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revision 1.80, Fri Feb 9 22:53:22 2007 UTC revision 1.98, Thu May 1 07:52:10 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);
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 159  Line 160 
160    
161  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
162  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
163  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
164  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
165  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
166  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
167  the tracing in your environment without stepping on other users.  the tracing in your environment without stepping on other users.
# Line 183  Line 184 
184    
185  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
186  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
187  using the L</StandardScript> or L</StandardSetup> methods, emergency tracing  using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
188  will be configured automatically.  will be configured automatically.
189    
 =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.  
   
190  =cut  =cut
191    
192  # Declare the configuration variables.  # Declare the configuration variables.
193    
194  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
195  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
196                              # standard output                              # standard output
197  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
198                              # hash of active category names                              # hash of active category names
199    my @LevelNames = qw(error warn notice info detail);
200  my $TraceLevel = 0;         # trace level; a higher trace level produces more  my $TraceLevel = 0;         # trace level; a higher trace level produces more
201                              # messages                              # messages
202  my @Queue = ();             # queued list of trace messages.  my @Queue = ();             # queued list of trace messages.
203  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
204    my $LastLevel = 0;          # level of the last test call
205  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
206  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
207    
208  =head2 Public Methods  =head2 Tracing Methods
209    
210    =head3 Setups
211    
212        my $count = Tracer::Setups();
213    
214    Return the number of times L</TSetup> has been called.
215    
216    This method allows for the creation of conditional tracing setups where, for example, we
217    may want to set up tracing if nobody else has done it before us.
218    
219    =cut
220    
221    sub Setups {
222        return $SetupCount;
223    }
224    
225  =head3 TSetup  =head3 TSetup
226    
227  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
228    
229  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
230  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 347  Line 274 
274          }          }
275      }      }
276      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
277      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
278      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
279        # the standard output (tee mode).
280      if ($target =~ m/^\+?>>?/) {      if ($target =~ m/^\+?>>?/) {
281          if ($target =~ m/^\+/) {          if ($target =~ m/^\+/) {
282              $TeeFlag = 1;              $TeeFlag = 1;
283              $target = substr($target, 1);              $target = substr($target, 1);
284          }          }
285          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
286                # We need to initialize the file (which clears it).
287              open TRACEFILE, $target;              open TRACEFILE, $target;
288              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
289              close TRACEFILE;              close TRACEFILE;
290                # Set to append mode now that the file has been cleared.
291              $Destination = ">$target";              $Destination = ">$target";
292          } else {          } else {
293              $Destination = $target;              $Destination = $target;
# Line 369  Line 299 
299      $SetupCount++;      $SetupCount++;
300  }  }
301    
302  =head3 StandardSetup  =head3 SetLevel
303    
304  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
305    
306  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.  
307    
308  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.  
309    
310  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  
311    
312      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
313    
314  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.  
315    
316  =over 4  =cut
317    
318  =item SQL  sub SetLevel {
319        $TraceLevel = $_[0];
320    }
321    
322  Traces SQL commands and activity.  =head3 ParseDate
323    
324  =item Tracer      my $time = Tracer::ParseDate($dateString);
325    
326  Traces error messages and call stacks.  Convert a date into a PERL time number. This method expects a date-like string
327    and parses it into a number. The string must be vaguely date-like or it will
328    return an undefined value. Our requirement is that a month and day be
329    present and that three pieces of the date string (time of day, month and day,
330    year) be separated by likely delimiters, such as spaces, commas, and such-like.
331    
332  =back  If a time of day is present, it must be in military time with two digits for
333    everything but the hour.
334    
335  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.  
336    
337      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
338    equally innocuous. This means, however, that a sufficiently long sentence with date-like
339    parts in it may be interpreted as a date. Hopefully this will not be a problem.
340    
341  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  
342    
343  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.  
344    
345      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  =over 4
346    
347  would send the trace output to C<traceBruce.log> in the temporary directory.  =item dateString
348    
349  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.  
350    
351  You can specify a different default trace level by setting C<$options->{trace}>  =item RETURN
 prior to calling this method.  
352    
353  An example at this point would help. Consider, for example, the command-line utility  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
354  C<TransactFeatures>. It accepts a list of positional parameters plus the options  the date string is invalid. A valid date string must contain a month and day.
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
355    
356      my ($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);  
357    
358    =cut
359    
360  The call to C<ParseCommand> specifies the default values for the options and  # Universal month conversion table.
361  stores the actual options in a hash that is returned as C<$options>. The  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
362  positional parameters are returned in C<@parameters>.                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
363                                Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
364                                Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
365                                May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
366                                Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
367                                Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
368                                Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
369                                Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
370                                Oct =>  9, October  =>   9, '10' =>  9,
371                                Nov => 10, November =>  10, '11' => 10,
372                                Dec => 11, December =>  11, '12' => 11
373                            };
374    
375  The following is a sample command line for C<TransactFeatures>.  sub ParseDate {
376        # Get the parameters.
377        my ($dateString) = @_;
378        # Declare the return variable.
379        my $retVal;
380        # Find the month and day of month. There are two ways that can happen. We check for the
381        # numeric style first. That way, if the user's done something like "Sun 12/22", then we
382        # won't be fooled into thinking the month is Sunday.
383        if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
384            my ($mon, $mday) = (MONTHS->{$1}, $2);
385            # Insist that the month and day are valid.
386            if (defined($mon) && $2 >= 1 && $2 <= 31) {
387                # Find the time.
388                my ($hour, $min, $sec) = (0, 0, 0);
389                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
390                    ($hour, $min, $sec) = ($1, $2, $3);
391                }
392                # Find the year.
393                my $year;
394                if ($dateString =~ /\b(\d{4})\b/) {
395                    $year = $1;
396                } else {
397                    # Get the default year, which is this one. Note we must convert it to
398                    # the four-digit value expected by "timelocal".
399                    (undef, undef, undef, undef, undef, $year) = localtime();
400                    $year += 1900;
401                }
402                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
403            }
404        }
405        # Return the result.
406        return $retVal;
407    }
408    
409      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  =head3 LogErrors
410    
411  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional      Tracer::LogErrors($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<$options> hash would be  
412    
413      { trace => 2, sql => 0, safe => 0,  Route the standard error output to a log file.
       noAlias => 1, start => ' ', tblFiles => 0 }  
414    
415  Use of C<StandardSetup> in this way provides a simple way of performing  =over 4
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
416    
417  If the C<background> option is specified on the command line, then the  =item fileName
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
418    
419      -user=Bruce -background  Name of the file to receive the error output.
420    
421  then the trace output would go to C<traceBruce.log>, the standard output to  =back
 C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to  
 simplify starting a command in the background.  
422    
423  The user name is also used as the tracing key for L</Emergency Tracing>.  =cut
 Specifying a value of C<E> for the trace level causes emergency tracing to  
 be used instead of custom tracing. If the user name is not specified,  
 the tracing key is taken from the C<Tracing> environment variable. If there  
 is no value for that variable, the tracing key will be computed from the PID.  
424    
425  Finally, if the special option C<-h> is specified, the option names will  sub LogErrors {
426  be traced at level 0 and the program will exit without processing.      # Get the file name.
427  This provides a limited help capability. For example, if the user enters      my ($fileName) = @_;
428        # Open the file as the standard error output.
429        open STDERR, '>', $fileName;
430    }
431    
432      TransactFeatures -h  =head3 Trace
433    
434  he would see the following output.      Trace($message);
435    
436      TransactFeatures [options] command transactionDirectory IDfile  Write a trace message to the target location specified in L</TSetup>. If there has not been
437          -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  
438    
439  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,  
440    
441      { trace => [0, "tracing level (default 0)"],  =item message
        ...  
442    
443  would set the default trace level to 0 instead of E, while  Message to write.
444    
445      { trace => ["2-", "tracing level (default 2)"],  =back
        ...  
446    
447  would set the default to 2, but trace only to the log file, not to the  =cut
 standard output.  
448    
449  The parameters to this method are as follows.  sub Trace {
450        # Get the parameters.
451        my ($message) = @_;
452        # Strip off any line terminators at the end of the message. We will add
453        # new-line stuff ourselves.
454        my $stripped = Strip($message);
455        # Compute the caller information.
456        my ($callPackage, $callFile, $callLine) = caller();
457        my $callFileTitle = basename($callFile);
458        # Check the caller.
459        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
460        # Get the timestamp.
461        my $timeStamp = Now();
462        # Build the prefix.
463        my $level = $LevelNames[$LastLevel] || "($LastLevel)";
464        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
465        # Format the message.
466        my $formatted = "$prefix $stripped";
467        # Process according to the destination.
468        if ($Destination eq "TEXT") {
469            # Write the message to the standard output.
470            print "$formatted\n";
471        } elsif ($Destination eq "ERROR") {
472            # Write the message to the error output. Here, we want our prefix fields.
473            print STDERR "$formatted\n";
474        } elsif ($Destination eq "WARN") {
475            # Emit the message to the standard error output. It is presumed that the
476            # error logger will add its own prefix fields, the notable exception being
477            # the caller info.
478            print STDERR "$callerInfo$stripped\n";
479        } elsif ($Destination eq "QUEUE") {
480            # Push the message into the queue.
481            push @Queue, "$formatted";
482        } elsif ($Destination eq "HTML") {
483            # Convert the message to HTML and write it to the standard output.
484            my $escapedMessage = CGI::escapeHTML($stripped);
485            print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
486        } elsif ($Destination =~ m/^>>/) {
487            # Write the trace message to an output file.
488            open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
489            print TRACING "$formatted\n";
490            close TRACING;
491            # If the Tee flag is on, echo it to the standard output.
492            if ($TeeFlag) {
493                print "$formatted\n";
494            }
495        }
496    }
497    
498  =over 4  =head3 T
499    
500  =item categories      my $switch = T($category, $traceLevel);
501    
502  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.  
503    
504  =item options      my $switch = T($traceLevel);
505    
506  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
507  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).  
508    
509  =item parmHelp  =over 4
510    
511  A string that vaguely describes the positional parameters. This is used  =item category
 if the user specifies the C<-h> option.  
512    
513  =item argv  Category to which the message belongs. If not specified, the caller's package name is
514    used.
515    
516  List of command line parameters, including the option switches, which must  =item traceLevel
517  precede the positional parameters and be prefixed by a hyphen.  
518    Relevant tracing level.
519    
520  =item RETURN  =item RETURN
521    
522  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.  
523    
524  =back  =back
525    
526  =cut  =cut
527    
528  sub StandardSetup {  sub T {
529        # Declare the return variable.
530        my $retVal = 0;
531        # Only proceed if tracing is turned on.
532        if ($Destination ne "NONE") {
533      # Get the parameters.      # Get the parameters.
534      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
535      # Get the default tracing key.          if (!defined $traceLevel) {
536      my $tkey = EmergencyKey();              # Here we have no category, so we need to get the calling package.
537      # Add the tracing options.              # The calling package is normally the first parameter. If it is
538      if (! exists $options->{trace}) {              # omitted, the first parameter will be the tracelevel. So, the
539          $options->{trace} = ['E', "tracing level (E for emergency tracing)"];              # first thing we do is shift the so-called category into the
540      }              # $traceLevel variable where it belongs.
541      $options->{sql} = [0, "turn on SQL tracing"];              $traceLevel = $category;
542      $options->{h} = [0, "display command-line options"];              my ($package, $fileName, $line) = caller;
543      $options->{user} = [$tkey, "tracing key"];              # If there is no calling package, we default to "main".
544      $options->{background} = [0, "spool standard and error output"];              if (!$package) {
545      # 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";  
546              } else {              } else {
547                  $traceMode = "WARN";                  my @cats = split /::/, $package;
548              }                  $category = $cats[$#cats];
549          }          }
         # Now set up the tracing.  
         TSetup("$traceLevel $cats", $traceMode);  
     }  
     # Check for the "h" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($retOptions->{h}) {  
         $0 =~ m#[/\\](\w+)(\.pl)?$#i;  
         print "$1 [options] $parmHelp\n";  
         for my $key (sort keys %{$options}) {  
             my $name = Pad($key, $longestName, 0, ' ');  
             my $desc = $options->{$key}->[1];  
             if ($options->{$key}->[0]) {  
                 $desc .= " (default " . $options->{$key}->[0] . ")";  
550              }              }
551              print "  $name $desc\n";          # Save the category name and level.
552            $LastCategory = $category;
553            $LastLevel = $traceLevel;
554            # Convert it to lower case before we hash it.
555            $category = lc $category;
556            # Use the category and tracelevel to compute the result.
557            if (ref $traceLevel) {
558                Confess("Bad trace level.");
559            } elsif (ref $TraceLevel) {
560                Confess("Bad trace config.");
561          }          }
562          exit(0);          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
563      }      }
564      # Return the parsed parameters.      # Return the computed result.
565      return ($retOptions, @retParameters);      return $retVal;
566  }  }
567    
568  =head3 Setups  =head3 QTrace
569    
570  C<< my $count = Tracer::Setups(); >>      my $data = QTrace($format);
571    
572  Return the number of times L</TSetup> has been called.  Return the queued trace data in the specified format.
573    
574  This method allows for the creation of conditional tracing setups where, for example, we  =over 4
575  may want to set up tracing if nobody else has done it before us.  
576    =item format
577    
578    C<html> to format the data as an HTML list, C<text> to format it as straight text.
579    
580    =back
581    
582  =cut  =cut
583    
584  sub Setups {  sub QTrace {
585      return $SetupCount;      # Get the parameter.
586        my ($format) = @_;
587        # Create the return variable.
588        my $retVal = "";
589        # Only proceed if there is an actual queue.
590        if (@Queue) {
591            # Process according to the format.
592            if ($format =~ m/^HTML$/i) {
593                # Convert the queue into an HTML list.
594                $retVal = "<ul>\n";
595                for my $line (@Queue) {
596                    my $escapedLine = CGI::escapeHTML($line);
597                    $retVal .= "<li>$escapedLine</li>\n";
598                }
599                $retVal .= "</ul>\n";
600            } elsif ($format =~ m/^TEXT$/i) {
601                # Convert the queue into a list of text lines.
602                $retVal = join("\n", @Queue) . "\n";
603            }
604            # Clear the queue.
605            @Queue = ();
606        }
607        # Return the formatted list.
608        return $retVal;
609  }  }
610    
611  =head3 Open  =head3 Confess
612    
613  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>      Confess($message);
614    
615  Open a file.  Trace the call stack and abort the program with the specified message. When used with
616    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
617    So, for example
618    
619  The I<$fileSpec> is essentially the second argument of the PERL C<open>      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
620    
621      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  Will abort the program with a stack trace if the value of C<$recNum> is negative.
622    
623  would open for output appended to the specified file, and  =over 4
624    
625      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  =item message
626    
627  would open a pipe that sorts the records written and removes duplicates. Note  Message to include in the trace.
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
628    
629      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =back
630    
631  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  =cut
 the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a  
 failed open will throw an exception and the third parameter will be used to construct  
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
632    
633      Could not open "/usr/spool/news/twitlog"  sub Confess {
634        # Get the parameters.
635        my ($message) = @_;
636        # Set up the category and level.
637        $LastCategory = "(confess)";
638        $LastLevel = 0;
639        if (! defined($FIG_Config::no_tool_hdr)) {
640            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
641            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
642            # Only proceed if the tool header file is actually present.
643            if (-f $toolHeaderFile) {
644                my $fh;
645                if (open $fh, "<$toolHeaderFile") {
646                    my @lines = <$fh>;
647                    Trace("Tool header has " . scalar(@lines) . " lines.");
648                }
649            }
650        }
651        # Trace the call stack.
652        Cluck($message);
653        # Abort the program.
654        croak(">>> $message");
655    }
656    
657  Note that the mode characters are automatically cleaned from the file name.  =head3 Assert
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
658    
659      Could not open "/usr/spool/news/twitlog": file not found.      Assert($condition1, $condition2, ... $conditionN);
660    
661  In some versions of PERL the only error message we get is a number, which  Return TRUE if all the conditions are true. This method can be used in conjunction with
662  corresponds to the C++ C<errno> value.  the OR operator and the L</Confess> method as a debugging assert.
663    So, for example
664    
665      Could not open "/usr/spool/news/twitlog": 6.      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
666    
667  =over 4  Will abort the program with a stack trace if the value of C<$recNum> is negative.
668    
669  =item fileHandle  =cut
670    sub Assert {
671        my $retVal = 1;
672        LOOP: for my $condition (@_) {
673            if (! $condition) {
674                $retVal = 0;
675                last LOOP;
676            }
677        }
678        return $retVal;
679    }
680    
681  File handle. If this parameter is C<undef>, a file handle will be generated  =head3 Cluck
 and returned as the value of this method.  
682    
683  =item fileSpec      Cluck($message);
684    
685  File name and mode, as per the PERL C<open> function.  Trace the call stack. Note that for best results, you should qualify the call with a
686    trace condition. For example,
687    
688  =item message (optional)      Cluck("Starting record parse.") if T(3);
689    
690  Error message to use if the open fails. If omitted, a standard error message  will only trace the stack if the trace level for the package is 3 or more.
 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>.  
691    
692  =item RETURN  =over 4
693    
694  Returns the name of the file handle assigned to the file, or C<undef> if the  =item message
695  open failed.  
696    Message to include in the trace.
697    
698  =back  =back
699    
700  =cut  =cut
701    
702  sub Open {  sub Cluck {
703      # Get the parameters.      # Get the parameters.
704      my ($fileHandle, $fileSpec, $message) = @_;      my ($message) = @_;
705      # Attempt to open the file.      # Trace what's happening.
706      my $rv = open $fileHandle, $fileSpec;      Trace("Stack trace for event: $message");
707      # If the open failed, generate an error message.      my $confession = longmess($message);
708      if (! $rv) {      # Convert the confession to a series of trace messages.
709          # Save the system error message.      for my $line (split /\s*\n/, $confession) {
710          my $sysMessage = $!;          # Only proceed if this call trace is for a method outside Tracer itself.
711          # See if we need a default message.          if ($line !~ /Tracer\.pm/) {
712          if (!$message) {              # Replace the leading tab with a series of spaces.
713              # Clean any obvious mode characters and leading spaces from the              $line =~ s/\t/    /;
714              # filename.              # Trace the line.
715              my ($fileName) = FindNamePart($fileSpec);              Trace($line);
             $message = "Could not open \"$fileName\"";  
716          }          }
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
717      }      }
     # Return the file handle.  
     return $fileHandle;  
718  }  }
719    
720  =head3 FindNamePart  =head3 ScriptSetup (deprecated)
   
 C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>  
   
 Extract the portion of a file specification that contains the file name.  
721    
722  A file specification is the string passed to an C<open> call. It specifies the file      my ($cgi, $varHash) = ScriptSetup($noTrace);
 mode and name. In a truly complex situation, it can specify a pipe sequence. This  
 method assumes that the file name is whatever follows the first angle bracket  
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
723    
724      >>/usr/fig/myfile.txt  Perform standard tracing and debugging setup for scripts. The value returned is
725      </usr/fig/myfile.txt  the CGI object followed by a pre-built variable hash. At the end of the script,
726      | sort -u > /usr/fig/myfile.txt  the client should call L</ScriptFinish> to output the web page.
727    
728  If the method cannot find a file name using its normal methods, it will return the  This method calls L</ETracing> to configure tracing, which allows the tracing
729  whole incoming string.  to be configured via the emergency tracing form on the debugging control panel.
730    Tracing will then be turned on automatically for all programs that use the L</ETracing>
731    method, which includes every program that uses this method or L</StandardSetup>.
732    
733  =over 4  =over 4
734    
735  =item fileSpec  =item noTrace (optional)
736    
737  File specification string from which the file name is to be extracted.  If specified, tracing will be suppressed. This is useful if the script wants to set up
738    tracing manually.
739    
740  =item RETURN  =item RETURN
741    
742  Returns a three-element list. The first element contains the file name portion of  Returns a two-element list consisting of a CGI query object and a variable hash for
743  the specified string, or the whole string if a file name cannot be found via normal  the output page.
 methods. The second element contains the start position of the file name portion and  
 the third element contains the length.  
744    
745  =back  =back
746    
747  =cut  =cut
748  #: Return Type $;  
749  sub FindNamePart {  sub ScriptSetup {
750      # Get the parameters.      # Get the parameters.
751      my ($fileSpec) = @_;      my ($noTrace) = @_;
752      # Default to the whole input string.      # Get the CGI query object.
753      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);      my $cgi = CGI->new();
754      # Parse out the file name if we can.      # Set up tracing if it's not suppressed.
755      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {      ETracing($cgi) unless $noTrace;
756          $retVal = $2;      # Create the variable hash.
757          $len = length $retVal;      my $varHash = { results => '' };
758          $pos = (length $fileSpec) - (length $3) - $len;      # Return the query object and variable hash.
759      }      return ($cgi, $varHash);
     # Return the result.  
     return ($retVal, $pos, $len);  
760  }  }
761    
762  =head3 OpenDir  =head3 ETracing
763    
764  C<< my @files = OpenDir($dirName, $filtered, $flag); >>      ETracing($parameter);
765    
766  Open a directory and return all the file names. This function essentially performs  Set up emergency tracing. Emergency tracing is tracing that is turned
767  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  on automatically for any program that calls this method. The emergency
768  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  tracing parameters are stored in a a file identified by a tracing key.
769  or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be  If this method is called with a CGI object, then the tracing key is
770  filtered out of the return list. If the directory does not open and I<$flag> is not  taken from a cookie. If it is called with no parameters, then the tracing
771  set, an exception is thrown. So, for example,  key is taken from an environment variable. If it is called with a string,
772    the tracing key is that string.
773    
774      my @files = OpenDir("/Volumes/fig/contigs", 1);  =over 4
775    
776  is effectively the same as  =item parameter
777    
778      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  A parameter from which the tracing key is computed. If it is a scalar,
779      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  that scalar is used as the tracing key. If it is a CGI object, the
780    tracing key is taken from the C<IP> cookie. If it is omitted, the
781    tracing key is taken from the C<TRACING> environment variable. If it
782    is a CGI object and emergency tracing is not on, the C<Trace> and
783    C<TF> parameters will be used to determine the type of tracing.
784    
785  Similarly, the following code  =back
786    
787      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  =cut
788    
789  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  sub ETracing {
790  automatically returns an empty list if the directory fails to open.      # Get the parameter.
791        my ($parameter) = @_;
792        # Check for CGI mode.
793        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
794        # Default to no tracing except errors.
795        my ($tracing, $dest) = ("0", "WARN");
796        # Check for emergency tracing.
797        my $tkey = EmergencyKey($parameter);
798        my $emergencyFile = EmergencyFileName($tkey);
799        if (-e $emergencyFile) {
800            # We have the file. Read in the data.
801            my @tracing = GetFile($emergencyFile);
802            # Pull off the time limit.
803            my $expire = shift @tracing;
804            # Convert it to seconds.
805            $expire *= 3600;
806            # Check the file data.
807            my $stat = stat($emergencyFile);
808            my ($now) = gettimeofday;
809            if ($now - $stat->mtime > $expire) {
810                # Delete the expired file.
811                unlink $emergencyFile;
812            } else {
813                # Emergency tracing is on. Pull off the destination and
814                # the trace level;
815                $dest = shift @tracing;
816                my $level = shift @tracing;
817                # Convert the destination to a real tracing destination.
818                # temp directory.
819                $dest = EmergencyTracingDest($tkey, $dest);
820                # Insure Tracer is specified.
821                my %moduleHash = map { $_ => 1 } @tracing;
822                $moduleHash{Tracer} = 1;
823                # Set the trace parameter.
824                $tracing = join(" ", $level, sort keys %moduleHash);
825            }
826        } elsif (defined $cgi) {
827            # There's no emergency tracing, but we have a CGI object, so check
828            # for tracing from the form parameters.
829            if ($cgi->param('Trace')) {
830                # Here the user has requested tracing via a form.
831                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
832                $tracing = $cgi->param('Trace') . " Tracer";
833            }
834        }
835        # Setup the tracing we've determined from all the stuff above.
836        TSetup($tracing, $dest);
837        # Check to see if we're a web script.
838        if (defined $cgi) {
839            # Yes we are. Trace the form and environment data.
840            TraceParms($cgi);
841            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
842            # emitted by the script in its raw form.
843            if (T(Raw => 3)) {
844                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
845            }
846        }
847    }
848    
849  =over 4  =head3 EmergencyFileName
850    
851  =item dirName      my $fileName = Tracer::EmergencyFileName($tkey);
852    
853  Name of the directory to open.  Return the emergency tracing file name. This is the file that specifies
854    the tracing information.
855    
856  =item filtered  =over 4
857    
858  TRUE if files whose names begin with a period (C<.>) should be automatically removed  =item tkey
 from the list, else FALSE.  
859    
860  =item flag  Tracing key for the current program.
861    
862  TRUE if a failure to open is okay, else FALSE  =item RETURN
863    
864    Returns the name of the file to contain the emergency tracing information.
865    
866  =back  =back
867    
868  =cut  =cut
869  #: Return Type @;  
870  sub OpenDir {  sub EmergencyFileName {
871      # Get the parameters.      # Get the parameters.
872      my ($dirName, $filtered, $flag) = @_;      my ($tkey) = @_;
873      # Declare the return variable.      # Compute the emergency tracing file name.
874      my @retVal = ();      return "$FIG_Config::temp/Emergency$tkey.txt";
     # Open the directory.  
     if (opendir(my $dirHandle, $dirName)) {  
         # The directory opened successfully. Get the appropriate list according to the  
         # strictures of the filter parameter.  
         if ($filtered) {  
             @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;  
         } else {  
             @retVal = readdir $dirHandle;  
         }  
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
     }  
     # Return the result.  
     return @retVal;  
875  }  }
876    
877  =head3 SetLevel  =head3 EmergencyFileTarget
878    
879  C<< Tracer::SetLevel($newLevel); >>      my $fileName = Tracer::EmergencyFileTarget($tkey);
880    
881  Modify the trace level. A higher trace level will cause more messages to appear.  Return the emergency tracing target file name. This is the file that receives
882    the tracing output for file-based tracing.
883    
884  =over 4  =over 4
885    
886  =item newLevel  =item tkey
   
 Proposed new trace level.  
   
 =back  
   
 =cut  
887    
888  sub SetLevel {  Tracing key for the current program.
     $TraceLevel = $_[0];  
 }  
889    
890  =head3 Now  =item RETURN
891    
892  C<< my $string = Tracer::Now(); >>  Returns the name of the file to contain the trace output.
893    
894  Return a displayable time stamp containing the local time.  =back
895    
896  =cut  =cut
897    
898  sub Now {  sub EmergencyFileTarget {
899      my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);      # Get the parameters.
900      my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .      my ($tkey) = @_;
901                   _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);      # Compute the emergency tracing file name.
902      return $retVal;      return "$FIG_Config::temp/trace$tkey.log";
 }  
   
 # Pad a number to 2 digits.  
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
903  }  }
904    
905  =head3 ParseTraceDate  =head3 EmergencyTracingDest
906    
907  C<< my $time = Tracer::ParseTraceDate($dateString); >>      my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
908    
909  Convert a date from the trace file into a PERL timestamp.  This method converts an emergency tracing destination to a real
910    tracing destination. The main difference is that if the
911    destination is C<FILE> or C<APPEND>, we convert it to file
912    output. If the destination is C<DUAL>, we convert it to file
913    and standard output.
914    
915  =over 4  =over 4
916    
917  =item dateString  =item tkey
918    
919    Tracing key for this environment.
920    
921  The date string from the trace file. The format of the string is determined by the  =item myDest
922  L</Now> method.  
923    Destination from the emergency tracing file.
924    
925  =item RETURN  =item RETURN
926    
927  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if  Returns a destination that can be passed into L</TSetup>.
 the time string is invalid.  
928    
929  =back  =back
930    
931  =cut  =cut
932    
933  sub ParseTraceDate {  sub EmergencyTracingDest {
934      # Get the parameters.      # Get the parameters.
935      my ($dateString) = @_;      my ($tkey, $myDest) = @_;
936      # Declare the return variable.      # Declare the return variable.
937      my $retVal;      my $retVal = $myDest;
938      # Parse the date.      # Process according to the destination value.
939      if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {      if ($myDest eq 'FILE') {
940          # Create a time object. Note we need to convert the day, month,          $retVal = ">" . EmergencyFileTarget($tkey);
941          # and year to a different base. Years count from 1900, and      } elsif ($myDest eq 'APPEND') {
942          # the internal month value is relocated to January = 0.          $retVal = ">>" . EmergencyFileTarget($tkey);
943          $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);      } elsif ($myDest eq 'DUAL') {
944            $retVal = "+>" . EmergencyFileTarget($tkey);
945        } elsif ($myDest eq 'WARN') {
946            $retVal = "WARN";
947      }      }
948      # Return the result.      # Return the result.
949      return $retVal;      return $retVal;
950  }  }
951    
952  =head3 LogErrors  =head3 Emergency
953    
954  C<< Tracer::LogErrors($fileName); >>      Emergency($key, $hours, $dest, $level, @modules);
955    
956  Route the standard error output to a log file.  Turn on emergency tracing. This method is normally invoked over the web from
957    a debugging console, but it can also be called by the C<trace.pl> script.
958    The caller specifies the duration of the emergency in hours, the desired tracing
959    destination, the trace level, and a list of the trace modules to activate.
960    For the length of the duration, when a program in an environment with the
961    specified tracing key active invokes a Sprout CGI script, tracing will be
962    turned on automatically. See L</TSetup> for more about tracing setup and
963    L</ETracing> for more about emergency tracing.
964    
965  =over 4  =over 4
966    
967  =item fileName  =item tkey
   
 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;  
 }  
   
 =head3 ReadOptions  
968    
969  C<< my %options = Tracer::ReadOptions($fileName); >>  The tracing key. This is used to identify the control file and the trace file.
970    
971  Read a set of options from a file. Each option is encoded in a line of text that has the  =item hours
 format  
972    
973  I<optionName>C<=>I<optionValue>C<; >I<comment>  Number of hours to keep emergency tracing alive.
974    
975  The option name must consist entirely of letters, digits, and the punctuation characters  =item dest
 C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  
 character is a semi-colon will be ignored. The return hash will map each option name to  
 the corresponding option value.  
976    
977  =over 4  Tracing destination. If no path information is specified for a file
978    destination, it is put in the FIG temporary directory.
979    
980  =item fileName  =item level
981    
982  Name of the file containing the option data.  Tracing level. A higher level means more trace messages.
983    
984  =item RETURN  =item modules
985    
986  Returns a hash mapping the option names specified in the file to their corresponding option  A list of the tracing modules to activate.
 value.  
987    
988  =back  =back
989    
990  =cut  =cut
991    
992  sub ReadOptions {  sub Emergency {
993      # Get the parameters.      # Get the parameters.
994      my ($fileName) = @_;      my ($tkey, $hours, $dest, $level, @modules) = @_;
995      # Open the file.      # Create the emergency file.
996      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");      my $specFile = EmergencyFileName($tkey);
997      # Count the number of records read.      my $outHandle = Open(undef, ">$specFile");
998      my ($records, $comments) = 0;      print $outHandle join("\n", $hours, $dest, $level, @modules, "");
     # Create the return hash.  
     my %retVal = ();  
     # Loop through the file, accumulating key-value pairs.  
     while (my $line = <CONFIGFILE>) {  
         # Denote we've read a line.  
         $records++;  
         # Determine the line type.  
         if ($line =~ /^\s*[\n\r]/) {  
             # A blank line is a comment.  
             $comments++;  
         } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {  
             # Here we have an option assignment.  
             retVal{$1} = $2;  
         } elsif ($line =~ /^\s*;/) {  
             # Here we have a text comment.  
             $comments++;  
         } else {  
             # Here we have an invalid line.  
             Trace("Invalid option statement in record $records.") if T(0);  
         }  
     }  
     # Return the hash created.  
     return %retVal;  
999  }  }
1000    
1001  =head3 GetOptions  =head3 EmergencyKey
   
 C<< Tracer::GetOptions(\%defaults, \%options); >>  
   
 Merge a specified set of options into a table of defaults. This method takes two hash references  
 as input and uses the data from the second to update the first. If the second does not exist,  
 there will be no effect. An error will be thrown if one of the entries in the second hash does not  
 exist in the first.  
   
 Consider the following example.  
   
 C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  
   
 In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  
 B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  
 B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and  
 the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  
 will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  
1002    
1003  C<< {databaseType => 'Oracle'} >>      my $tkey = EmergencyKey($parameter);
1004    
1005  an error will occur because the B<databaseType> option does not exist.  Return the Key to be used for emergency tracing. This could be an IP address,
1006     a session ID, or a user name, depending on the environment.
1007    
1008  =over 4  =over 4
1009    
1010  =item defaults  =item parameter
   
 Table of default option values.  
   
 =item options  
1011    
1012  Table of overrides, if any.  Parameter defining the method for finding the tracing key. If it is a scalar,
1013    then it is presumed to be the tracing key itself. If it is a CGI object, then
1014    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1015    taken from the C<TRACING> environment variable.
1016    
1017  =item RETURN  =item RETURN
1018    
1019  Returns a reference to the default table passed in as the first parameter.  Returns the key to be used for labels in emergency tracing.
1020    
1021  =back  =back
1022    
1023  =cut  =cut
1024    
1025  sub GetOptions {  sub EmergencyKey {
1026      # Get the parameters.      # Get the parameters.
1027      my ($defaults, $options) = @_;      my ($parameter) = @_;
1028      # Check for overrides.      # Declare the return variable.
1029      if ($options) {      my $retVal;
1030          # Loop through the overrides.      # Determine the parameter type.
1031          while (my ($option, $setting) = each %{$options}) {      if (! defined $parameter) {
1032              # Insure this override exists.          # Here we're supposed to check the environment.
1033              if (!exists $defaults->{$option}) {          $retVal = $ENV{TRACING};
                 croak "Unrecognized option $option encountered.";  
1034              } else {              } else {
1035                  # Apply the override.          my $ptype = ref $parameter;
1036                  $defaults->{$option} = $setting;          if ($ptype eq 'CGI') {
1037                # Here we were invoked from a web page. Look for a cookie.
1038                $retVal = $parameter->cookie('IP');
1039            } elsif (! $ptype) {
1040                # Here the key was passed in.
1041                $retVal = $parameter;
1042              }              }
1043          }          }
1044        # If no luck finding a key, use the PID.
1045        if (! defined $retVal) {
1046            $retVal = $$;
1047      }      }
1048      # Return the merged table.      # Return the result.
1049      return $defaults;      return $retVal;
1050  }  }
1051    
 =head3 MergeOptions  
   
 C<< Tracer::MergeOptions(\%table, \%defaults); >>  
1052    
1053  Merge default values into a hash table. This method looks at the key-value pairs in the  =head3 TraceParms
 second (default) hash, and if a matching key is not found in the first hash, the default  
 pair is copied in. The process is similar to L</GetOptions>, but there is no error-  
 checking and no return value.  
1054    
1055  =over 4      Tracer::TraceParms($cgi);
1056    
1057  =item table  Trace the CGI parameters at trace level CGI => 3 and the environment variables
1058    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1059    
1060  Hash table to be updated with the default values.  =over 4
1061    
1062  =item defaults  =item cgi
1063    
1064  Default values to be merged into the first hash table if they are not already present.  CGI query object containing the parameters to trace.
1065    
1066  =back  =back
1067    
1068  =cut  =cut
1069    
1070  sub MergeOptions {  sub TraceParms {
1071      # Get the parameters.      # Get the parameters.
1072      my ($table, $defaults) = @_;      my ($cgi) = @_;
1073      # Loop through the defaults.      if (T(CGI => 2)) {
1074      while (my ($key, $value) = each %{$defaults}) {          # Here we trace the GET-style URL for the script.
1075          if (!exists $table->{$key}) {          Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1076              $table->{$key} = $value;      }
1077        if (T(CGI => 3)) {
1078            # Here we want to trace the parameter data.
1079            my @names = $cgi->param;
1080            for my $parmName (sort @names) {
1081                # Note we skip the Trace parameters, which are for our use only.
1082                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1083                    my @values = $cgi->param($parmName);
1084                    Trace("[CGI] $parmName = " . join(", ", @values));
1085                }
1086            }
1087            # Display the request method.
1088            my $method = $cgi->request_method();
1089            Trace("Method: $method");
1090        }
1091        if (T(CGI => 4)) {
1092            # Here we want the environment data too.
1093            for my $envName (sort keys %ENV) {
1094                Trace("[ENV] $envName = $ENV{$envName}");
1095          }          }
1096      }      }
1097  }  }
1098    
1099  =head3 Trace  =head3 TraceImages
1100    
1101  C<< Trace($message); >>      Tracer::TraceImages($htmlString);
1102    
1103  Write a trace message to the target location specified in L</TSetup>. If there has not been  Trace information about all of an html document's images. The tracing
1104  any prior call to B<TSetup>.  will be for type "IMG" at level 3. The image's source string
1105    will be displayed. This is generally either the URL of the image or
1106    raw data for the image itself. If the source is too long, only the first 300
1107    characters will be shown at trace level 3. The entire source will be shown,
1108    however, at trace level 4. This method is not very smart, and might catch
1109    Javascript code, but it is still useful when debugging the arcane
1110    behavior of images in multiple browser environments.
1111    
1112  =over 4  =over 4
1113    
1114  =item message  =item htmlString
1115    
1116  Message to write.  HTML text for an outgoing web page.
1117    
1118  =back  =back
1119    
1120  =cut  =cut
1121    
1122  sub Trace {  sub TraceImages {
1123      # Get the parameters.      # Only proceed if we're at the proper trace level.
1124      my ($message) = @_;      if (T(IMG => 3)) {
1125      # Get the timestamp.          # For performance reasons we're manipulating $_[0] instead of retrieving the string
1126      my $timeStamp = Now();          # into a variable called "$htmlString". This is because we expect html strings to be
1127      # Format the message. Note we strip off any line terminators at the end.          # long, and don't want to copy them any more than we have to.
1128      my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);          Trace(length($_[0]) . " characters in web page.");
1129      # Process according to the destination.          # Loop through the HTML, culling image tags.
1130      if ($Destination eq "TEXT") {          while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1131          # Write the message to the standard output.              # Extract the source string and determine whether or not it's too long.
1132          print "$formatted\n";              my $srcString = $1;
1133      } elsif ($Destination eq "ERROR") {              my $pos = pos($_[0]) - length($srcString);
1134          # Write the message to the error output.              my $excess = length($srcString) - 300;
1135          print STDERR "$formatted\n";              # We'll put the display string in here.
1136      } elsif ($Destination eq "QUEUE") {              my $srcDisplay = $srcString;
1137          # Push the message into the queue.              # If it's a data string, split it at the comma.
1138          push @Queue, "$formatted";              $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1139      } elsif ($Destination eq "HTML") {              # If there's no excess or we're at trace level 4, we're done. At level 3 with
1140          # Convert the message to HTML and write it to the standard output.              # a long string, however, we only show the first 300 characters.
1141          my $escapedMessage = CGI::escapeHTML($message);              if ($excess > 0 && ! T(IMG => 4)) {
1142          print "<p>$formatted</p>\n";                  $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1143      } elsif ($Destination eq "WARN") {              }
1144         # Emit the message as a warning.              # Output the trace message.
1145         warn $message;              Trace("Image tag at position $pos:\n$srcDisplay");
     } elsif ($Destination =~ m/^>>/) {  
         # Write the trace message to an output file.  
         (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";  
         print TRACING "$formatted\n";  
         close TRACING;  
         # If the Tee flag is on, echo it to the standard output.  
         if ($TeeFlag) {  
             print "$formatted\n";  
1146          }          }
1147      }      }
1148  }  }
1149    
 =head3 T  
   
 C<< my $switch = T($category, $traceLevel); >>  
1150    
1151      or  =head3 ScriptFinish (deprecated)
1152    
1153  C<< my $switch = T($traceLevel); >>      ScriptFinish($webData, $varHash);
1154    
1155  Return TRUE if the trace level is at or above a specified value and the specified category  Output a web page at the end of a script. Either the string to be output or the
1156  is active, else FALSE. If no category is specified, the caller's package name is used.  name of a template file can be specified. If the second parameter is omitted,
1157    it is assumed we have a string to be output; otherwise, it is assumed we have the
1158    name of a template file. The template should have the variable C<DebugData>
1159    specified in any form that invokes a standard script. If debugging mode is turned
1160    on, a form field will be put in that allows the user to enter tracing data.
1161    Trace messages will be placed immediately before the terminal C<BODY> tag in
1162    the output, formatted as a list.
1163    
1164  =over 4  A typical standard script would loook like the following.
1165    
1166  =item category      BEGIN {
1167            # Print the HTML header.
1168            print "CONTENT-TYPE: text/html\n\n";
1169        }
1170        use Tracer;
1171        use CGI;
1172        use FIG;
1173        # ... more uses ...
1174    
1175  Category to which the message belongs. If not specified, the caller's package name is      my ($cgi, $varHash) = ScriptSetup();
1176  used.      eval {
1177            # ... get data from $cgi, put it in $varHash ...
1178        };
1179        if ($@) {
1180            Trace("Script Error: $@") if T(0);
1181        }
1182        ScriptFinish("Html/MyTemplate.html", $varHash);
1183    
1184  =item traceLevel  The idea here is that even if the script fails, you'll see trace messages and
1185    useful output.
1186    
1187  Relevant tracing level.  =over 4
1188    
1189  =item RETURN  =item webData
1190    
1191  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  A string containing either the full web page to be written to the output or the
1192    name of a template file from which the page is to be constructed. If the name
1193    of a template file is specified, then the second parameter must be present;
1194    otherwise, it must be absent.
1195    
1196    =item varHash (optional)
1197    
1198    If specified, then a reference to a hash mapping variable names for a template
1199    to their values. The template file will be read into memory, and variable markers
1200    will be replaced by data in this hash reference.
1201    
1202  =back  =back
1203    
1204  =cut  =cut
1205    
1206  sub T {  sub ScriptFinish {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
1207          # Get the parameters.          # Get the parameters.
1208          my ($category, $traceLevel) = @_;      my ($webData, $varHash) = @_;
1209          if (!defined $traceLevel) {      # Check for a template file situation.
1210              # Here we have no category, so we need to get the calling package.      my $outputString;
1211              # The calling package is normally the first parameter. If it is      if (defined $varHash) {
1212              # omitted, the first parameter will be the tracelevel. So, the          # Here we have a template file. We need to determine the template type.
1213              # first thing we do is shift the so-called category into the          my $template;
1214              # $traceLevel variable where it belongs.          if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1215              $traceLevel = $category;              $template = "$FIG_Config::template_url/$webData";
             my ($package, $fileName, $line) = caller;  
             # If there is no calling package, we default to "main".  
             if (!$package) {  
                 $category = "main";  
1216              } else {              } else {
1217                  $category = $package;              $template = "<<$webData";
1218              }              }
1219            $outputString = PageBuilder::Build($template, $varHash, "Html");
1220        } else {
1221            # Here the user gave us a raw string.
1222            $outputString = $webData;
1223          }          }
1224          # Save the category name.      # Check for trace messages.
1225          $LastCategory = $category;      if ($Destination ne "NONE" && $TraceLevel > 0) {
1226          # Convert it to lower case before we hash it.          # We have trace messages, so we want to put them at the end of the body. This
1227          $category = lc $category;          # is either at the end of the whole string or at the beginning of the BODY
1228          # Use the category and tracelevel to compute the result.          # end-tag.
1229          if (ref $traceLevel) {          my $pos = length $outputString;
1230              Confess("Bad trace level.");          if ($outputString =~ m#</body>#gi) {
1231          } elsif (ref $TraceLevel) {              $pos = (pos $outputString) - 7;
             Confess("Bad trace config.");  
1232          }          }
1233          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));          # If the trace messages were queued, we unroll them. Otherwise, we display the
1234            # destination.
1235            my $traceHtml;
1236            if ($Destination eq "QUEUE") {
1237                $traceHtml = QTrace('Html');
1238            } elsif ($Destination =~ /^>>(.+)$/) {
1239                # Here the tracing output it to a file. We code it as a hyperlink so the user
1240                # can copy the file name into the clipboard easily.
1241                my $actualDest = $1;
1242                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1243            } else {
1244                # Here we have one of the special destinations.
1245                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1246      }      }
1247      # Return the computed result.          substr $outputString, $pos, 0, $traceHtml;
1248      return $retVal;      }
1249        # Write the output string.
1250        print $outputString;
1251  }  }
1252    
1253  =head3 ParseCommand  =head2 Command-Line Utility Methods
   
 C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  
   
 Parse a command line consisting of a list of parameters. The initial parameters may be option  
 specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  
 off and merged into a table of default options. The remainder of the command line is  
 returned as a list of positional arguments. For example, consider the following invocation.  
   
 C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  
1254    
1255  In this case, the list @words will be treated as a command line. There are two options available,  =head3 SendSMS
 B<errors> and B<logFile>. If @words has the following format  
   
 C<< -logFile=error.log apple orange rutabaga >>  
1256    
1257  then at the end of the invocation, C<$options> will be      my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1258    
1259  C<< { errors => 0, logFile => 'error.log' } >>  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1260    user name, password, and API ID for the relevant account in the hash reference variable
1261    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1262    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1263    is C<2561022>, then the FIG_Config file must contain
1264    
1265  and C<@arguments> will contain      $phone =  { user => 'BruceTheHumanPet',
1266                    password => 'silly',
1267                    api_id => '2561022' };
1268    
1269  C<< apple orange rutabaga >>  The original purpose of this method was to insure Bruce would be notified immediately when the
1270    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1271    when you call this method.
1272    
1273  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The message ID will be returned if successful, and C<undef> if an error occurs.
 support for quote characters.  
1274    
1275  =over 4  =over 4
1276    
1277  =item optionTable  =item phoneNumber
1278    
1279  Table of default options.  Phone number to receive the message, in international format. A United States phone number
1280    would be prefixed by "1". A British phone number would be prefixed by "44".
1281    
1282  =item inputList  =item msg
1283    
1284  List of words on the command line.  Message to send to the specified phone.
1285    
1286  =item RETURN  =item RETURN
1287    
1288  Returns a reference to the option table and a list of the positional arguments.  Returns the message ID if successful, and C<undef> if the message could not be sent.
1289    
1290  =back  =back
1291    
1292  =cut  =cut
1293    
1294  sub ParseCommand {  sub SendSMS {
1295      # Get the parameters.      # Get the parameters.
1296      my ($optionTable, @inputList) = @_;      my ($phoneNumber, $msg) = @_;
1297      # Process any options in the input list.      # Declare the return variable. If we do not change it, C<undef> will be returned.
1298      my %overrides = ();      my $retVal;
1299      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      # Only proceed if we have phone support.
1300          # Get the current option.      if (! defined $FIG_Config::phone) {
1301          my $arg = shift @inputList;          Trace("Phone support not present in FIG_Config.") if T(1);
         # Pull out the option name.  
         $arg =~ /^-([^=]*)/g;  
         my $name = $1;  
         # Check for an option value.  
         if ($arg =~ /\G=(.*)$/g) {  
             # Here we have a value for the option.  
             $overrides{$name} = UnEscape($1);  
1302          } else {          } else {
1303              # Here there is no value, so we use 1.          # Get the phone data.
1304              $overrides{$name} = 1;          my $parms = $FIG_Config::phone;
1305            # Get the Clickatell URL.
1306            my $url = "http://api.clickatell.com/http/";
1307            # Create the user agent.
1308            my $ua = LWP::UserAgent->new;
1309            # Request a Clickatell session.
1310            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1311                                         password => $parms->{password},
1312                                         api_id => $parms->{api_id},
1313                                         to => $phoneNumber,
1314                                         text => $msg});
1315            # Check for an error.
1316            if (! $resp->is_success) {
1317                Trace("Alert failed.") if T(1);
1318            } else {
1319                # Get the message ID.
1320                my $rstring = $resp->content;
1321                if ($rstring =~ /^ID:\s+(.*)$/) {
1322                    $retVal = $1;
1323                } else {
1324                    Trace("Phone attempt failed with $rstring") if T(1);
1325          }          }
1326      }      }
     # Merge the options into the defaults.  
     GetOptions($optionTable, \%overrides);  
     # Translate the remaining parameters.  
     my @retVal = ();  
     for my $inputParm (@inputList) {  
         push @retVal, UnEscape($inputParm);  
1327      }      }
1328      # Return the results.      # Return the result.
1329      return ($optionTable, @retVal);      return $retVal;
1330  }  }
1331    
1332  =head3 Escape  =head3 StandardSetup
1333    
1334  C<< my $codedString = Tracer::Escape($realString); >>      my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1335    
1336  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  This method performs standard command-line parsing and tracing setup. The return
1337  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  values are a hash of the command-line options and a list of the positional
1338  result is to reverse the effect of L</UnEscape>.  parameters. Tracing is automatically set up and the command-line options are
1339    validated.
1340    
1341    This is a complex method that does a lot of grunt work. The parameters can
1342    be more easily understood, however, once they are examined individually.
1343    
1344    The I<categories> parameter is the most obtuse. It is a reference to a list of
1345    special-purpose tracing categories. Most tracing categories are PERL package
1346    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1347    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1348    
1349        ["Sprout", "SproutLoad", "ERDB"]
1350    
1351    This would cause trace messages in the specified three packages to appear in
1352    the output. There are two special tracing categories that are automatically
1353    handled by this method. In other words, if you used L</TSetup> you would need
1354    to include these categories manually, but if you use this method they are turned
1355    on automatically.
1356    
1357  =over 4  =over 4
1358    
1359  =item realString  =item SQL
1360    
1361  String to escape.  Traces SQL commands and activity.
1362    
1363    =item Tracer
1364    
1365    Traces error messages and call stacks.
1366    
1367    =back
1368    
1369    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1370    The trace level is specified using the C<-trace> command-line option. For example,
1371    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1372    all tracing at level 3.
1373    
1374        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1375    
1376    Standard tracing is output to the standard output and echoed to the file
1377    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1378    process ID. You can also specify the C<user> parameter to put a user ID
1379    instead of a process ID in the trace file name. So, for example
1380    
1381    The default trace level is 2. To get all messages, specify a trace level of 4.
1382    For a genome-by-genome update, use 3.
1383    
1384        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1385    
1386    would send the trace output to C<traceBruce.log> in the temporary directory.
1387    
1388    The I<options> parameter is a reference to a hash containing the command-line
1389    options, their default values, and an explanation of what they mean. Command-line
1390    options may be in the form of switches or keywords. In the case of a switch, the
1391    option value is 1 if it is specified and 0 if it is not specified. In the case
1392    of a keyword, the value is separated from the option name by an equal sign. You
1393    can see this last in the command-line example above.
1394    
1395    You can specify a different default trace level by setting C<$options->{trace}>
1396    prior to calling this method.
1397    
1398    An example at this point would help. Consider, for example, the command-line utility
1399    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1400    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1401    the following code.
1402    
1403        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1404                            { safe => [0, "use database transactions"],
1405                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1406                              start => [' ', "start with this genome"],
1407                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1408                            "<command> <transactionDirectory> <IDfile>",
1409                          @ARGV);
1410    
1411    
1412    The call to C<ParseCommand> specifies the default values for the options and
1413    stores the actual options in a hash that is returned as C<$options>. The
1414    positional parameters are returned in C<@parameters>.
1415    
1416    The following is a sample command line for C<TransactFeatures>.
1417    
1418        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1419    
1420    Single and double hyphens are equivalent. So, you could also code the
1421    above command as
1422    
1423        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1424    
1425    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1426    parameters, and would find themselves in I<@parameters> after executing the
1427    above code fragment. The tracing would be set to level 2, and the categories
1428    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1429    and C<DocUtils> was included because it came in within the first parameter
1430    to this method. The I<$options> hash would be
1431    
1432        { trace => 2, sql => 0, safe => 0,
1433          noAlias => 1, start => ' ', tblFiles => 0 }
1434    
1435    Use of C<StandardSetup> in this way provides a simple way of performing
1436    standard tracing setup and command-line parsing. Note that the caller is
1437    not even aware of the command-line switches C<-trace> and C<-sql>, which
1438    are used by this method to control the tracing. If additional tracing features
1439    need to be added in the future, they can be processed by this method without
1440    upsetting the command-line utilities.
1441    
1442    If the C<background> option is specified on the command line, then the
1443    standard and error outputs will be directed to files in the temporary
1444    directory, using the same suffix as the trace file. So, if the command
1445    line specified
1446    
1447        -user=Bruce -background
1448    
1449    then the trace output would go to C<traceBruce.log>, the standard output to
1450    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1451    simplify starting a command in the background.
1452    
1453    The user name is also used as the tracing key for L</Emergency Tracing>.
1454    Specifying a value of C<E> for the trace level causes emergency tracing to
1455    be used instead of custom tracing. If the user name is not specified,
1456    the tracing key is taken from the C<Tracing> environment variable. If there
1457    is no value for that variable, the tracing key will be computed from the PID.
1458    
1459    Finally, if the special option C<-help> is specified, the option
1460    names will be traced at level 0 and the program will exit without processing.
1461    This provides a limited help capability. For example, if the user enters
1462    
1463        TransactFeatures -help
1464    
1465    he would see the following output.
1466    
1467        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1468            -trace    tracing level (default E)
1469            -sql      trace SQL commands
1470            -safe     use database transactions
1471            -noAlias  do not expect aliases in CHANGE transactions
1472            -start    start with this genome
1473            -tblFiles output TBL files containing the corrected IDs
1474    
1475    The caller has the option of modifying the tracing scheme by placing a value
1476    for C<trace> in the incoming options hash. The default value can be overridden,
1477    or the tracing to the standard output can be turned off by suffixing a minus
1478    sign to the trace level. So, for example,
1479    
1480        { trace => [0, "tracing level (default 0)"],
1481           ...
1482    
1483    would set the default trace level to 0 instead of E, while
1484    
1485        { trace => ["2-", "tracing level (default 2)"],
1486           ...
1487    
1488    would set the default to 2, but trace only to the log file, not to the
1489    standard output.
1490    
1491    The parameters to this method are as follows.
1492    
1493    =over 4
1494    
1495    =item categories
1496    
1497    Reference to a list of tracing category names. These should be names of
1498    packages whose internal workings will need to be debugged to get the
1499    command working.
1500    
1501    =item options
1502    
1503    Reference to a hash containing the legal options for the current command mapped
1504    to their default values and descriptions. The user can override the defaults
1505    by specifying the options as command-line switches prefixed by a hyphen.
1506    Tracing-related options may be added to this hash. If the C<-h> option is
1507    specified on the command line, the option descriptions will be used to
1508    explain the options. To turn off tracing to the standard output, add a
1509    minus sign to the value for C<trace> (see above).
1510    
1511    =item parmHelp
1512    
1513    A string that vaguely describes the positional parameters. This is used
1514    if the user specifies the C<-h> option.
1515    
1516    =item argv
1517    
1518    List of command line parameters, including the option switches, which must
1519    precede the positional parameters and be prefixed by a hyphen.
1520    
1521  =item RETURN  =item RETURN
1522    
1523  Escaped equivalent of the real string.  Returns a list. The first element of the list is the reference to a hash that
1524    maps the command-line option switches to their values. These will either be the
1525    default values or overrides specified on the command line. The remaining
1526    elements of the list are the position parameters, in order.
1527    
1528  =back  =back
1529    
1530  =cut  =cut
1531    
1532  sub Escape {  sub StandardSetup {
1533      # Get the parameter.      # Get the parameters.
1534      my ($realString) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
1535      # Initialize the return variable.      # Get the default tracing key.
1536      my $retVal = "";      my $tkey = EmergencyKey();
1537      # Loop through the parameter string, looking for sequences to escape.      # Add the tracing options.
1538      while (length $realString > 0) {      if (! exists $options->{trace}) {
1539          # Look for the first sequence to escape.          $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1540          if ($realString =~ /^(.*?)([\n\t\r\\])/) {      }
1541              # Here we found it. The text preceding the sequence is in $1. The sequence      $options->{sql} = [0, "turn on SQL tracing"];
1542              # itself is in $2. First, move the clear text to the return variable.      $options->{help} = [0, "display command-line options"];
1543              $retVal .= $1;      $options->{user} = [$tkey, "tracing key"];
1544              # Strip the processed section off the real string.      $options->{background} = [0, "spool standard and error output"];
1545              $realString = substr $realString, (length $2) + (length $1);      # Create a parsing hash from the options hash. The parsing hash
1546              # Get the matched character.      # contains the default values rather than the default value
1547              my $char = $2;      # and the description. While we're at it, we'll memorize the
1548              # If we have a CR, we are done.      # length of the longest option name.
1549              if ($char ne "\r") {      my $longestName = 0;
1550                  # It's not a CR, so encode the escape sequence.      my %parseOptions = ();
1551                  $char =~ tr/\t\n/tn/;      for my $key (keys %{$options}) {
1552                  $retVal .= "\\" . $char;          if (length $key > $longestName) {
1553                $longestName = length $key;
1554            }
1555            $parseOptions{$key} = $options->{$key}->[0];
1556        }
1557        # Parse the command line.
1558        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1559        # Get the logfile suffix.
1560        my $suffix = $retOptions->{user};
1561        # Check for background mode.
1562        if ($retOptions->{background}) {
1563            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1564            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1565            open STDOUT, ">$outFileName";
1566            open STDERR, ">$errFileName";
1567            # Check for phone support. If we have phone support and a phone number,
1568            # we want to turn it on.
1569            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1570                $retOptions->{phone} = $ENV{PHONE};
1571            }
1572        }
1573        # Now we want to set up tracing. First, we need to know if the user
1574        # wants emergency tracing.
1575        if ($retOptions->{trace} eq 'E') {
1576            ETracing($retOptions->{user});
1577        } else {
1578            # Here the tracing is controlled from the command line.
1579            my @cats = @{$categories};
1580            if ($retOptions->{sql}) {
1581                push @cats, "SQL";
1582            }
1583            # Add the default categories.
1584            push @cats, "Tracer";
1585            # Next, we create the category string by joining the categories.
1586            my $cats = join(" ", @cats);
1587            # Check to determine whether or not the caller wants to turn off tracing
1588            # to the standard output.
1589            my $traceLevel = $retOptions->{trace};
1590            my $textOKFlag = 1;
1591            if ($traceLevel =~ /^(.)-/) {
1592                $traceLevel = $1;
1593                $textOKFlag = 0;
1594            }
1595            # Now we set up the trace mode.
1596            my $traceMode;
1597            # Verify that we can open a file in the FIG temporary directory.
1598            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1599            if (open TESTTRACE, ">$traceFileName") {
1600                # Here we can trace to a file.
1601                $traceMode = ">$traceFileName";
1602                if ($textOKFlag) {
1603                    # Echo to standard output if the text-OK flag is set.
1604                    $traceMode = "+$traceMode";
1605                }
1606                # Close the test file.
1607                close TESTTRACE;
1608            } else {
1609                # Here we can't trace to a file. Complain about this.
1610                warn "Could not open trace file $traceFileName: $!\n";
1611                # We trace to the standard output if it's
1612                # okay, and the error log otherwise.
1613                if ($textOKFlag) {
1614                    $traceMode = "TEXT";
1615                } else {
1616                    $traceMode = "WARN";
1617                }
1618            }
1619            # Now set up the tracing.
1620            TSetup("$traceLevel $cats", $traceMode);
1621        }
1622        # Check for the "help" option. If it is specified, dump the command-line
1623        # options and exit the program.
1624        if ($retOptions->{help}) {
1625            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1626            print "$1 [options] $parmHelp\n";
1627            for my $key (sort keys %{$options}) {
1628                my $name = Pad($key, $longestName, 0, ' ');
1629                my $desc = $options->{$key}->[1];
1630                if ($options->{$key}->[0]) {
1631                    $desc .= " (default " . $options->{$key}->[0] . ")";
1632              }              }
1633          } else {              print "  $name $desc\n";
             # Here there are no more escape sequences. The rest of the string is  
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
1634          }          }
1635            exit(0);
1636      }      }
1637      # Return the result.      # Trace the options, if applicable.
1638      return $retVal;      if (T(3)) {
1639            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1640            Trace("Selected options: " . join(", ", sort @parms) . ".");
1641        }
1642        # Return the parsed parameters.
1643        return ($retOptions, @retParameters);
1644  }  }
1645    
1646  =head3 UnEscape  =head3 ReadOptions
1647    
1648  C<< my $realString = Tracer::UnEscape($codedString); >>      my %options = Tracer::ReadOptions($fileName);
1649    
1650  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Read a set of options from a file. Each option is encoded in a line of text that has the
1651  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  format
1652  be deleted.  
1653    I<optionName>C<=>I<optionValue>C<; >I<comment>
1654    
1655    The option name must consist entirely of letters, digits, and the punctuation characters
1656    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1657    character is a semi-colon will be ignored. The return hash will map each option name to
1658    the corresponding option value.
1659    
1660  =over 4  =over 4
1661    
1662  =item codedString  =item fileName
1663    
1664  String to un-escape.  Name of the file containing the option data.
1665    
1666  =item RETURN  =item RETURN
1667    
1668  Returns a copy of the original string with the escape sequences converted to their actual  Returns a hash mapping the option names specified in the file to their corresponding option
1669  values.  value.
1670    
1671  =back  =back
1672    
1673  =cut  =cut
1674    
1675  sub UnEscape {  sub ReadOptions {
1676      # Get the parameter.      # Get the parameters.
1677      my ($codedString) = @_;      my ($fileName) = @_;
1678      # Initialize the return variable.      # Open the file.
1679      my $retVal = "";      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1680      # Only proceed if the incoming string is nonempty.      # Count the number of records read.
1681      if (defined $codedString) {      my ($records, $comments) = 0;
1682          # Loop through the parameter string, looking for escape sequences. We can't do      # Create the return hash.
1683          # translating because it causes problems with the escaped slash. ("\\t" becomes      my %retVal = ();
1684          # "\<tab>" no matter what we do.)      # Loop through the file, accumulating key-value pairs.
1685          while (length $codedString > 0) {      while (my $line = <CONFIGFILE>) {
1686              # Look for the first escape sequence.          # Denote we've read a line.
1687              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {          $records++;
1688                  # Here we found it. The text preceding the sequence is in $1. The sequence          # Determine the line type.
1689                  # itself is in $2. First, move the clear text to the return variable.          if ($line =~ /^\s*[\n\r]/) {
1690                  $retVal .= $1;              # A blank line is a comment.
1691                  $codedString = substr $codedString, (2 + length $1);              $comments++;
1692                  # Get the escape value.          } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1693                  my $char = $2;              # Here we have an option assignment.
1694                  # If we have a "\r", we are done.              retVal{$1} = $2;
1695                  if ($char ne 'r') {          } elsif ($line =~ /^\s*;/) {
1696                      # Here it's not an 'r', so we convert it.              # Here we have a text comment.
1697                      $char =~ tr/\\tn/\\\t\n/;              $comments++;
                     $retVal .= $char;  
                 }  
1698              } else {              } else {
1699                  # Here there are no more escape sequences. The rest of the string is              # Here we have an invalid line.
1700                  # transferred unmodified.              Trace("Invalid option statement in record $records.") if T(0);
                 $retVal .= $codedString;  
                 $codedString = "";  
             }  
1701          }          }
1702      }      }
1703      # Return the result.      # Return the hash created.
1704      return $retVal;      return %retVal;
1705  }  }
1706    
1707  =head3 ParseRecord  =head3 GetOptions
1708    
1709  C<< my @fields = Tracer::ParseRecord($line); >>      Tracer::GetOptions(\%defaults, \%options);
1710    
1711  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Merge a specified set of options into a table of defaults. This method takes two hash references
1712  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  as input and uses the data from the second to update the first. If the second does not exist,
1713  These will automatically be converted.  there will be no effect. An error will be thrown if one of the entries in the second hash does not
1714    exist in the first.
1715    
1716    Consider the following example.
1717    
1718        my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1719    
1720    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1721    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1722    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1723    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1724    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1725    
1726        {databaseType => 'Oracle'}
1727    
1728    an error will occur because the B<databaseType> option does not exist.
1729    
1730  =over 4  =over 4
1731    
1732  =item line  =item defaults
1733    
1734  Line of data containing the tab-delimited fields.  Table of default option values.
1735    
1736    =item options
1737    
1738    Table of overrides, if any.
1739    
1740  =item RETURN  =item RETURN
1741    
1742  Returns a list of the fields found in the data line.  Returns a reference to the default table passed in as the first parameter.
1743    
1744  =back  =back
1745    
1746  =cut  =cut
1747    
1748  sub ParseRecord {  sub GetOptions {
1749      # Get the parameter.      # Get the parameters.
1750      my ($line) = @_;      my ($defaults, $options) = @_;
1751      # Remove the trailing new-line, if any.      # Check for overrides.
1752      chomp $line;      if ($options) {
1753      # Split the line read into pieces using the tab character.          # Loop through the overrides.
1754      my @retVal = split /\t/, $line;          while (my ($option, $setting) = each %{$options}) {
1755      # Trim and fix the escapes in each piece.              # Insure this override exists.
1756      for my $value (@retVal) {              if (!exists $defaults->{$option}) {
1757          # Trim leading whitespace.                  croak "Unrecognized option $option encountered.";
1758          $value =~ s/^\s+//;              } else {
1759          # Trim trailing whitespace.                  # Apply the override.
1760          $value =~ s/\s+$//;                  $defaults->{$option} = $setting;
         # Delete the carriage returns.  
         $value =~ s/\r//g;  
         # Convert the escapes into their real values.  
         $value =~ s/\\t/"\t"/ge;  
         $value =~ s/\\n/"\n"/ge;  
1761      }      }
1762      # Return the result.          }
1763      return @retVal;      }
1764        # Return the merged table.
1765        return $defaults;
1766  }  }
1767    
1768  =head3 Merge  =head3 MergeOptions
1769    
1770  C<< my @mergedList = Tracer::Merge(@inputList); >>      Tracer::MergeOptions(\%table, \%defaults);
1771    
1772  Sort a list of strings and remove duplicates.  Merge default values into a hash table. This method looks at the key-value pairs in the
1773    second (default) hash, and if a matching key is not found in the first hash, the default
1774    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1775    checking and no return value.
1776    
1777  =over 4  =over 4
1778    
1779  =item inputList  =item table
1780    
1781  List of scalars to sort and merge.  Hash table to be updated with the default values.
1782    
1783  =item RETURN  =item defaults
1784    
1785  Returns a list containing the same elements sorted in ascending order with duplicates  Default values to be merged into the first hash table if they are not already present.
 removed.  
1786    
1787  =back  =back
1788    
1789  =cut  =cut
1790    
1791  sub Merge {  sub MergeOptions {
1792      # Get the input list in sort order.      # Get the parameters.
1793      my @inputList = sort @_;      my ($table, $defaults) = @_;
1794      # Only proceed if the list has at least two elements.      # Loop through the defaults.
1795      if (@inputList > 1) {      while (my ($key, $value) = each %{$defaults}) {
1796          # Now we want to move through the list splicing out duplicates.          if (!exists $table->{$key}) {
1797          my $i = 0;              $table->{$key} = $value;
         while ($i < @inputList) {  
             # Get the current entry.  
             my $thisEntry = $inputList[$i];  
             # Find out how many elements duplicate the current entry.  
             my $j = $i + 1;  
             my $dup1 = $i + 1;  
             while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };  
             # If the number is nonzero, splice out the duplicates found.  
             if ($j > $dup1) {  
                 splice @inputList, $dup1, $j - $dup1;  
             }  
             # Now the element at position $dup1 is different from the element before it  
             # at position $i. We push $i forward one position and start again.  
             $i++;  
1798          }          }
1799      }      }
     # Return the merged list.  
     return @inputList;  
1800  }  }
1801    
1802  =head3 Percent  =head3 ParseCommand
1803    
1804  C<< my $percent = Tracer::Percent($number, $base); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1805    
1806  Returns the percent of the base represented by the given number. If the base  Parse a command line consisting of a list of parameters. The initial parameters may be option
1807  is zero, returns zero.  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1808    off and merged into a table of default options. The remainder of the command line is
1809    returned as a list of positional arguments. For example, consider the following invocation.
1810    
1811        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1812    
1813    In this case, the list @words will be treated as a command line and there are two options available,
1814    B<errors> and B<logFile>. If @words has the following format
1815    
1816        -logFile=error.log apple orange rutabaga
1817    
1818    then at the end of the invocation, C<$options> will be
1819    
1820        { errors => 0, logFile => 'error.log' }
1821    
1822    and C<@arguments> will contain
1823    
1824        apple orange rutabaga
1825    
1826    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1827    support for quote characters. Options can be specified with single or double hyphens.
1828    
1829  =over 4  =over 4
1830    
1831  =item number  =item optionTable
1832    
1833  Percent numerator.  Table of default options.
1834    
1835  =item base  =item inputList
1836    
1837  Percent base.  List of words on the command line.
1838    
1839  =item RETURN  =item RETURN
1840    
1841  Returns the percentage of the base represented by the numerator.  Returns a reference to the option table and a list of the positional arguments.
1842    
1843  =back  =back
1844    
1845  =cut  =cut
1846    
1847  sub Percent {  sub ParseCommand {
1848      # Get the parameters.      # Get the parameters.
1849      my ($number, $base) = @_;      my ($optionTable, @inputList) = @_;
1850      # Declare the return variable.      # Process any options in the input list.
1851      my $retVal = 0;      my %overrides = ();
1852      # Compute the percent.      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1853      if ($base != 0) {          # Get the current option.
1854          $retVal = $number * 100 / $base;          my $arg = shift @inputList;
1855            # Pull out the option name.
1856            $arg =~ /^--?([^=]*)/g;
1857            my $name = $1;
1858            # Check for an option value.
1859            if ($arg =~ /\G=(.*)$/g) {
1860                # Here we have a value for the option.
1861                $overrides{$name} = UnEscape($1);
1862            } else {
1863                # Here there is no value, so we use 1.
1864                $overrides{$name} = 1;
1865      }      }
     # Return the result.  
     return $retVal;  
1866  }  }
1867        # Merge the options into the defaults.
1868        GetOptions($optionTable, \%overrides);
1869        # Translate the remaining parameters.
1870        my @retVal = ();
1871        for my $inputParm (@inputList) {
1872            push @retVal, UnEscape($inputParm);
1873        }
1874        # Return the results.
1875        return ($optionTable, @retVal);
1876    }
1877    
1878    
1879    =head2 File Utility Methods
1880    
1881  =head3 GetFile  =head3 GetFile
1882    
1883  C<< my @fileContents = Tracer::GetFile($fileName); >>      my @fileContents = Tracer::GetFile($fileName);
1884    
1885      or      or
1886    
1887  C<< my $fileContents = Tracer::GetFile($fileName); >>      my $fileContents = Tracer::GetFile($fileName);
1888    
1889  Return the entire contents of a file. In list context, line-ends are removed and  Return the entire contents of a file. In list context, line-ends are removed and
1890  each line is a list element. In scalar context, line-ends are replaced by C<\n>.  each line is a list element. In scalar context, line-ends are replaced by C<\n>.
# Line 1648  Line 1934 
1934    
1935  =head3 PutFile  =head3 PutFile
1936    
1937  C<< Tracer::PutFile($fileName, \@lines); >>      Tracer::PutFile($fileName, \@lines);
1938    
1939  Write out a file from a list of lines of text.  Write out a file from a list of lines of text.
1940    
# Line 1691  Line 1977 
1977      close $handle;      close $handle;
1978  }  }
1979    
1980  =head3 QTrace  =head3 ParseRecord
1981    
1982  C<< my $data = QTrace($format); >>      my @fields = Tracer::ParseRecord($line);
1983    
1984  Return the queued trace data in the specified format.  Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1985    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1986    These will automatically be converted.
1987    
1988  =over 4  =over 4
1989    
1990  =item format  =item line
1991    
1992  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Line of data containing the tab-delimited fields.
1993    
1994    =item RETURN
1995    
1996    Returns a list of the fields found in the data line.
1997    
1998  =back  =back
1999    
2000  =cut  =cut
2001    
2002  sub QTrace {  sub ParseRecord {
2003      # Get the parameter.      # Get the parameter.
2004      my ($format) = @_;      my ($line) = @_;
2005      # Create the return variable.      # Remove the trailing new-line, if any.
2006      my $retVal = "";      chomp $line;
2007      # Only proceed if there is an actual queue.      # Split the line read into pieces using the tab character.
2008      if (@Queue) {      my @retVal = split /\t/, $line;
2009          # Process according to the format.      # Trim and fix the escapes in each piece.
2010          if ($format =~ m/^HTML$/i) {      for my $value (@retVal) {
2011              # Convert the queue into an HTML list.          # Trim leading whitespace.
2012              $retVal = "<ul>\n";          $value =~ s/^\s+//;
2013              for my $line (@Queue) {          # Trim trailing whitespace.
2014                  my $escapedLine = CGI::escapeHTML($line);          $value =~ s/\s+$//;
2015                  $retVal .= "<li>$escapedLine</li>\n";          # Delete the carriage returns.
2016            $value =~ s/\r//g;
2017            # Convert the escapes into their real values.
2018            $value =~ s/\\t/"\t"/ge;
2019            $value =~ s/\\n/"\n"/ge;
2020              }              }
2021              $retVal .= "</ul>\n";      # Return the result.
2022          } elsif ($format =~ m/^TEXT$/i) {      return @retVal;
             # Convert the queue into a list of text lines.  
             $retVal = join("\n", @Queue) . "\n";  
2023          }          }
2024          # Clear the queue.  
2025          @Queue = ();  =head3 Merge
2026    
2027        my @mergedList = Tracer::Merge(@inputList);
2028    
2029    Sort a list of strings and remove duplicates.
2030    
2031    =over 4
2032    
2033    =item inputList
2034    
2035    List of scalars to sort and merge.
2036    
2037    =item RETURN
2038    
2039    Returns a list containing the same elements sorted in ascending order with duplicates
2040    removed.
2041    
2042    =back
2043    
2044    =cut
2045    
2046    sub Merge {
2047        # Get the input list in sort order.
2048        my @inputList = sort @_;
2049        # Only proceed if the list has at least two elements.
2050        if (@inputList > 1) {
2051            # Now we want to move through the list splicing out duplicates.
2052            my $i = 0;
2053            while ($i < @inputList) {
2054                # Get the current entry.
2055                my $thisEntry = $inputList[$i];
2056                # Find out how many elements duplicate the current entry.
2057                my $j = $i + 1;
2058                my $dup1 = $i + 1;
2059                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2060                # If the number is nonzero, splice out the duplicates found.
2061                if ($j > $dup1) {
2062                    splice @inputList, $dup1, $j - $dup1;
2063      }      }
2064      # Return the formatted list.              # Now the element at position $dup1 is different from the element before it
2065      return $retVal;              # at position $i. We push $i forward one position and start again.
2066                $i++;
2067            }
2068        }
2069        # Return the merged list.
2070        return @inputList;
2071  }  }
2072    
2073  =head3 Confess  =head3 Open
2074    
2075  C<< Confess($message); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2076    
2077  Trace the call stack and abort the program with the specified message. When used with  Open a file.
2078  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
2079  So, for example  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2080    function. The mode is specified using Unix-like shell information. So, for
2081    example,
2082    
2083  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2084    
2085  Will abort the program with a stack trace if the value of C<$recNum> is negative.  would open for output appended to the specified file, and
2086    
2087        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2088    
2089    would open a pipe that sorts the records written and removes duplicates. Note
2090    the use of file handle syntax in the Open call. To use anonymous file handles,
2091    code as follows.
2092    
2093        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2094    
2095    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2096    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2097    failed open will throw an exception and the third parameter will be used to construct
2098    an error message. If the parameter is omitted, a standard message is constructed
2099    using the file spec.
2100    
2101        Could not open "/usr/spool/news/twitlog"
2102    
2103    Note that the mode characters are automatically cleaned from the file name.
2104    The actual error message from the file system will be captured and appended to the
2105    message in any case.
2106    
2107        Could not open "/usr/spool/news/twitlog": file not found.
2108    
2109    In some versions of PERL the only error message we get is a number, which
2110    corresponds to the C++ C<errno> value.
2111    
2112        Could not open "/usr/spool/news/twitlog": 6.
2113    
2114  =over 4  =over 4
2115    
2116  =item message  =item fileHandle
2117    
2118  Message to include in the trace.  File handle. If this parameter is C<undef>, a file handle will be generated
2119    and returned as the value of this method.
2120    
2121    =item fileSpec
2122    
2123    File name and mode, as per the PERL C<open> function.
2124    
2125    =item message (optional)
2126    
2127    Error message to use if the open fails. If omitted, a standard error message
2128    will be generated. In either case, the error information from the file system
2129    is appended to the message. To specify a conditional open that does not throw
2130    an error if it fails, use C<0>.
2131    
2132    =item RETURN
2133    
2134    Returns the name of the file handle assigned to the file, or C<undef> if the
2135    open failed.
2136    
2137  =back  =back
2138    
2139  =cut  =cut
2140    
2141  sub Confess {  sub Open {
2142      # Get the parameters.      # Get the parameters.
2143      my ($message) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2144      # Trace the call stack.      # Attempt to open the file.
2145      Cluck($message);      my $rv = open $fileHandle, $fileSpec;
2146      # Abort the program.      # If the open failed, generate an error message.
2147      croak(">>> $message");      if (! $rv) {
2148            # Save the system error message.
2149            my $sysMessage = $!;
2150            # See if we need a default message.
2151            if (!$message) {
2152                # Clean any obvious mode characters and leading spaces from the
2153                # filename.
2154                my ($fileName) = FindNamePart($fileSpec);
2155                $message = "Could not open \"$fileName\"";
2156            }
2157            # Terminate with an error using the supplied message and the
2158            # error message from the file system.
2159            Confess("$message: $!");
2160        }
2161        # Return the file handle.
2162        return $fileHandle;
2163  }  }
2164    
2165  =head3 Assert  =head3 FindNamePart
2166    
2167  C<< Assert($condition1, $condition2, ... $conditionN); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2168    
2169  Return TRUE if all the conditions are true. This method can be used in conjunction with  Extract the portion of a file specification that contains the file name.
2170  the OR operator and the L</Confess> method as a debugging assert.  
2171  So, for example  A file specification is the string passed to an C<open> call. It specifies the file
2172    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2173    method assumes that the file name is whatever follows the first angle bracket
2174    sequence.  So, for example, in the following strings the file name is
2175    C</usr/fig/myfile.txt>.
2176    
2177  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      >>/usr/fig/myfile.txt
2178        </usr/fig/myfile.txt
2179        | sort -u > /usr/fig/myfile.txt
2180    
2181  Will abort the program with a stack trace if the value of C<$recNum> is negative.  If the method cannot find a file name using its normal methods, it will return the
2182    whole incoming string.
2183    
2184    =over 4
2185    
2186    =item fileSpec
2187    
2188    File specification string from which the file name is to be extracted.
2189    
2190    =item RETURN
2191    
2192    Returns a three-element list. The first element contains the file name portion of
2193    the specified string, or the whole string if a file name cannot be found via normal
2194    methods. The second element contains the start position of the file name portion and
2195    the third element contains the length.
2196    
2197    =back
2198    
2199  =cut  =cut
2200  sub Assert {  #: Return Type $;
2201      my $retVal = 1;  sub FindNamePart {
2202      LOOP: for my $condition (@_) {      # Get the parameters.
2203          if (! $condition) {      my ($fileSpec) = @_;
2204              $retVal = 0;      # Default to the whole input string.
2205              last LOOP;      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2206          }      # Parse out the file name if we can.
2207        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2208            $retVal = $2;
2209            $len = length $retVal;
2210            $pos = (length $fileSpec) - (length $3) - $len;
2211      }      }
2212      return $retVal;      # Return the result.
2213        return ($retVal, $pos, $len);
2214  }  }
2215    
2216  =head3 Cluck  =head3 OpenDir
   
 C<< Cluck($message); >>  
   
 Trace the call stack. Note that for best results, you should qualify the call with a  
 trace condition. For example,  
   
 C<< Cluck("Starting record parse.") if T(3); >>  
2217    
2218  will only trace the stack if the trace level for the package is 3 or more.      my @files = OpenDir($dirName, $filtered, $flag);
2219    
2220  =over 4  Open a directory and return all the file names. This function essentially performs
2221    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2222    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2223    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2224    filtered out of the return list. If the directory does not open and I<$flag> is not
2225    set, an exception is thrown. So, for example,
2226    
2227  =item message      my @files = OpenDir("/Volumes/fig/contigs", 1);
2228    
2229  Message to include in the trace.  is effectively the same as
2230    
2231  =back      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2232        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2233    
2234  =cut  Similarly, the following code
2235    
2236  sub Cluck {      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
     # Get the parameters.  
     my ($message) = @_;  
     # Trace what's happening.  
     Trace("Stack trace for event: $message");  
     my $confession = longmess($message);  
     # Convert the confession to a series of trace messages. Note we skip any  
     # messages relating to calls into Tracer.  
     for my $line (split /\s*\n/, $confession) {  
         Trace($line) if ($line !~ /Tracer\.pm/);  
     }  
 }  
2237    
2238  =head3 Min  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2239    automatically returns an empty list if the directory fails to open.
2240    
2241  C<< my $min = Min($value1, $value2, ... $valueN); >>  =over 4
2242    
2243  Return the minimum argument. The arguments are treated as numbers.  =item dirName
2244    
2245  =over 4  Name of the directory to open.
2246    
2247  =item $value1, $value2, ... $valueN  =item filtered
2248    
2249  List of numbers to compare.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2250    from the list, else FALSE.
2251    
2252  =item RETURN  =item flag
2253    
2254  Returns the lowest number in the list.  TRUE if a failure to open is okay, else FALSE
2255    
2256  =back  =back
2257    
2258  =cut  =cut
2259    #: Return Type @;
2260  sub Min {  sub OpenDir {
2261      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2262      my ($retVal, @values) = @_;      my ($dirName, $filtered, $flag) = @_;
2263      # Loop through the remaining parameters, looking for the lowest.      # Declare the return variable.
2264      for my $value (@values) {      my @retVal = ();
2265          if ($value < $retVal) {      # Open the directory.
2266              $retVal = $value;      if (opendir(my $dirHandle, $dirName)) {
2267            # The directory opened successfully. Get the appropriate list according to the
2268            # strictures of the filter parameter.
2269            if ($filtered) {
2270                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2271            } else {
2272                @retVal = readdir $dirHandle;
2273          }          }
2274        } elsif (! $flag) {
2275            # Here the directory would not open and it's considered an error.
2276            Confess("Could not open directory $dirName.");
2277      }      }
2278      # Return the minimum found.      # Return the result.
2279      return $retVal;      return @retVal;
2280  }  }
2281    
 =head3 Max  
2282    
2283  C<< my $max = Max($value1, $value2, ... $valueN); >>  =head3 Insure
2284    
2285        Insure($dirName, $chmod);
2286    
2287  Return the maximum argument. The arguments are treated as numbers.  Insure a directory is present.
2288    
2289  =over 4  =over 4
2290    
2291  =item $value1, $value2, ... $valueN  =item dirName
2292    
2293  List of numbers to compare.  Name of the directory to check. If it does not exist, it will be created.
2294    
2295  =item RETURN  =item chmod (optional)
2296    
2297  Returns the highest number in the list.  Security privileges to be given to the directory if it is created.
2298    
2299  =back  =back
2300    
2301  =cut  =cut
2302    
2303  sub Max {  sub Insure {
2304      # Get the parameters. Note that we prime the return value with the first parameter.      my ($dirName, $chmod) = @_;
2305      my ($retVal, @values) = @_;      if (! -d $dirName) {
2306      # Loop through the remaining parameters, looking for the highest.          Trace("Creating $dirName directory.") if T(2);
2307      for my $value (@values) {          eval {
2308          if ($value > $retVal) {              mkpath $dirName;
2309              $retVal = $value;              # If we have permissions specified, set them here.
2310                if (defined($chmod)) {
2311                    chmod $chmod, $dirName;
2312                }
2313            };
2314            if ($@) {
2315                Confess("Error creating $dirName: $@");
2316          }          }
2317      }      }
     # Return the maximum found.  
     return $retVal;  
2318  }  }
2319    
2320  =head3 AddToListMap  =head3 ChDir
2321    
2322  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>      ChDir($dirName);
2323    
2324  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Change to the specified directory.
 is created for the key. Otherwise, the new value is pushed onto the list.  
2325    
2326  =over 4  =over 4
2327    
2328  =item hash  =item dirName
   
 Reference to the target hash.  
   
 =item key  
   
 Key for which the value is to be added.  
   
 =item value1, value2, ... valueN  
2329    
2330  List of values to add to the key's value list.  Name of the directory to which we want to change.
2331    
2332  =back  =back
2333    
2334  =cut  =cut
2335    
2336  sub AddToListMap {  sub ChDir {
2337      # Get the parameters.      my ($dirName) = @_;
2338      my ($hash, $key, @values) = @_;      if (! -d $dirName) {
2339      # Process according to whether or not the key already has a value.          Confess("Cannot change to directory $dirName: no such directory.");
     if (! exists $hash->{$key}) {  
         $hash->{$key} = [@values];  
2340      } else {      } else {
2341          push @{$hash->{$key}}, @values;          Trace("Changing to directory $dirName.") if T(File => 4);
2342            my $okFlag = chdir $dirName;
2343            if (! $okFlag) {
2344                Confess("Error switching to directory $dirName.");
2345            }
2346      }      }
2347  }  }
2348    
2349  =head3 DebugMode  =head3 SetPermissions
2350    
2351  C<< if (Tracer::DebugMode) { ...code... } >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2352    
2353  Return TRUE if debug mode has been turned on, else abort.  Set the permissions for a directory and all the files and folders inside it.
2354    In addition, the group ownership will be changed to the specified value.
2355    
2356  Certain CGI scripts are too dangerous to exist in the production  This method is more vulnerable than most to permission and compatability
2357  environment. This method provides a simple way to prevent them  problems, so it does internal error recovery.
 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.  
2358    
2359  =cut  =over 4
2360    
2361  sub DebugMode {  =item dirName
     # Declare the return variable.  
     my $retVal = 0;  
     # Check the debug configuration.  
     my $password = CGI::cookie("DebugMode");  
     my $encrypted = Digest::MD5::md5_hex($password);  
     if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {  
         $retVal = 1;  
     } else {  
         # Here debug mode is off, so we generate an error.  
         Confess("Cannot use this facility without logging in.");  
     }  
     # Return the determination indicator.  
     return $retVal;  
 }  
2362    
2363  =head3 Strip  Name of the directory to process.
2364    
2365  C<< my $string = Tracer::Strip($line); >>  =item group
2366    
2367  Strip all line terminators off a string. This is necessary when dealing with files  Name of the group to be assigned.
 that may have been transferred back and forth several times among different  
 operating environments.  
2368    
2369  =over 4  =item mask
2370    
2371  =item line  Permission mask. Bits that are C<1> in this mask will be ORed into the
2372    permission bits of any file or directory that does not already have them
2373    set to 1.
2374    
2375  Line of text to be stripped.  =item otherMasks
2376    
2377  =item RETURN  Map of search patterns to permission masks. If a directory name matches
2378    one of the patterns, that directory and all its members and subdirectories
2379    will be assigned the new pattern. For example, the following would
2380    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2381    
2382  The same line of text with all the line-ending characters chopped from the end.      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2383    
2384    The list is ordered, so the following would use 0777 for C<tmp1> and
2385    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2386    
2387        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2388                                                       '^tmp' => 0666);
2389    
2390    Note that the pattern matches are all case-insensitive, and only directory
2391    names are matched, not file names.
2392    
2393  =back  =back
2394    
2395  =cut  =cut
2396    
2397  sub Strip {  sub SetPermissions {
2398      # Get a copy of the parameter string.      # Get the parameters.
2399      my ($string) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2400      my $retVal = (defined $string ? $string : "");      # Set up for error recovery.
2401      # Strip the line terminator characters.      eval {
2402      $retVal =~ s/(\r|\n)+$//g;          # Switch to the specified directory.
2403      # Return the result.          ChDir($dirName);
2404      return $retVal;          # Get the group ID.
2405            my $gid = getgrnam($group);
2406            # Get the mask for tracing.
2407            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2408            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2409            my $fixCount = 0;
2410            my $lookCount = 0;
2411            # @dirs will be a stack of directories to be processed.
2412            my @dirs = (getcwd());
2413            while (scalar(@dirs) > 0) {
2414                # Get the current directory.
2415                my $dir = pop @dirs;
2416                # Check for a match to one of the specified directory names. To do
2417                # that, we need to pull the individual part of the name off of the
2418                # whole path.
2419                my $simpleName = $dir;
2420                if ($dir =~ m!/([^/]+)$!) {
2421                    $simpleName = $1;
2422                }
2423                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2424                # Search for a match.
2425                my $match = 0;
2426                my $i;
2427                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2428                    my $pattern = $otherMasks[$i];
2429                    if ($simpleName =~ /$pattern/i) {
2430                        $match = 1;
2431                    }
2432                }
2433                # Check for a match. Note we use $i-1 because the loop added 2
2434                # before terminating due to the match.
2435                if ($match && $otherMasks[$i-1] != $mask) {
2436                    # This directory matches one of the incoming patterns, and it's
2437                    # a different mask, so we process it recursively with that mask.
2438                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2439                } else {
2440                    # Here we can process normally. Get all of the non-hidden members.
2441                    my @submems = OpenDir($dir, 1);
2442                    for my $submem (@submems) {
2443                        # Get the full name.
2444                        my $thisMem = "$dir/$submem";
2445                        Trace("Checking member $thisMem.") if T(4);
2446                        $lookCount++;
2447                        if ($lookCount % 1000 == 0) {
2448                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2449                        }
2450                        # Fix the group.
2451                        chown -1, $gid, $thisMem;
2452                        # Insure this member is not a symlink.
2453                        if (! -l $thisMem) {
2454                            # Get its info.
2455                            my $fileInfo = stat $thisMem;
2456                            # Only proceed if we got the info. Otherwise, it's a hard link
2457                            # and we want to skip it anyway.
2458                            if ($fileInfo) {
2459                                my $fileMode = $fileInfo->mode;
2460                                if (($fileMode & $mask) != $mask) {
2461                                    # Fix this member.
2462                                    $fileMode |= $mask;
2463                                    chmod $fileMode, $thisMem;
2464                                    $fixCount++;
2465                                }
2466                                # If it's a subdirectory, stack it.
2467                                if (-d $thisMem) {
2468                                    push @dirs, $thisMem;
2469                                }
2470                            }
2471                        }
2472                    }
2473                }
2474            }
2475            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2476        };
2477        # Check for an error.
2478        if ($@) {
2479            Confess("SetPermissions error: $@");
2480        }
2481  }  }
2482    
2483  =head3 Pad  =head3 GetLine
2484    
2485  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      my @data = Tracer::GetLine($handle);
2486    
2487  Pad a string to a specified length. The pad character will be a  Read a line of data from a tab-delimited file.
 space, and the padding will be on the right side unless specified  
 in the third parameter.  
2488    
2489  =over 4  =over 4
2490    
2491  =item string  =item handle
   
 String to be padded.  
   
 =item len  
   
 Desired length of the padded string.  
   
 =item left (optional)  
   
 TRUE if the string is to be left-padded; otherwise it will be padded on the right.  
   
 =item padChar (optional)  
2492    
2493  Character to use for padding. The default is a space.  Open file handle from which to read.
2494    
2495  =item RETURN  =item RETURN
2496    
2497  Returns a copy of the original string with the pad character added to the  Returns a list of the fields in the record read. The fields are presumed to be
2498  specified end so that it achieves the desired length.  tab-delimited. If we are at the end of the file, then an empty list will be
2499    returned. If an empty line is read, a single list item consisting of a null
2500    string will be returned.
2501    
2502  =back  =back
2503    
2504  =cut  =cut
2505    
2506  sub Pad {  sub GetLine {
2507      # Get the parameters.      # Get the parameters.
2508      my ($string, $len, $left, $padChar) = @_;      my ($handle) = @_;
2509      # Compute the padding character.      # Declare the return variable.
2510      if (! defined $padChar) {      my @retVal = ();
2511          $padChar = " ";      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2512        # Read from the file.
2513        my $line = <$handle>;
2514        # Only proceed if we found something.
2515        if (defined $line) {
2516            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2517            # upload control and have a nonstandard EOL combination.
2518            $line =~ s/(\r|\n)+$//;
2519            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2520            if (T(File => 4)) {
2521                my $escapedLine = $line;
2522                $escapedLine =~ s/\n/\\n/g;
2523                $escapedLine =~ s/\r/\\r/g;
2524                $escapedLine =~ s/\t/\\t/g;
2525                Trace("Line read: -->$escapedLine<--");
2526      }      }
2527      # Compute the number of spaces needed.          # If the line is empty, return a single empty string; otherwise, parse
2528      my $needed = $len - length $string;          # it into fields.
2529      # Copy the string into the return variable.          if ($line eq "") {
2530      my $retVal = $string;              push @retVal, "";
     # Only proceed if padding is needed.  
     if ($needed > 0) {  
         # Create the pad string.  
         my $pad = $padChar x $needed;  
         # Affix it to the return value.  
         if ($left) {  
             $retVal = $pad . $retVal;  
2531          } else {          } else {
2532              $retVal .= $pad;              push @retVal, split /\t/,$line;
2533          }          }
2534        } else {
2535            # Trace the reason the read failed.
2536            Trace("End of file: $!") if T(File => 3);
2537      }      }
2538      # Return the result.      # Return the result.
2539      return $retVal;      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";  
2540  }  }
2541    
2542  =head3 TICK  =head3 PutLine
   
 C<< my @results = TICK($commandString); >>  
   
 Perform a back-tick operation on a command. If this is a Windows environment, any leading  
 dot-slash (C<./> will be removed. So, for example, if you were doing  
2543    
2544      `./protein.cgi`      Tracer::PutLine($handle, \@fields, $eol);
2545    
2546  from inside a CGI script, it would work fine in Unix, but would issue an error message  Write a line of data to a tab-delimited file. The specified field values will be
2547  in Windows complaining that C<'.'> is not a valid command. If instead you code  output in tab-separated form, with a trailing new-line.
2548    
2549      TICK("./protein.cgi")  =over 4
2550    
2551  it will work correctly in both environments.  =item handle
2552    
2553  =over 4  Output file handle.
2554    
2555  =item commandString  =item fields
2556    
2557  The command string to pass to the system.  List of field values.
2558    
2559  =item RETURN  =item eol (optional)
2560    
2561  Returns the standard output from the specified command, as a list.  End-of-line character (default is "\n").
2562    
2563  =back  =back
2564    
2565  =cut  =cut
2566  #: Return Type @;  
2567  sub TICK {  sub PutLine {
2568      # Get the parameters.      # Get the parameters.
2569      my ($commandString) = @_;      my ($handle, $fields, $eol) = @_;
2570      # Chop off the dot-slash if this is Windows.      # Write the data.
2571      if ($FIG_Config::win_mode) {      print $handle join("\t", @{$fields}) . ($eol || "\n");
         $commandString =~ s!^\./!!;  
     }  
     # Activate the command and return the result.  
     return `$commandString`;  
2572  }  }
2573    
 =head3 ScriptSetup  
   
 C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  
2574    
2575  Perform standard tracing and debugging setup for scripts. The value returned is  =head3 PrintLine
 the CGI object followed by a pre-built variable hash.  
2576    
2577  The C<Trace> form parameter is used to determine whether or not tracing is active and      Tracer::PrintLine($line);
 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.  
2578    
2579  In some situations, it is not practical to invoke tracing via form parameters. For this  Print a line of text with a trailing new-line.
 situation, you can turn on emergency tracing from the debugging control panel.  
 Tracing will then be turned on automatically for all programs that use the L</ETracing>  
 method, which includes every program that uses this method or L</StandardSetup>.  
2580    
2581  =over 4  =over 4
2582    
2583  =item noTrace (optional)  =item line
   
 If specified, tracing will be suppressed. This is useful if the script wants to set up  
 tracing manually.  
   
 =item RETURN  
2584    
2585  Returns a two-element list consisting of a CGI query object and a variable hash for  Line of text to print.
 the output page.  
2586    
2587  =back  =back
2588    
2589  =cut  =cut
2590    
2591  sub ScriptSetup {  sub PrintLine {
2592      # Get the parameters.      # Get the parameters.
2593      my ($noTrace) = @_;      my ($line) = @_;
2594      # Get the CGI query object.      # Print the line.
2595      my $cgi = CGI->new();      print "$line\n";
     # Set up tracing if it's not suppressed.  
     ETracing($cgi) unless $noTrace;  
     # Create the variable hash.  
     my $varHash = { results => '' };  
     # Return the query object and variable hash.  
     return ($cgi, $varHash);  
2596  }  }
2597    
 =head3 ETracing  
2598    
2599  C<< ETracing($parameter); >>  =head2 Other Useful Methods
2600    
2601  Set up emergency tracing. Emergency tracing is tracing that is turned  =head3 ParseParm
2602  on automatically for any program that calls this method. The emergency  
2603  tracing parameters are stored in a a file identified by a tracing key.      my $listValue = Tracer::ParseParm($string);
2604  If this method is called with a CGI object, then the tracing key is  
2605  taken from a cookie. If it is called with no parameters, then the tracing  Convert a parameter into a list reference. If the parameter is undefined,
2606  key is taken from an environment variable. If it is called with a string,  an undefined value will be returned. Otherwise, it will be parsed as a
2607  the tracing key is that string.  comma-separated list of values.
2608    
2609  =over 4  =over 4
2610    
2611  =item parameter  =item string
2612    
2613  A parameter from which the tracing key is computed. If it is a scalar,  Incoming string.
2614  that scalar is used as the tracing key. If it is a CGI object, the  
2615  tracing key is taken from the C<IP> cookie. If it is omitted, the  =item RETURN
2616  tracing key is taken from the C<TRACING> environment variable. If it  
2617  is a CGI object and emergency tracing is not on, the C<Trace> and  Returns a reference to a list of values, or C<undef> if the incoming value
2618  C<TF> parameters will be used to determine the type of tracing.  was undefined.
2619    
2620  =back  =back
2621    
2622  =cut  =cut
2623    
2624  sub ETracing {  sub ParseParm {
2625      # Get the parameter.      # Get the parameters.
2626      my ($parameter) = @_;      my ($string) = @_;
2627      # Check for CGI mode.      # Declare the return variable.
2628      my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);      my $retVal;
2629      # Default to no tracing except errors.      # Check for data.
2630      my ($tracing, $dest) = ("0", "WARN");      if (defined $string) {
2631      # Check for emergency tracing.          # We have some, so split it into a list.
2632      my $tkey = EmergencyKey($parameter);          $retVal = [ split /\s*,\s*/, $string];
     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);  
2633      }      }
2634        # Return the result.
2635        return $retVal;
2636  }  }
2637    
2638  =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  
2639    
2640  Returns the name of the file to contain the emergency tracing information.      my $string = Tracer::Now();
2641    
2642  =back  Return a displayable time stamp containing the local time. Whatever format this
2643    method produces must be parseable by L</ParseDate>.
2644    
2645  =cut  =cut
2646    
2647  sub EmergencyFileName {  sub Now {
2648      # Get the parameters.      return DisplayTime(time);
     my ($tkey) = @_;  
     # Compute the emergency tracing file name.  
     return "$FIG_Config::temp/Emergency$tkey.txt";  
2649  }  }
2650    
2651  =head3 EmergencyFileTarget  =head3 DisplayTime
2652    
2653  C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>      my $string = Tracer::DisplayTime($time);
2654    
2655  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
2656  the tracing output for file-based tracing.  method produces must be parseable by L</ParseDate>.
2657    
2658  =over 4  =over 4
2659    
2660  =item tkey  =item time
2661    
2662  Tracing key for the current program.  Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2663    
2664  =item RETURN  =item RETURN
2665    
2666  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.
2667    
2668  =back  =back
2669    
2670  =cut  =cut
2671    
2672  sub EmergencyFileTarget {  sub DisplayTime {
2673      # Get the parameters.      my ($time) = @_;
2674      my ($tkey) = @_;      my $retVal = "(n/a)";
2675      # Compute the emergency tracing file name.      if (defined $time) {
2676      return "$FIG_Config::temp/trace$tkey.log";          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2677            $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2678                      _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2679        }
2680        return $retVal;
2681  }  }
2682    
2683  =head3 EmergencyTracingDest  # Pad a number to 2 digits.
2684    sub _p2 {
2685  C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>      my ($value) = @_;
2686        $value = "0$value" if ($value < 10);
2687        return $value;
2688    }
2689    
2690  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.  
2691    
2692  =over 4      my $codedString = Tracer::Escape($realString);
2693    
2694  =item tkey  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2695    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2696    result is to reverse the effect of L</UnEscape>.
2697    
2698  Tracing key for this environment.  =over 4
2699    
2700  =item myDest  =item realString
2701    
2702  Destination from the emergency tracing file.  String to escape.
2703    
2704  =item RETURN  =item RETURN
2705    
2706  Returns a destination that can be passed into L</TSetup>.  Escaped equivalent of the real string.
2707    
2708  =back  =back
2709    
2710  =cut  =cut
2711    
2712  sub EmergencyTracingDest {  sub Escape {
2713      # Get the parameters.      # Get the parameter.
2714      my ($tkey, $myDest) = @_;      my ($realString) = @_;
2715      # Declare the return variable.      # Initialize the return variable.
2716      my $retVal;      my $retVal = "";
2717      # Process according to the destination value.      # Loop through the parameter string, looking for sequences to escape.
2718      if ($myDest eq 'FILE') {      while (length $realString > 0) {
2719          $retVal = ">" . EmergencyFileTarget($tkey);          # Look for the first sequence to escape.
2720      } elsif ($myDest eq 'APPEND') {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2721          $retVal = ">>" . EmergencyFileTarget($tkey);              # Here we found it. The text preceding the sequence is in $1. The sequence
2722                # itself is in $2. First, move the clear text to the return variable.
2723                $retVal .= $1;
2724                # Strip the processed section off the real string.
2725                $realString = substr $realString, (length $2) + (length $1);
2726                # Get the matched character.
2727                my $char = $2;
2728                # If we have a CR, we are done.
2729                if ($char ne "\r") {
2730                    # It's not a CR, so encode the escape sequence.
2731                    $char =~ tr/\t\n/tn/;
2732                    $retVal .= "\\" . $char;
2733                }
2734      } else {      } else {
2735          $retVal = $myDest;              # Here there are no more escape sequences. The rest of the string is
2736                # transferred unmodified.
2737                $retVal .= $realString;
2738                $realString = "";
2739            }
2740      }      }
2741      # Return the result.      # Return the result.
2742      return $retVal;      return $retVal;
2743  }  }
2744    
2745  =head3 Emergency  =head3 UnEscape
2746    
2747  C<< Emergency($key, $hours, $dest, $level, @modules); >>      my $realString = Tracer::UnEscape($codedString);
2748    
2749  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
2750  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
2751  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.  
2752    
2753  =over 4  =over 4
2754    
2755  =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  
2756    
2757  Tracing level. A higher level means more trace messages.  String to un-escape.
2758    
2759  =item modules  =item RETURN
2760    
2761  A list of the tracing modules to activate.  Returns a copy of the original string with the escape sequences converted to their actual
2762    values.
2763    
2764  =back  =back
2765    
2766  =cut  =cut
2767    
2768  sub Emergency {  sub UnEscape {
2769      # Get the parameters.      # Get the parameter.
2770      my ($tkey, $hours, $dest, $level, @modules) = @_;      my ($codedString) = @_;
2771      # Create the emergency file.      # Initialize the return variable.
2772      my $specFile = EmergencyFileName($tkey);      my $retVal = "";
2773      my $outHandle = Open(undef, ">$specFile");      # Only proceed if the incoming string is nonempty.
2774      print $outHandle join("\n", $hours, $dest, $level, @modules, "");      if (defined $codedString) {
2775            # Loop through the parameter string, looking for escape sequences. We can't do
2776            # translating because it causes problems with the escaped slash. ("\\t" becomes
2777            # "\<tab>" no matter what we do.)
2778            while (length $codedString > 0) {
2779                # Look for the first escape sequence.
2780                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2781                    # Here we found it. The text preceding the sequence is in $1. The sequence
2782                    # itself is in $2. First, move the clear text to the return variable.
2783                    $retVal .= $1;
2784                    $codedString = substr $codedString, (2 + length $1);
2785                    # Get the escape value.
2786                    my $char = $2;
2787                    # If we have a "\r", we are done.
2788                    if ($char ne 'r') {
2789                        # Here it's not an 'r', so we convert it.
2790                        $char =~ tr/\\tn/\\\t\n/;
2791                        $retVal .= $char;
2792                    }
2793                } else {
2794                    # Here there are no more escape sequences. The rest of the string is
2795                    # transferred unmodified.
2796                    $retVal .= $codedString;
2797                    $codedString = "";
2798                }
2799            }
2800        }
2801        # Return the result.
2802        return $retVal;
2803  }  }
2804    
2805  =head3 EmergencyKey  =head3 Percent
2806    
2807  C<< my $tkey = EmergencyKey($parameter); >>      my $percent = Tracer::Percent($number, $base);
2808    
2809  Return the Key to be used for emergency tracing. This could be an IP address,  Returns the percent of the base represented by the given number. If the base
2810   a session ID, or a user name, depending on the environment.  is zero, returns zero.
2811    
2812  =over 4  =over 4
2813    
2814  =item parameter  =item number
2815    
2816  Parameter defining the method for finding the tracing key. If it is a scalar,  Percent numerator.
2817  then it is presumed to be the tracing key itself. If it is a CGI object, then  
2818  the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is  =item base
2819  taken from the C<TRACING> environment variable.  
2820    Percent base.
2821    
2822  =item RETURN  =item RETURN
2823    
2824  Returns the key to be used for labels in emergency tracing.  Returns the percentage of the base represented by the numerator.
2825    
2826  =back  =back
2827    
2828  =cut  =cut
2829    
2830  sub EmergencyKey {  sub Percent {
2831      # Get the parameters.      # Get the parameters.
2832      my ($parameter) = @_;      my ($number, $base) = @_;
2833      # Declare the return variable.      # Declare the return variable.
2834      my $retVal;      my $retVal = 0;
2835      # Determine the parameter type.      # Compute the percent.
2836      if (! defined $parameter) {      if ($base != 0) {
2837          # 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 = $$;  
2838      }      }
2839      # Return the result.      # Return the result.
2840      return $retVal;      return $retVal;
2841  }  }
2842    
2843    =head3 Constrain
2844    
2845  =head3 TraceParms      my $constrained = Constrain($value, $min, $max);
   
 C<< Tracer::TraceParms($cgi); >>  
2846    
2847  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Modify a numeric value to bring it to a point in between a maximum and a minimum.
 at level CGI => 4.  
2848    
2849  =over 4  =over 4
2850    
2851  =item cgi  =item value
2852    
2853  CGI query object containing the parameters to trace.  Value to constrain.
2854    
2855  =back  =item min (optional)
2856    
2857  =cut  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
2858    
2859  sub TraceParms {  =item max (optional)
     # Get the parameters.  
     my ($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}");  
         }  
     }  
 }  
2860    
2861  =head3 ScriptFinish  Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
2862    
2863  C<< ScriptFinish($webData, $varHash); >>  =item RETURN
2864    
2865  Output a web page at the end of a script. Either the string to be output or the  Returns the incoming value, constrained according to the other parameters.
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
2866    
2867  A typical standard script would loook like the following.  =back
2868    
2869      BEGIN {  =cut
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
2870    
2871      my ($cgi, $varHash) = ScriptSetup();  sub Constrain {
2872      eval {      # Get the parameters.
2873          # ... get data from $cgi, put it in $varHash ...      my ($value, $min, $max) = @_;
2874      };      # Declare the return variable.
2875      if ($@) {      my $retVal = $value;
2876          Trace("Script Error: $@") if T(0);      # Apply the minimum constraint.
2877        if (defined $min && $retVal < $min) {
2878            $retVal = $min;
2879        }
2880        # Apply the maximum constraint.
2881        if (defined $max && $retVal > $max) {
2882            $retVal = $max;
2883        }
2884        # Return the result.
2885        return $retVal;
2886      }      }
     ScriptFinish("Html/MyTemplate.html", $varHash);  
2887    
2888  The idea here is that even if the script fails, you'll see trace messages and  =head3 Min
2889  useful output.  
2890        my $min = Min($value1, $value2, ... $valueN);
2891    
2892    Return the minimum argument. The arguments are treated as numbers.
2893    
2894  =over 4  =over 4
2895    
2896  =item webData  =item $value1, $value2, ... $valueN
2897    
2898  A string containing either the full web page to be written to the output or the  List of numbers to compare.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
2899    
2900  =item varHash (optional)  =item RETURN
2901    
2902  If specified, then a reference to a hash mapping variable names for a template  Returns the lowest number in the list.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
2903    
2904  =back  =back
2905    
2906  =cut  =cut
2907    
2908  sub ScriptFinish {  sub Min {
2909      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
2910      my ($webData, $varHash) = @_;      my ($retVal, @values) = @_;
2911      # Check for a template file situation.      # Loop through the remaining parameters, looking for the lowest.
2912      my $outputString;      for my $value (@values) {
2913      if (defined $varHash) {          if ($value < $retVal) {
2914          # 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";  
2915          }          }
         substr $outputString, $pos, 0, $traceHtml;  
2916      }      }
2917      # Write the output string.      # Return the minimum found.
2918      print $outputString;      return $retVal;
2919  }  }
2920    
2921  =head3 Insure  =head3 Max
2922    
2923  C<< Insure($dirName); >>      my $max = Max($value1, $value2, ... $valueN);
2924    
2925  Insure a directory is present.  Return the maximum argument. The arguments are treated as numbers.
2926    
2927  =over 4  =over 4
2928    
2929  =item dirName  =item $value1, $value2, ... $valueN
2930    
2931  Name of the directory to check. If it does not exist, it will be created.  List of numbers to compare.
2932    
2933    =item RETURN
2934    
2935    Returns the highest number in the list.
2936    
2937  =back  =back
2938    
2939  =cut  =cut
2940    
2941  sub Insure {  sub Max {
2942      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
2943      if (! -d $dirName) {      my ($retVal, @values) = @_;
2944          Trace("Creating $dirName directory.") if T(File => 2);      # Loop through the remaining parameters, looking for the highest.
2945          eval { mkpath $dirName; };      for my $value (@values) {
2946          if ($@) {          if ($value > $retVal) {
2947              Confess("Error creating $dirName: $@");              $retVal = $value;
2948          }          }
2949      }      }
2950        # Return the maximum found.
2951        return $retVal;
2952  }  }
2953    
 =head3 ChDir  
2954    
2955  C<< ChDir($dirName); >>  =head3 Strip
2956    
2957  Change to the specified directory.      my $string = Tracer::Strip($line);
2958    
2959    Strip all line terminators off a string. This is necessary when dealing with files
2960    that may have been transferred back and forth several times among different
2961    operating environments.
2962    
2963  =over 4  =over 4
2964    
2965  =item dirName  =item line
2966    
2967  Name of the directory to which we want to change.  Line of text to be stripped.
2968    
2969    =item RETURN
2970    
2971    The same line of text with all the line-ending characters chopped from the end.
2972    
2973  =back  =back
2974    
2975  =cut  =cut
2976    
2977  sub ChDir {  sub Strip {
2978      my ($dirName) = @_;      # Get a copy of the parameter string.
2979      if (! -d $dirName) {      my ($string) = @_;
2980          Confess("Cannot change to directory $dirName: no such directory.");      my $retVal = (defined $string ? $string : "");
2981      } else {      # Strip the line terminator characters.
2982          Trace("Changing to directory $dirName.") if T(File => 4);      $retVal =~ s/(\r|\n)+$//g;
2983          my $okFlag = chdir $dirName;      # Return the result.
2984          if (! $okFlag) {      return $retVal;
             Confess("Error switching to directory $dirName.");  
         }  
     }  
2985  }  }
2986    
2987  =head3 SendSMS  =head3 Pad
2988    
2989  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
2990    
2991  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  Pad a string to a specified length. The pad character will be a
2992  user name, password, and API ID for the relevant account in the hash reference variable  space, and the padding will be on the right side unless specified
2993  I<$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  
2994    
2995      $phone =  { user => 'BruceTheHumanPet',  =over 4
                 password => 'silly',  
                 api_id => '2561022' };  
2996    
2997  The original purpose of this method was to insure Bruce would be notified immediately when the  =item string
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
2998    
2999  The message ID will be returned if successful, and C<undef> if an error occurs.  String to be padded.
3000    
3001  =over 4  =item len
3002    
3003  =item phoneNumber  Desired length of the padded string.
3004    
3005  Phone number to receive the message, in international format. A United States phone number  =item left (optional)
 would be prefixed by "1". A British phone number would be prefixed by "44".  
3006    
3007  =item msg  TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3008    
3009  Message to send to the specified phone.  =item padChar (optional)
3010    
3011    Character to use for padding. The default is a space.
3012    
3013  =item RETURN  =item RETURN
3014    
3015  Returns the message ID if successful, and C<undef> if the message could not be sent.  Returns a copy of the original string with the pad character added to the
3016    specified end so that it achieves the desired length.
3017    
3018  =back  =back
3019    
3020  =cut  =cut
3021    
3022  sub SendSMS {  sub Pad {
3023      # Get the parameters.      # Get the parameters.
3024      my ($phoneNumber, $msg) = @_;      my ($string, $len, $left, $padChar) = @_;
3025      # Declare the return variable. If we do not change it, C<undef> will be returned.      # Compute the padding character.
3026      my $retVal;      if (! defined $padChar) {
3027      # Only proceed if we have phone support.          $padChar = " ";
     if (! defined $FIG_Config::phone) {  
         Trace("Phone support not present in FIG_Config.") if T(1);  
     } else {  
         # Get the phone data.  
         my $parms = $FIG_Config::phone;  
         # Get the Clickatell URL.  
         my $url = "http://api.clickatell.com/http/";  
         # Create the user agent.  
         my $ua = LWP::UserAgent->new;  
         # Request a Clickatell session.  
         my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},  
                                      password => $parms->{password},  
                                      api_id => $parms->{api_id},  
                                      to => $phoneNumber,  
                                      text => $msg});  
         # Check for an error.  
         if (! $resp->is_success) {  
             Trace("Alert failed.") if T(1);  
         } else {  
             # Get the message ID.  
             my $rstring = $resp->content;  
             if ($rstring =~ /^ID:\s+(.*)$/) {  
                 $retVal = $1;  
             } else {  
                 Trace("Phone attempt failed with $rstring") if T(1);  
3028              }              }
3029        # Compute the number of spaces needed.
3030        my $needed = $len - length $string;
3031        # Copy the string into the return variable.
3032        my $retVal = $string;
3033        # Only proceed if padding is needed.
3034        if ($needed > 0) {
3035            # Create the pad string.
3036            my $pad = $padChar x $needed;
3037            # Affix it to the return value.
3038            if ($left) {
3039                $retVal = $pad . $retVal;
3040            } else {
3041                $retVal .= $pad;
3042          }          }
3043      }      }
3044      # Return the result.      # Return the result.
3045      return $retVal;      return $retVal;
3046  }  }
3047    
3048    =head3 EOF
3049    
3050    This is a constant that is lexically greater than any useful string.
3051    
3052    =cut
3053    
3054    sub EOF {
3055        return "\xFF\xFF\xFF\xFF\xFF";
3056    }
3057    
3058    =head3 TICK
3059    
3060        my @results = TICK($commandString);
3061    
3062    Perform a back-tick operation on a command. If this is a Windows environment, any leading
3063    dot-slash (C<./> will be removed. So, for example, if you were doing
3064    
3065        `./protein.cgi`
3066    
3067    from inside a CGI script, it would work fine in Unix, but would issue an error message
3068    in Windows complaining that C<'.'> is not a valid command. If instead you code
3069    
3070        TICK("./protein.cgi")
3071    
3072    it will work correctly in both environments.
3073    
3074    =over 4
3075    
3076    =item commandString
3077    
3078    The command string to pass to the system.
3079    
3080    =item RETURN
3081    
3082    Returns the standard output from the specified command, as a list.
3083    
3084    =back
3085    
3086    =cut
3087    #: Return Type @;
3088    sub TICK {
3089        # Get the parameters.
3090        my ($commandString) = @_;
3091        # Chop off the dot-slash if this is Windows.
3092        if ($FIG_Config::win_mode) {
3093            $commandString =~ s!^\./!!;
3094        }
3095        # Activate the command and return the result.
3096        return `$commandString`;
3097    }
3098    
3099    
3100  =head3 CommaFormat  =head3 CommaFormat
3101    
3102  C<< my $formatted = Tracer::CommaFormat($number); >>      my $formatted = Tracer::CommaFormat($number);
3103    
3104  Insert commas into a number.  Insert commas into a number.
3105    
# Line 2740  Line 3132 
3132      # Return the result.      # Return the result.
3133      return $retVal;      return $retVal;
3134  }  }
 =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  
   
 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  
3135    
 =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(File => 2);  
         my $fixCount = 0;  
         my $lookCount = 0;  
         # @dirs will be a stack of directories to be processed.  
         my @dirs = (getcwd());  
         while (scalar(@dirs) > 0) {  
             # Get the current directory.  
             my $dir = pop @dirs;  
             # Check for a match to one of the specified directory names. To do  
             # that, we need to pull the individual part of the name off of the  
             # whole path.  
             my $simpleName = $dir;  
             if ($dir =~ m!/([^/]+)$!) {  
                 $simpleName = $1;  
             }  
             Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);  
             # Search for a match.  
             my $match = 0;  
             my $i;  
             for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {  
                 my $pattern = $otherMasks[$i];  
                 if ($simpleName =~ /$pattern/i) {  
                     $match = 1;  
                 }  
             }  
             # Check for a match. Note we use $i-1 because the loop added 2  
             # before terminating due to the match.  
             if ($match && $otherMasks[$i-1] != $mask) {  
                 # This directory matches one of the incoming patterns, and it's  
                 # a different mask, so we process it recursively with that mask.  
                 SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);  
             } else {  
                 # Here we can process normally. Get all of the non-hidden members.  
                 my @submems = OpenDir($dir, 1);  
                 for my $submem (@submems) {  
                     # Get the full name.  
                     my $thisMem = "$dir/$submem";  
                     Trace("Checking member $thisMem.") if T(4);  
                     $lookCount++;  
                     if ($lookCount % 1000 == 0) {  
                         Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);  
                     }  
                     # Fix the group.  
                     chown -1, $gid, $thisMem;  
                     # Insure this member is not a symlink.  
                     if (! -l $thisMem) {  
                         # Get its info.  
                         my $fileInfo = stat $thisMem;  
                         # Only proceed if we got the info. Otherwise, it's a hard link  
                         # and we want to skip it anyway.  
                         if ($fileInfo) {  
                             my $fileMode = $fileInfo->mode;  
                             if (($fileMode & $mask) != $mask) {  
                                 # Fix this member.  
                                 $fileMode |= $mask;  
                                 chmod $fileMode, $thisMem;  
                                 $fixCount++;  
                             }  
                             # If it's a subdirectory, stack it.  
                             if (-d $thisMem) {  
                                 push @dirs, $thisMem;  
                             }  
                         }  
                     }  
                 }  
             }  
         }  
         Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);  
     };  
     # Check for an error.  
     if ($@) {  
         Confess("SetPermissions error: $@");  
     }  
 }  
3136    
3137  =head3 CompareLists  =head3 CompareLists
3138    
3139  C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3140    
3141  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
3142  are presumed to be sorted alphabetically by the value in the $keyIndex column.  are presumed to be sorted alphabetically by the value in the $keyIndex column.
# Line 2941  Line 3201 
3201      return ($inserted, $deleted);      return ($inserted, $deleted);
3202  }  }
3203    
 =head3 GetLine  
   
 C<< my @data = Tracer::GetLine($handle); >>  
   
 Read a line of data from a tab-delimited file.  
   
 =over 4  
   
 =item handle  
   
 Open file handle from which to read.  
   
 =item RETURN  
   
 Returns a list of the fields in the record read. The fields are presumed to be  
 tab-delimited. If we are at the end of the file, then an empty list will be  
 returned. If an empty line is read, a single list item consisting of a null  
 string will be returned.  
   
 =back  
   
 =cut  
   
 sub GetLine {  
     # Get the parameters.  
     my ($handle) = @_;  
     # Declare the return variable.  
     my @retVal = ();  
     Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);  
     # Read from the file.  
     my $line = <$handle>;  
     # Only proceed if we found something.  
     if (defined $line) {  
         # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an  
         # upload control and have a nonstandard EOL combination.  
         $line =~ s/(\r|\n)+$//;  
         # Here we do some fancy tracing to help in debugging complicated EOL marks.  
         if (T(File => 4)) {  
             my $escapedLine = $line;  
             $escapedLine =~ s/\n/\\n/g;  
             $escapedLine =~ s/\r/\\r/g;  
             $escapedLine =~ s/\t/\\t/g;  
             Trace("Line read: -->$escapedLine<--");  
         }  
         # If the line is empty, return a single empty string; otherwise, parse  
         # it into fields.  
         if ($line eq "") {  
             push @retVal, "";  
         } else {  
             push @retVal, split /\t/,$line;  
         }  
     } else {  
         # Trace the reason the read failed.  
         Trace("End of file: $!") if T(File => 3);  
     }  
     # Return the result.  
     return @retVal;  
 }  
   
 =head3 PutLine  
   
 C<< Tracer::PutLine($handle, \@fields); >>  
   
 Write a line of data to a tab-delimited file. The specified field values will be  
 output in tab-separated form, with a trailing new-line.  
   
 =over 4  
   
 =item handle  
   
 Output file handle.  
   
 =item fields  
   
 List of field values.  
   
 =back  
   
 =cut  
   
 sub PutLine {  
     # Get the parameters.  
     my ($handle, $fields) = @_;  
     # Write the data.  
     print $handle join("\t", @{$fields}) . "\n";  
 }  
   
3204  =head3 GenerateURL  =head3 GenerateURL
3205    
3206  C<< my $queryUrl = Tracer::GenerateURL($page, %parameters); >>      my $queryUrl = Tracer::GenerateURL($page, %parameters);
3207    
3208  Generate a GET-style URL for the specified page with the specified parameter  Generate a GET-style URL for the specified page with the specified parameter
3209  names and values. The values will be URL-escaped automatically. So, for  names and values. The values will be URL-escaped automatically. So, for
# Line 3078  Line 3251 
3251    
3252  =head3 ApplyURL  =head3 ApplyURL
3253    
3254  C<< Tracer::ApplyURL($table, $target, $url); >>      Tracer::ApplyURL($table, $target, $url);
3255    
3256  Run through a two-dimensional table (or more accurately, a list of lists), converting the  Run through a two-dimensional table (or more accurately, a list of lists), converting the
3257  I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The  I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
# Line 3121  Line 3294 
3294    
3295  =head3 CombineURL  =head3 CombineURL
3296    
3297  C<< my $combinedHtml = Tracer::CombineURL($text, $url); >>      my $combinedHtml = Tracer::CombineURL($text, $url);
3298    
3299  This method will convert the specified text into HTML hyperlinked to the specified  This method will convert the specified text into HTML hyperlinked to the specified
3300  URL. The hyperlinking will only take place if the URL looks legitimate: that is, it  URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
# Line 3162  Line 3335 
3335      return $retVal;      return $retVal;
3336  }  }
3337    
3338    =head3 Cmp
3339    
3340        my $cmp = Tracer::Cmp($a, $b);
3341    
3342    This method performs a universal sort comparison. Each value coming in is
3343    separated into a leading text part and a trailing number part. The text
3344    part is string compared, and if both parts are equal, then the number
3345    parts are compared numerically. A stream of just numbers or a stream of
3346    just strings will sort correctly, and a mixed stream will sort with the
3347    numbers first. Strings with a label and a number will sort in the
3348    expected manner instead of lexically.
3349    
3350    =over 4
3351    
3352    =item a
3353    
3354    First item to compare.
3355    
3356    =item b
3357    
3358    Second item to compare.
3359    
3360    =item RETURN
3361    
3362    Returns a negative number if the first item should sort first (is less), a positive
3363    number if the first item should sort second (is greater), and a zero if the items are
3364    equal.
3365    
3366    =back
3367    
3368    =cut
3369    
3370    sub Cmp {
3371        # Get the parameters.
3372        my ($a, $b) = @_;
3373        # Declare the return value.
3374        my $retVal;
3375        # Check for nulls.
3376        if (! defined($a)) {
3377            $retVal = (! defined($b) ? 0 : -1);
3378        } elsif (! defined($b)) {
3379            $retVal = 1;
3380        } else {
3381            # Here we have two real values. Parse the two strings.
3382            $a =~ /^(\D*)(\d*)$/;
3383            my $aParsed = [$1, $2];
3384            $b =~ /^(\D*)(\d*)$/;
3385            my $bParsed = [$1, $2];
3386            # Compare the string parts.
3387            $retVal = $aParsed->[0] cmp $bParsed->[0];
3388            if (! $retVal) {
3389                $retVal = $aParsed->[1] <=> $bParsed->[1];
3390            }
3391        }
3392        # Return the result.
3393        return $retVal;
3394    }
3395    
3396    
3397    =head3 TrackingCode
3398    
3399        my $html = Tracer::TrackingCode();
3400    
3401    Returns the HTML code for doing web page traffic monitoring. If the
3402    current environment is a test system, then it returns a null string;
3403    otherwise, it returns a bunch of javascript containing code for turning
3404    on SiteMeter and Google Analytics.
3405    
3406    =cut
3407    
3408    sub TrackingCode {
3409        # Declare the return variable.
3410        my $retVal = "<!-- tracking off -->";
3411        # Determine if we're in production.
3412        if ($FIG_Config::site_meter) {
3413            $retVal = <<END_HTML
3414            <!-- Site Meter -->
3415            <script type="text/javascript" src="http://s20.sitemeter.com/js/counter.js?site=s20nmpdr">
3416            </script>
3417            <noscript>
3418            <a href="http://s20.sitemeter.com/stats.asp?site=s20nmpdr" target="_top">
3419            <img src="http://s20.sitemeter.com/meter.asp?site=s20nmpdr" alt="Site Meter" border="0"/></a>
3420            </noscript>
3421            <!-- Copyright (c)2006 Site Meter -->
3422    END_HTML
3423        }
3424        return $retVal;
3425    }
3426    
3427    
3428  1;  1;

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