887  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>      my ($value) = @_;
2888        $value = "0$value" if ($value < 10);
2889        return $value;
2890    }
2891    
2892  This method converts an emergency tracing destination to a real  =head3 Escape
 tracing destination. The main difference is that if the  
 destination is C<FILE> or C<APPEND>, we convert it to file  
 output.  
2893    
2894  =over 4      my $codedString = Tracer::Escape($realString);
2895    
2896  =item tkey  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2897    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2898    result is to reverse the effect of L</UnEscape>.
2899    
2900  Tracing key for this environment.  =over 4
2901    
2902  =item myDest  =item realString
2903    
2904  Destination from the emergency tracing file.  String to escape.
2905    
2906  =item RETURN  =item RETURN
2907    
2908  Returns a destination that can be passed into L</TSetup>.  Escaped equivalent of the real string.
2909    
2910  =back  =back
2911    
2912  =cut  =cut
2913    
2914  sub EmergencyTracingDest {  sub Escape {
2915      # Get the parameters.      # Get the parameter.
2916      my ($tkey, $myDest) = @_;      my ($realString) = @_;
2917      # Declare the return variable.      # Initialize the return variable.
2918      my $retVal;      my $retVal = "";
2919      # Process according to the destination value.      # Loop through the parameter string, looking for sequences to escape.
2920      if ($myDest eq 'FILE') {      while (length $realString > 0) {
2921          $retVal = ">" . EmergencyFileTarget($tkey);          # Look for the first sequence to escape.
2922      } elsif ($myDest eq 'APPEND') {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2923          $retVal = ">>" . EmergencyFileTarget($tkey);              # Here we found it. The text preceding the sequence is in $1. The sequence
2924                # itself is in $2. First, move the clear text to the return variable.
2925                $retVal .= $1;
2926                # Strip the processed section off the real string.
2927                $realString = substr $realString, (length $2) + (length $1);
2928                # Get the matched character.
2929                my $char = $2;
2930                # If we have a CR, we are done.
2931                if ($char ne "\r") {
2932                    # It's not a CR, so encode the escape sequence.
2933                    $char =~ tr/\t\n/tn/;
2934                    $retVal .= "\\" . $char;
2935                }
2936      } else {      } else {
2937          $retVal = $myDest;              # Here there are no more escape sequences. The rest of the string is
2938                # transferred unmodified.
2939                $retVal .= $realString;
2940                $realString = "";
2941            }
2942      }      }
2943      # Return the result.      # Return the result.
2944      return $retVal;      return $retVal;
2945  }  }
2946    
2947  =head3 Emergency  =head3 UnEscape
2948    
2949  C<< Emergency($key, $hours, $dest, $level, @modules); >>      my $realString = Tracer::UnEscape($codedString);
2950    
2951  Turn on emergency tracing. This method can only be invoked over the web and is  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2952  should not be called if debug mode is off. The caller specifies the duration of the  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2953  emergency in hours, the desired tracing destination, the trace level,  be deleted.
 and a list of the trace modules to activate. For the length of the duration, when a  
 program in an environment with the specified tracing key active invokes a Sprout  
 CGI script, tracing will be turned on automatically. See L</TSetup> for more  
 about tracing setup and L</ETracing> for more about emergency tracing.  
2954    
2955  =over 4  =over 4
2956    
2957  =item tkey  =item codedString
   
 The tracing key. This is used to identify the control file and the trace file.  
   
 =item hours  
   
 Number of hours to keep emergency tracing alive.  
   
 =item dest  
   
 Tracing destination. If no path information is specified for a file  
 destination, it is put in the FIG temporary directory.  
   
 =item level  
2958    
2959  Tracing level. A higher level means more trace messages.  String to un-escape.
2960    
2961  =item modules  =item RETURN
2962    
2963  A list of the tracing modules to activate.  Returns a copy of the original string with the escape sequences converted to their actual
2964    values.
2965    
2966  =back  =back
2967    
2968  =cut  =cut
2969    
2970  sub Emergency {  sub UnEscape {
2971      # Get the parameters.      # Get the parameter.
2972      my ($tkey, $hours, $dest, $level, @modules) = @_;      my ($codedString) = @_;
2973      # Create the emergency file.      # Initialize the return variable.
2974      my $specFile = EmergencyFileName($tkey);      my $retVal = "";
2975      my $outHandle = Open(undef, ">$specFile");      # Only proceed if the incoming string is nonempty.
2976      print $outHandle join("\n", $hours, $dest, $level, @modules, "");      if (defined $codedString) {
2977            # Loop through the parameter string, looking for escape sequences. We can't do
2978            # translating because it causes problems with the escaped slash. ("\\t" becomes
2979            # "\<tab>" no matter what we do.)
2980            while (length $codedString > 0) {
2981                # Look for the first escape sequence.
2982                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2983                    # Here we found it. The text preceding the sequence is in $1. The sequence
2984                    # itself is in $2. First, move the clear text to the return variable.
2985                    $retVal .= $1;
2986                    $codedString = substr $codedString, (2 + length $1);
2987                    # Get the escape value.
2988                    my $char = $2;
2989                    # If we have a "\r", we are done.
2990                    if ($char ne 'r') {
2991                        # Here it's not an 'r', so we convert it.
2992                        $char =~ tr/\\tn/\\\t\n/;
2993                        $retVal .= $char;
2994                    }
2995                } else {
2996                    # Here there are no more escape sequences. The rest of the string is
2997                    # transferred unmodified.
2998                    $retVal .= $codedString;
2999                    $codedString = "";
3000                }
3001            }
3002        }
3003        # Return the result.
3004        return $retVal;
3005  }  }
3006    
3007  =head3 EmergencyKey  =head3 Percent
3008    
3009  C<< my $tkey = EmergencyKey($parameter); >>      my $percent = Tracer::Percent($number, $base);
3010    
3011  Return the Key to be used for emergency tracing. This could be an IP address,  Returns the percent of the base represented by the given number. If the base
3012   a session ID, or a user name, depending on the environment.  is zero, returns zero.
3013    
3014  =over 4  =over 4
3015    
3016  =item parameter  =item number
3017    
3018  Parameter defining the method for finding the tracing key. If it is a scalar,  Percent numerator.
3019  then it is presumed to be the tracing key itself. If it is a CGI object, then  
3020  the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is  =item base
3021  taken from the C<TRACING> environment variable.  
3022    Percent base.
3023    
3024  =item RETURN  =item RETURN
3025    
3026  Returns the key to be used for labels in emergency tracing.  Returns the percentage of the base represented by the numerator.
3027    
3028  =back  =back
3029    
3030  =cut  =cut
3031    
3032  sub EmergencyKey {  sub Percent {
3033      # Get the parameters.      # Get the parameters.
3034      my ($parameter) = @_;      my ($number, $base) = @_;
3035      # Declare the return variable.      # Declare the return variable.
3036      my $retVal;      my $retVal = 0;
3037      # Determine the parameter type.      # Compute the percent.
3038      if (! defined $parameter) {      if ($base != 0) {
3039          # Here we're supposed to check the environment.          $retVal = $number * 100 / $base;
         $retVal = $ENV{TRACING};  
     } else {  
         my $ptype = ref $parameter;  
         if ($ptype eq 'CGI') {  
             # Here we were invoked from a web page. Look for a cookie.  
             $retVal = $parameter->cookie('IP');  
         } elsif (! $ptype) {  
             # Here the key was passed in.  
             $retVal = $parameter;  
         }  
     }  
     # If no luck finding a key, use the PID.  
     if (! defined $retVal) {  
         $retVal = $$;  
3040      }      }
3041      # Return the result.      # Return the result.
3042      return $retVal;      return $retVal;
3043  }  }
3044    
3045    =head3 Constrain
3046    
3047  =head3 TraceParms      my $constrained = Constrain($value, $min, $max);
   
 C<< Tracer::TraceParms($cgi); >>  
3048    
3049  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Modify a numeric value to bring it to a point in between a maximum and a minimum.
 at level CGI => 4.  
3050    
3051  =over 4  =over 4
3052    
3053  =item cgi  =item value
3054    
3055  CGI query object containing the parameters to trace.  Value to constrain.
3056    
3057  =back  =item min (optional)
3058    
3059  =cut  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3060    
3061  sub TraceParms {  =item max (optional)
     # Get the parameters.  
     my ($cgi) = @_;  
     if (T(CGI => 3)) {  
         # Here we want to trace the parameter data.  
         my @names = $cgi->param;  
         for my $parmName (sort @names) {  
             # Note we skip the Trace parameters, which are for our use only.  
             if ($parmName ne 'Trace' && $parmName ne 'TF') {  
                 my @values = $cgi->param($parmName);  
                 Trace("CGI: $parmName = " . join(", ", @values));  
             }  
         }  
         # Display the request method.  
         my $method = $cgi->request_method();  
         Trace("Method: $method");  
     }  
     if (T(CGI => 4)) {  
         # Here we want the environment data too.  
         for my $envName (sort keys %ENV) {  
             Trace("ENV: $envName = $ENV{$envName}");  
         }  
     }  
 }  
3062    
3063  =head3 ScriptFinish  Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3064    
3065  C<< ScriptFinish($webData, $varHash); >>  =item RETURN
3066    
3067  Output a web page at the end of a script. Either the string to be output or the  Returns the incoming value, constrained according to the other parameters.
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
3068    
3069  A typical standard script would loook like the following.  =back
3070    
3071      BEGIN {  =cut
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
3072    
3073      my ($cgi, $varHash) = ScriptSetup();  sub Constrain {
3074      eval {      # Get the parameters.
3075          # ... get data from $cgi, put it in $varHash ...      my ($value, $min, $max) = @_;
3076      };      # Declare the return variable.
3077      if ($@) {      my $retVal = $value;
3078          Trace("Script Error: $@") if T(0);      # Apply the minimum constraint.
3079        if (defined $min && $retVal < $min) {
3080            $retVal = $min;
3081        }
3082        # Apply the maximum constraint.
3083        if (defined $max && $retVal > $max) {
3084            $retVal = $max;
3085        }
3086        # Return the result.
3087        return $retVal;
3088      }      }
     ScriptFinish("Html/MyTemplate.html", $varHash);  
3089    
3090  The idea here is that even if the script fails, you'll see trace messages and  =head3 Min
3091  useful output.  
3092        my $min = Min($value1, $value2, ... $valueN);
3093    
3094    Return the minimum argument. The arguments are treated as numbers.
3095    
3096  =over 4  =over 4
3097    
3098  =item webData  =item $value1, $value2, ... $valueN
3099    
3100  A string containing either the full web page to be written to the output or the  List of numbers to compare.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3101    
3102  =item varHash (optional)  =item RETURN
3103    
3104  If specified, then a reference to a hash mapping variable names for a template  Returns the lowest number in the list.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
3105    
3106  =back  =back
3107    
3108  =cut  =cut
3109    
3110  sub ScriptFinish {  sub Min {
3111      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3112      my ($webData, $varHash) = @_;      my ($retVal, @values) = @_;
3113      # Check for a template file situation.      # Loop through the remaining parameters, looking for the lowest.
3114      my $outputString;      for my $value (@values) {
3115      if (defined $varHash) {          if ($value < $retVal) {
3116          # Here we have a template file. We need to determine the template type.              $retVal = $value;
         my $template;  
         if ($FIG_Config::template_url && $webData =~ /\.php$/) {  
             $template = "$FIG_Config::template_url/$webData";  
         } else {  
             $template = "<<$webData";  
         }  
         $outputString = PageBuilder::Build($template, $varHash, "Html");  
     } else {  
         # Here the user gave us a raw string.  
         $outputString = $webData;  
     }  
     # Check for trace messages.  
     if ($Destination ne "NONE" && $TraceLevel > 0) {  
         # We have trace messages, so we want to put them at the end of the body. This  
         # is either at the end of the whole string or at the beginning of the BODY  
         # end-tag.  
         my $pos = length $outputString;  
         if ($outputString =~ m#</body>#gi) {  
             $pos = (pos $outputString) - 7;  
         }  
         # If the trace messages were queued, we unroll them. Otherwise, we display the  
         # destination.  
         my $traceHtml;  
         if ($Destination eq "QUEUE") {  
             $traceHtml = QTrace('Html');  
         } elsif ($Destination =~ /^>>(.+)$/) {  
             # Here the tracing output it to a file. We code it as a hyperlink so the user  
             # can copy the file name into the clipboard easily.  
             my $actualDest = $1;  
             $traceHtml = "<p>Tracing output to $actualDest.</p>\n";  
         } else {  
             # Here we have one of the special destinations.  
             $traceHtml = "<P>Tracing output type is $Destination.</p>\n";  
3117          }          }
         substr $outputString, $pos, 0, $traceHtml;  
3118      }      }
3119      # Write the output string.      # Return the minimum found.
3120      print $outputString;      return $retVal;
3121  }  }
3122    
3123  =head3 Insure  =head3 Max
3124    
3125  C<< Insure($dirName); >>      my $max = Max($value1, $value2, ... $valueN);
3126    
3127  Insure a directory is present.  Return the maximum argument. The arguments are treated as numbers.
3128    
3129  =over 4  =over 4
3130    
3131  =item dirName  =item $value1, $value2, ... $valueN
3132    
3133  Name of the directory to check. If it does not exist, it will be created.  List of numbers to compare.
3134    
3135    =item RETURN
3136    
3137    Returns the highest number in the list.
3138    
3139  =back  =back
3140    
3141  =cut  =cut
3142    
3143  sub Insure {  sub Max {
3144      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
3145      if (! -d $dirName) {      my ($retVal, @values) = @_;
3146          Trace("Creating $dirName directory.") if T(2);      # Loop through the remaining parameters, looking for the highest.
3147          eval { mkpath $dirName; };      for my $value (@values) {
3148          if ($@) {          if ($value > $retVal) {
3149              Confess("Error creating $dirName: $@");              $retVal = $value;
3150          }          }
3151      }      }
3152        # Return the maximum found.
3153        return $retVal;
3154  }  }
3155    
 =head3 ChDir  
3156    
3157  C<< ChDir($dirName); >>  =head3 Strip
3158    
3159        my $string = Tracer::Strip($line);
3160    
3161  Change to the specified directory.  Strip all line terminators off a string. This is necessary when dealing with files
3162    that may have been transferred back and forth several times among different
3163    operating environments.
3164    
3165  =over 4  =over 4
3166    
3167  =item dirName  =item line
3168    
3169  Name of the directory to which we want to change.  Line of text to be stripped.
3170    
3171    =item RETURN
3172    
3173    The same line of text with all the line-ending characters chopped from the end.
3174    
3175  =back  =back
3176    
3177  =cut  =cut
3178    
3179  sub ChDir {  sub Strip {
3180      my ($dirName) = @_;      # Get a copy of the parameter string.
3181      if (! -d $dirName) {      my ($string) = @_;
3182          Confess("Cannot change to directory $dirName: no such directory.");      my $retVal = (defined $string ? $string : "");
3183      } else {      # Strip the line terminator characters.
3184          Trace("Changing to directory $dirName.") if T(4);      $retVal =~ s/(\r|\n)+$//g;
3185          my $okFlag = chdir $dirName;      # Return the result.
3186          if (! $okFlag) {      return $retVal;
             Confess("Error switching to directory $dirName.");  
         }  
     }  
3187  }  }
3188    
3189  =head3 SendSMS  =head3 Pad
3190    
3191  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3192    
3193  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  Pad a string to a specified length. The pad character will be a
3194  user name, password, and API ID for the relevant account in the hash reference variable  space, and the padding will be on the right side unless specified
3195  I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For  in the third parameter.
 example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID  
 is C<2561022>, then the FIG_Config file must contain  
3196    
3197      $phone =  { user => 'BruceTheHumanPet',  =over 4
                 password => 'silly',  
                 api_id => '2561022' };  
3198    
3199  The original purpose of this method was to insure Bruce would be notified immediately when the  =item string
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
3200    
3201  The message ID will be returned if successful, and C<undef> if an error occurs.  String to be padded.
3202    
3203  =over 4  =item len
3204    
3205  =item phoneNumber  Desired length of the padded string.
3206    
3207  Phone number to receive the message, in international format. A United States phone number  =item left (optional)
 would be prefixed by "1". A British phone number would be prefixed by "44".  
3208    
3209  =item msg  TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3210    
3211  Message to send to the specified phone.  =item padChar (optional)
3212    
3213    Character to use for padding. The default is a space.
3214    
3215  =item RETURN  =item RETURN
3216    
3217  Returns the message ID if successful, and C<undef> if the message could not be sent.  Returns a copy of the original string with the pad character added to the
3218    specified end so that it achieves the desired length.
3219    
3220  =back  =back
3221    
3222  =cut  =cut
3223    
3224  sub SendSMS {  sub Pad {
3225      # Get the parameters.      # Get the parameters.
3226      my ($phoneNumber, $msg) = @_;      my ($string, $len, $left, $padChar) = @_;
3227      # Declare the return variable. If we do not change it, C<undef> will be returned.      # Compute the padding character.
3228      my $retVal;      if (! defined $padChar) {
3229      # Only proceed if we have phone support.          $padChar = " ";
3230      if (! defined $FIG_Config::phone) {      }
3231          Trace("Phone support not present in FIG_Config.") if T(1);      # Compute the number of spaces needed.
3232      } else {      my $needed = $len - length $string;
3233          # Get the phone data.      # Copy the string into the return variable.
3234          my $parms = $FIG_Config::phone;      my $retVal = $string;
3235          # Get the Clickatell URL.      # Only proceed if padding is needed.
3236          my $url = "http://api.clickatell.com/http/";      if ($needed > 0) {
3237          # Create the user agent.          # Create the pad string.
3238          my $ua = LWP::UserAgent->new;          my $pad = $padChar x $needed;
3239          # Request a Clickatell session.          # Affix it to the return value.
3240          my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},          if ($left) {
3241                                       password => $parms->{password},              $retVal = $pad . $retVal;
                                      api_id => $parms->{api_id},  
                                      to => $phoneNumber,  
                                      text => $msg});  
         # Check for an error.  
         if (! $resp->is_success) {  
             Trace("Alert failed.") if T(1);  
         } else {  
             # Get the message ID.  
             my $rstring = $resp->content;  
             if ($rstring =~ /^ID:\s+(.*)$/) {  
                 $retVal = $1;  
3242              } else {              } else {
3243                  Trace("Phone attempt failed with $rstring") if T(1);              $retVal .= $pad;
3244              }              }
3245          }          }
3246        # Return the result.
3247        return $retVal;
3248    }
3249    
3250    =head3 EOF
3251    
3252    This is a constant that is lexically greater than any useful string.
3253    
3254    =cut
3255    
3256    sub EOF {
3257        return "\xFF\xFF\xFF\xFF\xFF";
3258    }
3259    
3260    =head3 TICK
3261    
3262        my @results = TICK($commandString);
3263    
3264    Perform a back-tick operation on a command. If this is a Windows environment, any leading
3265    dot-slash (C<./> will be removed. So, for example, if you were doing
3266    
3267        `./protein.cgi`
3268    
3269    from inside a CGI script, it would work fine in Unix, but would issue an error message
3270    in Windows complaining that C<'.'> is not a valid command. If instead you code
3271    
3272        TICK("./protein.cgi")
3273    
3274    it will work correctly in both environments.
3275    
3276    =over 4
3277    
3278    =item commandString
3279    
3280    The command string to pass to the system.
3281    
3282    =item RETURN
3283    
3284    Returns the standard output from the specified command, as a list.
3285    
3286    =back
3287    
3288    =cut
3289    #: Return Type @;
3290    sub TICK {
3291        # Get the parameters.
3292        my ($commandString) = @_;
3293        # Chop off the dot-slash if this is Windows.
3294        if ($FIG_Config::win_mode) {
3295            $commandString =~ s!^\./!!;
3296      }      }
3297      # Return the result.      # Activate the command and return the result.
3298      return $retVal;      return `$commandString`;
3299  }  }
3300    
3301    
3302  =head3 CommaFormat  =head3 CommaFormat
3303    
3304  C<< my $formatted = Tracer::CommaFormat($number); >>      my $formatted = Tracer::CommaFormat($number);
3305    
3306  Insert commas into a number.  Insert commas into a number.
3307    
# Line 2695  Line 3334 
3334      # Return the result.      # Return the result.
3335      return $retVal;      return $retVal;
3336  }  }
 =head3 SetPermissions  
   
 C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  
   
 Set the permissions for a directory and all the files and folders inside it.  
 In addition, the group ownership will be changed to the specified value.  
   
 This method is more vulnerable than most to permission and compatability  
 problems, so it does internal error recovery.  
   
 =over 4  
   
 =item dirName  
   
 Name of the directory to process.  
   
 =item group  
   
 Name of the group to be assigned.  
   
 =item mask  
   
 Permission mask. Bits that are C<1> in this mask will be ORed into the  
 permission bits of any file or directory that does not already have them  
 set to 1.  
   
 =item otherMasks  
3337    
 Map of search patterns to permission masks. If a directory name matches  
 one of the patterns, that directory and all its members and subdirectories  
 will be assigned the new pattern. For example, the following would  
 assign 01664 to most files, but would use 01777 for directories named C<tmp>.  
   
     Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  
   
 The list is ordered, so the following would use 0777 for C<tmp1> and  
 0666 for C<tmp>, C<tmp2>, or C<tmp3>.  
   
     Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  
                                                    '^tmp' => 0666);  
   
 Note that the pattern matches are all case-insensitive, and only directory  
 names are matched, not file names.  
   
 =back  
   
 =cut  
   
 sub SetPermissions {  
     # Get the parameters.  
     my ($dirName, $group, $mask, @otherMasks) = @_;  
     # Set up for error recovery.  
     eval {  
         # Switch to the specified directory.  
         ChDir($dirName);  
         # Get the group ID.  
         my $gid = getgrnam($group);  
         # Get the mask for tracing.  
         my $traceMask = sprintf("%04o", $mask) . "($mask)";  
         Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(2);  
         my $fixCount = 0;  
         my $lookCount = 0;  
         # @dirs will be a stack of directories to be processed.  
         my @dirs = (getcwd());  
         while (scalar(@dirs) > 0) {  
             # Get the current directory.  
             my $dir = pop @dirs;  
             # Check for a match to one of the specified directory names. To do  
             # that, we need to pull the individual part of the name off of the  
             # whole path.  
             my $simpleName = $dir;  
             if ($dir =~ m!/([^/]+)$!) {  
                 $simpleName = $1;  
             }  
             Trace("Simple directory name for $dir is $simpleName.") if T(4);  
             # Search for a match.  
             my $match = 0;  
             my $i;  
             for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {  
                 my $pattern = $otherMasks[$i];  
                 if ($simpleName =~ /$pattern/i) {  
                     $match = 1;  
                 }  
             }  
             # Check for a match. Note we use $i-1 because the loop added 2  
             # before terminating due to the match.  
             if ($match && $otherMasks[$i-1] != $mask) {  
                 # This directory matches one of the incoming patterns, and it's  
                 # a different mask, so we process it recursively with that mask.  
                 SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);  
             } else {  
                 # Here we can process normally. Get all of the non-hidden members.  
                 my @submems = OpenDir($dir, 1);  
                 for my $submem (@submems) {  
                     # Get the full name.  
                     my $thisMem = "$dir/$submem";  
                     Trace("Checking member $thisMem.") if T(4);  
                     $lookCount++;  
                     if ($lookCount % 1000 == 0) {  
                         Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(3);  
                     }  
                     # Fix the group.  
                     chown -1, $gid, $thisMem;  
                     # Insure this member is not a symlink.  
                     if (! -l $thisMem) {  
                         # Get its info.  
                         my $fileInfo = stat $thisMem;  
                         # Only proceed if we got the info. Otherwise, it's a hard link  
                         # and we want to skip it anyway.  
                         if ($fileInfo) {  
                             my $fileMode = $fileInfo->mode;  
                             if (($fileMode & $mask) != $mask) {  
                                 # Fix this member.  
                                 $fileMode |= $mask;  
                                 chmod $fileMode, $thisMem;  
                                 $fixCount++;  
                             }  
                             # If it's a subdirectory, stack it.  
                             if (-d $thisMem) {  
                                 push @dirs, $thisMem;  
                             }  
                         }  
                     }  
                 }  
             }  
         }  
         Trace("$lookCount files and directories processed, $fixCount fixed.") if T(2);  
     };  
     # Check for an error.  
     if ($@) {  
         Confess("SetPermissions error: $@");  
     }  
 }  
3338    
3339  =head3 CompareLists  =head3 CompareLists
3340    
3341  C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3342    
3343  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
3344  are presumed to be sorted alphabetically by the value in the $keyIndex column.  are presumed to be sorted alphabetically by the value in the $keyIndex column.
# Line 2896  Line 3403 
3403      return ($inserted, $deleted);      return ($inserted, $deleted);
3404  }  }
3405    
3406  =head3 GetLine  =head3 GenerateURL
3407    
3408  C<< my @data = Tracer::GetLine($handle); >>      my $queryUrl = Tracer::GenerateURL($page, %parameters);
3409    
3410  Read a line of data from a tab-delimited file.  Generate a GET-style URL for the specified page with the specified parameter
3411    names and values. The values will be URL-escaped automatically. So, for
3412    example
3413    
3414        Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3415    
3416    would return
3417    
3418        form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3419    
3420  =over 4  =over 4
3421    
3422  =item handle  =item page
3423    
3424  Open file handle from which to read.  Page URL.
3425    
3426    =item parameters
3427    
3428    Hash mapping parameter names to parameter values.
3429    
3430  =item RETURN  =item RETURN
3431    
3432  Returns a list of the fields in the record read. The fields are presumed to be  Returns a GET-style URL that goes to the specified page and passes in the
3433  tab-delimited. If we are at the end of the file, then an empty list will be  specified parameters and values.
 returned. If an empty line is read, a single list item consisting of a null