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

Diff of /FigKernelPackages/Tracer.pm

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

revision 1.92, Thu Dec 6 13:59:04 2007 UTC revision 1.98, Thu May 1 07:52:10 2008 UTC
# Line 1  Line 1 
1  #  # -*- perl -*-
2    ########################################################################
3  # Copyright (c) 2003-2006 University of Chicago and Fellowship  # Copyright (c) 2003-2006 University of Chicago and Fellowship
4  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
5  #  #
# Line 13  Line 14 
14  # at info@ci.uchicago.edu or the Fellowship for Interpretation of  # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15  # Genomes at veronika@thefig.info or download a copy from  # Genomes at veronika@thefig.info or download a copy from
16  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
17  #  ########################################################################
18    
19  package Tracer;  package Tracer;
20    
21      require Exporter;      require Exporter;
22      @ISA = ('Exporter');      @ISA = ('Exporter');
23      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency);
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    
 NOTE: to configure emergency tracing from the command line instead of the Debugging  
 Control Panel (see below), use the C<trace.pl> script.  
   
 =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 $SetupCount;
223    }
224    
225  =head3 TSetup  =head3 TSetup
226    
# Line 350  Line 274 
274          }          }
275      }      }
276      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
277      # cases are the single ">", which requires we clear the file first, and the      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
278      # "+" prefix which indicates a double echo.      # ">>" (append). A leading "+" for either indicates that we are also writing to
279        # the standard output (tee mode).
280      if ($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 372  Line 299 
299      $SetupCount++;      $SetupCount++;
300  }  }
301    
302  =head3 StandardSetup  =head3 SetLevel
303    
304      my ($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 $retVal;
407    }
408    
409      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  =head3 LogErrors
410    
411  Single and double hyphens are equivalent. So, you could also code the      Tracer::LogErrors($fileName);
 above command as  
412    
413      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl  Route the standard error output to a log file.
414    
415  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  =over 4
 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<$options> hash would be  
416    
417      { trace => 2, sql => 0, safe => 0,  =item fileName
       noAlias => 1, start => ' ', tblFiles => 0 }  
418    
419  Use of C<StandardSetup> in this way provides a simple way of performing  Name of the file to receive the error output.
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
420    
421  If the C<background> option is specified on the command line, then the  =back
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
422    
423      -user=Bruce -background  =cut
424    
425  then the trace output would go to C<traceBruce.log>, the standard output to  sub LogErrors {
426  C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to      # Get the file name.
427  simplify starting a command in the background.      my ($fileName) = @_;
428        # Open the file as the standard error output.
429        open STDERR, '>', $fileName;
430    }
431    
432  The user name is also used as the tracing key for L</Emergency Tracing>.  =head3 Trace
 Specifying a value of C<E> for the trace level causes emergency tracing to  
 be used instead of custom tracing. If the user name is not specified,  
 the tracing key is taken from the C<Tracing> environment variable. If there  
 is no value for that variable, the tracing key will be computed from the PID.  
433    
434  Finally, if the special option C<-help> is specified, the option      Trace($message);
 names will be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
435    
436      TransactFeatures -help  Write a trace message to the target location specified in L</TSetup>. If there has not been
437    any prior call to B<TSetup>.
438    
439  he would see the following output.  =over 4
440    
441      TransactFeatures [options] <command> <transactionDirectory> <IDfile>  =item message
         -trace    tracing level (default E)  
         -sql      trace SQL commands  
         -safe     use database transactions  
         -noAlias  do not expect aliases in CHANGE transactions  
         -start    start with this genome  
         -tblFiles output TBL files containing the corrected IDs  
442    
443  The caller has the option of modifying the tracing scheme by placing a value  Message to write.
 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,  
444    
445      { trace => [0, "tracing level (default 0)"],  =back
        ...  
446    
447  would set the default trace level to 0 instead of E, while  =cut
448    
449      { trace => ["2-", "tracing level (default 2)"],  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  would set the default to 2, but trace only to the log file, not to the  =head3 T
 standard output.  
499    
500  The parameters to this method are as follows.      my $switch = T($category, $traceLevel);
501    
502  =over 4      or
503    
504  =item categories      my $switch = T($traceLevel);
505    
506  Reference to a list of tracing category names. These should be names of  Return TRUE if the trace level is at or above a specified value and the specified category
507  packages whose internal workings will need to be debugged to get the  is active, else FALSE. If no category is specified, the caller's package name is used.
 command working.  
508    
509  =item options  =over 4
510    
511  Reference to a hash containing the legal options for the current command mapped  =item category
 to their default values and descriptions. The user can override the defaults  
 by specifying the options as command-line switches prefixed by a hyphen.  
 Tracing-related options may be added to this hash. If the C<-h> option is  
 specified on the command line, the option descriptions will be used to  
 explain the options. To turn off tracing to the standard output, add a  
 minus sign to the value for C<trace> (see above).  
   
 =item parmHelp  
512    
513  A string that vaguely describes the positional parameters. This is used  Category to which the message belongs. If not specified, the caller's package name is
514  if the user specifies the C<-h> option.  used.
515    
516  =item argv  =item traceLevel
517    
518  List of command line parameters, including the option switches, which must  Relevant tracing level.
 precede the positional parameters and be prefixed by a hyphen.  
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} = ['2', "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      $options->{help} = [0, "display command-line options"];              my ($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, ">$errFileName";  
         # Check for phone support. If we have phone support and a phone number,  
         # we want to turn it on.  
         if ($ENV{PHONE} && defined($FIG_Config::phone)) {  
             $retOptions->{phone} = $ENV{PHONE};  
         }  
     }  
     # Now we want to set up tracing. First, we need to know if the user  
     # wants emergency tracing.  
     if ($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];
         }  
         # Now set up the tracing.  
         TSetup("$traceLevel $cats", $traceMode);  
     }  
     # Check for the "help" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($retOptions->{help}) {  
         $0 =~ m#[/\\](\w+)(\.pl)?$#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] . ")";  
549              }              }
             print "  $name $desc\n";  
550          }          }
551          exit(0);          # 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      # Trace the options, if applicable.          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
     if (T(3)) {  
         my @parms = grep { $retOptions->{$_} } keys %{$retOptions};  
         Trace("Selected options: " . join(", ", sort @parms) . ".");  
563      }      }
564      # Return the parsed parameters.      # Return the computed result.
565      return ($retOptions, @retParameters);      return $retVal;
566  }  }
567    
568  =head3 Setups  =head3 QTrace
569    
570      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
 may want to set up tracing if nobody else has done it before us.  
575    
576  =cut  =item format
577    
578  sub Setups {  C<html> to format the data as an HTML list, C<text> to format it as straight text.
     return $SetupCount;  
 }  
579    
580  =head3 Open  =back
581    
582      my $handle = Open($fileHandle, $fileSpec, $message);  =cut
583    
584  Open a file.  sub QTrace {
585        # Get the parameter.
586        my ($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 $retVal;
609    }
610    
611  The I<$fileSpec> is essentially the second argument of the PERL C<open>  =head3 Confess
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
612    
613      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");      Confess($message);
614    
615  would open for output appended to the specified file, and  Trace the call stack and abort the program with the specified message. When used with
616    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
617    So, for example
618    
619      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
620    
621  would open a pipe that sorts the records written and removes duplicates. Note  Will abort the program with a stack trace if the value of C<$recNum> is negative.
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
622    
623      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =over 4
624    
625  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  =item message
 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.  
626    
627      Could not open "/usr/spool/news/twitlog"  Message to include in the trace.
628    
629  Note that the mode characters are automatically cleaned from the file name.  =back
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
630    
631      Could not open "/usr/spool/news/twitlog": file not found.  =cut
632    
633  In some versions of PERL the only error message we get is a number, which  sub Confess {
634  corresponds to the C++ C<errno> value.      # 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(">>> $message");
655    }
656    
657      Could not open "/usr/spool/news/twitlog": 6.  =head3 Assert
658    
659  =over 4      Assert($condition1, $condition2, ... $conditionN);
660    
661  =item fileHandle  Return TRUE if all the conditions are true. This method can be used in conjunction with
662    the OR operator and the L</Confess> method as a debugging assert.
663    So, for example
664    
665  File handle. If this parameter is C<undef>, a file handle will be generated      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
 and returned as the value of this method.  
666    
667  =item fileSpec  Will abort the program with a stack trace if the value of C<$recNum> is negative.
668    
669  File name and mode, as per the PERL C<open> function.  =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 $retVal;
679    }
680    
681  =item message (optional)  =head3 Cluck
682    
683  Error message to use if the open fails. If omitted, a standard error message      Cluck($message);
 will be generated. In either case, the error information from the file system  
 is appended to the message. To specify a conditional open that does not throw  
 an error if it fails, use C<0>.  
684    
685  =item RETURN  Trace the call stack. Note that for best results, you should qualify the call with a
686    trace condition. For example,
687    
688  Returns the name of the file handle assigned to the file, or C<undef> if the      Cluck("Starting record parse.") if T(3);
689  open failed.  
690    will only trace the stack if the trace level for the package is 3 or more.
691    
692    =over 4
693    
694    =item message
695    
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)
   
     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
   
     my @files = OpenDir($dirName, $filtered, $flag);  
   
 Open a directory and return all the file names. This function essentially performs  
 the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  
 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  
 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be  
 filtered out of the return list. If the directory does not open and I<$flag> is not  
 set, an exception is thrown. So, for example,  
   
     my @files = OpenDir("/Volumes/fig/contigs", 1);  
   
 is effectively the same as  
   
     opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
   
 Similarly, the following code  
763    
764      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);      ETracing($parameter);
765    
766  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  Set up emergency tracing. Emergency tracing is tracing that is turned
767  automatically returns an empty list if the directory fails to open.  on automatically for any program that calls this method. The emergency
768    tracing parameters are stored in a a file identified by a tracing key.
769    If this method is called with a CGI object, then the tracing key is
770    taken from a cookie. If it is called with no parameters, then the tracing
771    key is taken from an environment variable. If it is called with a string,
772    the tracing key is that string.
773    
774  =over 4  =over 4
775    
776  =item dirName  =item parameter
   
 Name of the directory to open.  
   
 =item filtered  
   
 TRUE if files whose names begin with a period (C<.>) should be automatically removed  
 from the list, else FALSE.  
   
 =item flag  
777    
778  TRUE if a failure to open is okay, else FALSE  A parameter from which the tracing key is computed. If it is a scalar,
779    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  =back  =back
786    
787  =cut  =cut
788  #: Return Type @;  
789  sub OpenDir {  sub ETracing {
790      # Get the parameters.      # Get the parameter.
791      my ($dirName, $filtered, $flag) = @_;      my ($parameter) = @_;
792      # Declare the return variable.      # Check for CGI mode.
793      my @retVal = ();      my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
794      # Open the directory.      # Default to no tracing except errors.
795      if (opendir(my $dirHandle, $dirName)) {      my ($tracing, $dest) = ("0", "WARN");
796          # The directory opened successfully. Get the appropriate list according to the      # Check for emergency tracing.
797          # strictures of the filter parameter.      my $tkey = EmergencyKey($parameter);
798          if ($filtered) {      my $emergencyFile = EmergencyFileName($tkey);
799              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;      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 {          } else {
813              @retVal = readdir $dirHandle;              # 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          }          }
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
846      }      }
     # Return the result.  
     return @retVal;  
847  }  }
848    
849  =head3 SetLevel  =head3 EmergencyFileName
850    
851      Tracer::SetLevel($newLevel);      my $fileName = Tracer::EmergencyFileName($tkey);
852    
853  Modify the trace level. A higher trace level will cause more messages to appear.  Return the emergency tracing file name. This is the file that specifies
854    the tracing information.
855    
856  =over 4  =over 4
857    
858  =item newLevel  =item tkey
859    
860  Proposed new trace level.  Tracing key for the current program.
861    
862    =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    
870  sub SetLevel {  sub EmergencyFileName {
871      $TraceLevel = $_[0];      # Get the parameters.
872        my ($tkey) = @_;
873        # Compute the emergency tracing file name.
874        return "$FIG_Config::temp/Emergency$tkey.txt";
875  }  }
876    
877  =head3 Now  =head3 EmergencyFileTarget
878    
879      my $string = Tracer::Now();      my $fileName = Tracer::EmergencyFileTarget($tkey);
880    
881  Return a displayable time stamp containing the local time.  Return the emergency tracing target file name. This is the file that receives
882    the tracing output for file-based tracing.
883    
884  =cut  =over 4
885    
886  sub Now {  =item tkey
     my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);  
     my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .  
                  _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);  
     return $retVal;  
 }  
887    
888  # Pad a number to 2 digits.  Tracing key for the current program.
889  sub _p2 {  
890      my ($value) = @_;  =item RETURN
891      $value = "0$value" if ($value < 10);  
892      return $value;  Returns the name of the file to contain the trace output.
893    
894    =back
895    
896    =cut
897    
898    sub EmergencyFileTarget {
899        # Get the parameters.
900        my ($tkey) = @_;
901        # Compute the emergency tracing file name.
902        return "$FIG_Config::temp/trace$tkey.log";
903  }  }
904    
905  =head3 ParseTraceDate  =head3 EmergencyTracingDest
906    
907      my $time = Tracer::ParseTraceDate($dateString);      my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
908    
909  Convert a date from the trace file into a PERL timestamp.  This method converts an emergency tracing destination to a real
910    tracing destination. The main difference is that if the
911    destination is C<FILE> or C<APPEND>, we convert it to file
912    output. If the destination is C<DUAL>, we convert it to file
913    and standard output.
914    
915  =over 4  =over 4
916    
917  =item dateString  =item tkey
918    
919    Tracing key for this environment.
920    
921    =item myDest
922    
923  The date string from the trace file. The format of the string is determined by the  Destination from the emergency tracing file.
 L</Now> method.  
924    
925  =item RETURN  =item RETURN
926    
927  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if  Returns a destination that can be passed into L</TSetup>.
 the time string is invalid.  
928    
929  =back  =back
930    
931  =cut  =cut
932    
933  sub ParseTraceDate {  sub EmergencyTracingDest {
934      # Get the parameters.      # Get the parameters.
935      my ($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 $retVal;
950  }  }
951    
952  =head3 LogErrors  =head3 Emergency
953    
954      Tracer::LogErrors($fileName);      Emergency($key, $hours, $dest, $level, @modules);
955    
956  Route the standard error output to a log file.  Turn on emergency tracing. This method is normally invoked over the web from
957    a debugging console, but it can also be called by the C<trace.pl> script.
958    The caller specifies the duration of the emergency in hours, the desired tracing
959    destination, the trace level, and a list of the trace modules to activate.
960    For the length of the duration, when a program in an environment with the
961    specified tracing key active invokes a Sprout CGI script, tracing will be
962    turned on automatically. See L</TSetup> for more about tracing setup and
963    L</ETracing> for more about emergency tracing.
964    
965  =over 4  =over 4
966    
967  =item fileName  =item tkey
968    
969  Name of the file to receive the error output.  The tracing key. This is used to identify the control file and the trace file.
970    
971    =item hours
972    
973    Number of hours to keep emergency tracing alive.
974    
975    =item dest
976    
977    Tracing destination. If no path information is specified for a file
978    destination, it is put in the FIG temporary directory.
979    
980    =item level
981    
982    Tracing level. A higher level means more trace messages.
983    
984    =item modules
985    
986    A list of the tracing modules to activate.
987    
988  =back  =back
989    
990  =cut  =cut
991    
992  sub LogErrors {  sub Emergency {
993      # Get the file name.      # Get the parameters.
994      my ($fileName) = @_;      my ($tkey, $hours, $dest, $level, @modules) = @_;
995      # Open the file as the standard error output.      # Create the emergency file.
996      open STDERR, '>', $fileName;      my $specFile = EmergencyFileName($tkey);
997        my $outHandle = Open(undef, ">$specFile");
998        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
999  }  }
1000    
1001  =head3 ReadOptions  =head3 EmergencyKey
   
     my %options = Tracer::ReadOptions($fileName);  
   
 Read a set of options from a file. Each option is encoded in a line of text that has the  
 format  
1002    
1003  I<optionName>C<=>I<optionValue>C<; >I<comment>      my $tkey = EmergencyKey($parameter);
1004    
1005  The option name must consist entirely of letters, digits, and the punctuation characters  Return the Key to be used for emergency tracing. This could be an IP address,
1006  C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank   a session ID, or a user name, depending on the environment.
 character is a semi-colon will be ignored. The return hash will map each option name to  
 the corresponding option value.  
1007    
1008  =over 4  =over 4
1009    
1010  =item fileName  =item parameter
1011    
1012  Name of the file containing the option data.  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 hash mapping the option names specified in the file to their corresponding option  Returns the key to be used for labels in emergency tracing.
 value.  
1020    
1021  =back  =back
1022    
1023  =cut  =cut
1024    
1025  sub ReadOptions {  sub EmergencyKey {
1026      # Get the parameters.      # Get the parameters.
1027      my ($fileName) = @_;      my ($parameter) = @_;
1028      # Open the file.      # Declare the return variable.
1029      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");      my $retVal;
1030      # Count the number of records read.      # Determine the parameter type.
1031      my ($records, $comments) = 0;      if (! defined $parameter) {
1032      # Create the return hash.          # Here we're supposed to check the environment.
1033      my %retVal = ();          $retVal = $ENV{TRACING};
     # 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++;  
1034          } else {          } else {
1035              # Here we have an invalid line.          my $ptype = ref $parameter;
1036              Trace("Invalid option statement in record $records.") if T(0);          if ($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      # Return the hash created.      # If no luck finding a key, use the PID.
1045      return %retVal;      if (! defined $retVal) {
1046            $retVal = $$;
1047        }
1048        # Return the result.
1049        return $retVal;
1050  }  }
1051    
 =head3 GetOptions  
1052    
1053      Tracer::GetOptions(\%defaults, \%options);  =head3 TraceParms
1054    
1055  Merge a specified set of options into a table of defaults. This method takes two hash references      Tracer::TraceParms($cgi);
 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.  
1056    
1057  Consider the following example.  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      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);  =over 4
1061    
1062  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  =item cgi
 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<$options> is defined as  
1063    
1064      {databaseType => 'Oracle'}  CGI query object containing the parameters to trace.
1065    
1066  an error will occur because the B<databaseType> option does not exist.  =back
1067    
1068  =over 4  =cut
1069    
1070  =item defaults  sub TraceParms {
1071        # Get the parameters.
1072        my ($cgi) = @_;
1073        if (T(CGI => 2)) {
1074            # Here we trace the GET-style URL for the script.
1075            Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1076        }
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  Table of default option values.  =head3 TraceImages
1100    
1101  =item options      Tracer::TraceImages($htmlString);
1102    
1103  Table of overrides, if any.  Trace information about all of an html document's images. The tracing
1104    will be for type "IMG" at level 3. The image's source string
1105    will be displayed. This is generally either the URL of the image or
1106    raw data for the image itself. If the source is too long, only the first 300
1107    characters will be shown at trace level 3. The entire source will be shown,
1108    however, at trace level 4. This method is not very smart, and might catch
1109    Javascript code, but it is still useful when debugging the arcane
1110    behavior of images in multiple browser environments.
1111    
1112  =item RETURN  =over 4
1113    
1114  Returns a reference to the default table passed in as the first parameter.  =item htmlString
1115    
1116    HTML text for an outgoing web page.
1117    
1118  =back  =back
1119    
1120  =cut  =cut
1121    
1122  sub GetOptions {  sub TraceImages {
1123      # Get the parameters.      # Only proceed if we're at the proper trace level.
1124      my ($defaults, $options) = @_;      if (T(IMG => 3)) {
1125      # Check for overrides.          # For performance reasons we're manipulating $_[0] instead of retrieving the string
1126      if ($options) {          # into a variable called "$htmlString". This is because we expect html strings to be
1127          # Loop through the overrides.          # long, and don't want to copy them any more than we have to.
1128          while (my ($option, $setting) = each %{$options}) {          Trace(length($_[0]) . " characters in web page.");
1129              # Insure this override exists.          # Loop through the HTML, culling image tags.
1130              if (!exists $defaults->{$option}) {          while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1131                  croak "Unrecognized option $option encountered.";              # Extract the source string and determine whether or not it's too long.
1132              } else {              my $srcString = $1;
1133                  # Apply the override.              my $pos = pos($_[0]) - length($srcString);
1134                  $defaults->{$option} = $setting;              my $excess = length($srcString) - 300;
1135                # We'll put the display string in here.
1136                my $srcDisplay = $srcString;
1137                # If it's a data string, split it at the comma.
1138                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1139                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1140                # a long string, however, we only show the first 300 characters.
1141                if ($excess > 0 && ! T(IMG => 4)) {
1142                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1143              }              }
1144                # Output the trace message.
1145                Trace("Image tag at position $pos:\n$srcDisplay");
1146          }          }
1147      }      }
     # Return the merged table.  
     return $defaults;  
1148  }  }
1149    
 =head3 MergeOptions  
   
     Tracer::MergeOptions(\%table, \%defaults);  
   
 Merge default values into a hash table. This method looks at the key-value pairs in the  
 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.  
1150    
1151  =over 4  =head3 ScriptFinish (deprecated)
   
 =item table  
   
 Hash table to be updated with the default values.  
   
 =item defaults  
1152    
1153  Default values to be merged into the first hash table if they are not already present.      ScriptFinish($webData, $varHash);
1154    
1155  =back  Output a web page at the end of a script. Either the string to be output or the
1156    name of a template file can be specified. If the second parameter is omitted,
1157    it is assumed we have a string to be output; otherwise, it is assumed we have the
1158    name of a template file. The template should have the variable C<DebugData>
1159    specified in any form that invokes a standard script. If debugging mode is turned
1160    on, a form field will be put in that allows the user to enter tracing data.
1161    Trace messages will be placed immediately before the terminal C<BODY> tag in
1162    the output, formatted as a list.
1163    
1164  =cut  A typical standard script would loook like the following.
1165    
1166  sub MergeOptions {      BEGIN {
1167      # Get the parameters.          # Print the HTML header.
1168      my ($table, $defaults) = @_;          print "CONTENT-TYPE: text/html\n\n";
     # Loop through the defaults.  
     while (my ($key, $value) = each %{$defaults}) {  
         if (!exists $table->{$key}) {  
             $table->{$key} = $value;  
         }  
1169      }      }
1170        use Tracer;
1171        use CGI;
1172        use FIG;
1173        # ... more uses ...
1174    
1175        my ($cgi, $varHash) = ScriptSetup();
1176        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", $varHash);
1183    
1184  =head3 Trace  The idea here is that even if the script fails, you'll see trace messages and
1185    useful output.
1186    
1187      Trace($message);  =over 4
1188    
1189  Write a trace message to the target location specified in L</TSetup>. If there has not been  =item webData
 any prior call to B<TSetup>.  
1190    
1191  =over 4  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 message  =item varHash (optional)
1197    
1198  Message to write.  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 Trace {  sub ScriptFinish {
1207      # Get the parameters.      # Get the parameters.
1208      my ($message) = @_;      my ($webData, $varHash) = @_;
1209      # Get the timestamp.      # Check for a template file situation.
1210      my $timeStamp = Now();      my $outputString;
1211      # Format the message. Note we strip off any line terminators at the end.      if (defined $varHash) {
1212      my $prefix = "[$timeStamp] <$LastCategory>: ";          # Here we have a template file. We need to determine the template type.
1213      my $formatted = $prefix . Strip($message);          my $template;
1214      # Process according to the destination.          if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1215      if ($Destination eq "TEXT") {              $template = "$FIG_Config::template_url/$webData";
1216          # Write the message to the standard output.          } else {
1217          print "$formatted\n";              $template = "<<$webData";
1218      } elsif ($Destination eq "ERROR") {          }
1219          # Write the message to the error output.          $outputString = PageBuilder::Build($template, $varHash, "Html");
1220          print STDERR "$formatted\n";      } else {
1221      } elsif ($Destination eq "QUEUE") {          # Here the user gave us a raw string.
1222          # Push the message into the queue.          $outputString = $webData;
1223          push @Queue, "$formatted";      }
1224      } elsif ($Destination eq "HTML") {      # Check for trace messages.
1225          # Convert the message to HTML and write it to the standard output.      if ($Destination ne "NONE" && $TraceLevel > 0) {
1226          my $escapedMessage = CGI::escapeHTML($message);          # We have trace messages, so we want to put them at the end of the body. This
1227          print "<p>$timeStamp $LastCategory: $escapedMessage</p>\n";          # is either at the end of the whole string or at the beginning of the BODY
1228      } elsif ($Destination eq "WARN") {          # end-tag.
1229         # Emit the message as a warning.          my $pos = length $outputString;
1230         warn $message;          if ($outputString =~ m#</body>#gi) {
1231      } elsif ($Destination =~ m/^>>/) {              $pos = (pos $outputString) - 7;
1232          # Write the trace message to an output file.          }
1233          (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";          # If the trace messages were queued, we unroll them. Otherwise, we display the
1234          print TRACING "$formatted\n";          # destination.
1235          close TRACING;          my $traceHtml;
1236          # If the Tee flag is on, echo it to the standard output.          if ($Destination eq "QUEUE") {
1237          if ($TeeFlag) {              $traceHtml = QTrace('Html');
1238              print "$formatted\n";          } 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            substr $outputString, $pos, 0, $traceHtml;
1248      }      }
1249        # Write the output string.
1250        print $outputString;
1251  }  }
1252    
1253  =head3 T  =head2 Command-Line Utility Methods
1254    
1255      my $switch = T($category, $traceLevel);  =head3 SendSMS
1256    
1257      or      my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1258    
1259      my $switch = T($traceLevel);  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  Return TRUE if the trace level is at or above a specified value and the specified category      $phone =  { user => 'BruceTheHumanPet',
1266  is active, else FALSE. If no category is specified, the caller's package name is used.                  password => 'silly',
1267                    api_id => '2561022' };
1268    
1269    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 message ID will be returned if successful, and C<undef> if an error occurs.
1274    
1275  =over 4  =over 4
1276    
1277  =item category  =item phoneNumber
1278    
1279  Category to which the message belongs. If not specified, the caller's package name is  Phone number to receive the message, in international format. A United States phone number
1280  used.  would be prefixed by "1". A British phone number would be prefixed by "44".
1281    
1282  =item traceLevel  =item msg
1283    
1284  Relevant tracing level.  Message to send to the specified phone.
1285    
1286  =item RETURN  =item RETURN
1287    
1288  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  Returns the message ID if successful, and C<undef> if the message could not be sent.
1289    
1290  =back  =back
1291    
1292  =cut  =cut
1293    
1294  sub T {  sub SendSMS {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
1295          # Get the parameters.          # Get the parameters.
1296          my ($category, $traceLevel) = @_;      my ($phoneNumber, $msg) = @_;
1297          if (!defined $traceLevel) {      # Declare the return variable. If we do not change it, C<undef> will be returned.
1298              # Here we have no category, so we need to get the calling package.      my $retVal;
1299              # The calling package is normally the first parameter. If it is      # Only proceed if we have phone support.
1300              # omitted, the first parameter will be the tracelevel. So, the      if (! defined $FIG_Config::phone) {
1301              # first thing we do is shift the so-called category into the          Trace("Phone support not present in FIG_Config.") if T(1);
             # $traceLevel variable where it belongs.  
             $traceLevel = $category;  
             my ($package, $fileName, $line) = caller;  
             # If there is no calling package, we default to "main".  
             if (!$package) {  
                 $category = "main";  
1302              } else {              } else {
1303                  my @cats = split /::/, $package;          # Get the phone data.
1304                  $category = $cats[$#cats];          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          }          }
         # Save the category name.  
         $LastCategory = $category;  
         # Convert it to lower case before we hash it.  
         $category = lc $category;  
         # Use the category and tracelevel to compute the result.  
         if (ref $traceLevel) {  
             Confess("Bad trace level.");  
         } elsif (ref $TraceLevel) {  
             Confess("Bad trace config.");  
1326          }          }
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
1327      }      }
1328      # Return the computed result.      # Return the result.
1329      return $retVal;      return $retVal;
1330  }  }
1331    
1332  =head3 ParseCommand  =head3 StandardSetup
   
     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.  
1333    
1334      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);      my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1335    
1336  In this case, the list @words will be treated as a command line and there are two options available,  This method performs standard command-line parsing and tracing setup. The return
1337  B<errors> and B<logFile>. If @words has the following format  values are a hash of the command-line options and a list of the positional
1338    parameters. Tracing is automatically set up and the command-line options are
1339    validated.
1340    
1341      -logFile=error.log apple orange rutabaga  This is a complex method that does a lot of grunt work. The parameters can
1342    be more easily understood, however, once they are examined individually.
1343    
1344  then at the end of the invocation, C<$options> will be  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      { errors => 0, logFile => 'error.log' }      ["Sprout", "SproutLoad", "ERDB"]
1350    
1351  and C<@arguments> will contain  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      apple orange rutabaga  =over 4
1358    
1359  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  =item SQL
 support for quote characters. Options can be specified with single or double hyphens.  
1360    
1361  =over 4  Traces SQL commands and activity.
1362    
1363  =item optionTable  =item Tracer
1364    
1365  Table of default options.  Traces error messages and call stacks.
1366    
1367  =item inputList  =back
1368    
1369  List of words on the command line.  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  =item RETURN      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1375    
1376  Returns a reference to the option table and a list of the positional arguments.  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  =back  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  =cut      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1385    
1386  sub ParseCommand {  would send the trace output to C<traceBruce.log> in the temporary directory.
     # Get the parameters.  
     my ($optionTable, @inputList) = @_;  
     # Process any options in the input list.  
     my %overrides = ();  
     while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {  
         # Get the current option.  
         my $arg = shift @inputList;  
         # 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);  
         } else {  
             # Here there is no value, so we use 1.  
             $overrides{$name} = 1;  
         }  
     }  
     # Merge the options into the defaults.  
     GetOptions($optionTable, \%overrides);  
     # Translate the remaining parameters.  
     my @retVal = ();  
     for my $inputParm (@inputList) {  
         push @retVal, UnEscape($inputParm);  
     }  
     # Return the results.  
     return ($optionTable, @retVal);  
 }  
1387    
1388  =head3 Escape  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      my $codedString = Tracer::Escape($realString);  You can specify a different default trace level by setting C<$options->{trace}>
1396    prior to calling this method.
1397    
1398  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  An example at this point would help. Consider, for example, the command-line utility
1399  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  C<TransactFeatures>. It accepts a list of positional parameters plus the options
1400  result is to reverse the effect of L</UnEscape>.  C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1401    the following code.
1402    
1403        my ($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  =over 4
1494    
1495  =item realString  =item categories
1496    
1497  String to escape.  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($retOptions->{user});
1577          } else {          } else {
1578              # Here there are no more escape sequences. The rest of the string is          # Here the tracing is controlled from the command line.
1579              # transferred unmodified.          my @cats = @{$categories};
1580              $retVal .= $realString;          if ($retOptions->{sql}) {
1581              $realString = "";              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      # Return the result.          }
1619      return $retVal;          # Now set up the tracing.
1620            TSetup("$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                print "  $name $desc\n";
1634            }
1635            exit(0);
1636        }
1637        # Trace the options, if applicable.
1638        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      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++;
1698                      $retVal .= $char;          } else {
1699                  }              # Here we have an invalid line.
1700              } else {              Trace("Invalid option statement in record $records.") if T(0);
                 # Here there are no more escape sequences. The rest of the string is  
                 # transferred unmodified.  
                 $retVal .= $codedString;  
                 $codedString = "";  
             }  
1701          }          }
1702      }      }
1703      # Return the result.      # Return the hash created.
1704      return $retVal;      return %retVal;
1705  }  }
1706    
1707  =head3 ParseRecord  =head3 GetOptions
1708    
1709      my @fields = Tracer::ParseRecord($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;
1761          # 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;  
1762      }      }
1763      # Return the result.      }
1764      return @retVal;      # Return the merged table.
1765        return $defaults;
1766  }  }
1767    
1768  =head3 Merge  =head3 MergeOptions
1769    
1770      my @mergedList = Tracer::Merge(@inputList);      Tracer::MergeOptions(\%table, \%defaults);
1771    
1772  Sort a list of strings and remove duplicates.  Merge default values into a hash table. This method looks at the key-value pairs in the
1773    second (default) hash, and if a matching key is not found in the first hash, the default
1774    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1775    checking and no return value.
1776    
1777  =over 4  =over 4
1778    
1779  =item inputList  =item table
1780    
1781  List of scalars to sort and merge.  Hash table to be updated with the default values.
1782    
1783  =item RETURN  =item defaults
1784    
1785  Returns a list containing the same elements sorted in ascending order with duplicates  Default values to be merged into the first hash table if they are not already present.
 removed.  
1786    
1787  =back  =back
1788    
1789  =cut  =cut
1790    
1791  sub Merge {  sub MergeOptions {
1792      # Get the input list in sort order.      # Get the parameters.
1793      my @inputList = sort @_;      my ($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      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    
# Line 1711  Line 1977 
1977      close $handle;      close $handle;
1978  }  }
1979    
1980  =head3 QTrace  =head3 ParseRecord
1981    
1982      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              $retVal .= "</ul>\n";          # Convert the escapes into their real values.
2018          } elsif ($format =~ m/^TEXT$/i) {          $value =~ s/\\t/"\t"/ge;
2019              # Convert the queue into a list of text lines.          $value =~ s/\\n/"\n"/ge;
             $retVal = join("\n", @Queue) . "\n";  
         }  
         # Clear the queue.  
         @Queue = ();  
2020      }      }
2021      # Return the formatted list.      # Return the result.
2022      return $retVal;      return @retVal;
2023  }  }
2024    
2025  =head3 Confess  =head3 Merge
2026    
2027      Confess($message);      my @mergedList = Tracer::Merge(@inputList);
2028    
2029  Trace the call stack and abort the program with the specified message. When used with  Sort a list of strings and remove duplicates.
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
2030    
2031      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");  =over 4
2032    
2033  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item inputList
2034    
2035  =over 4  List of scalars to sort and merge.
2036    
2037  =item message  =item RETURN
2038    
2039  Message to include in the trace.  Returns a list containing the same elements sorted in ascending order with duplicates
2040    removed.
2041    
2042  =back  =back
2043    
2044  =cut  =cut
2045    
2046  sub Confess {  sub Merge {
2047      # Get the parameters.      # Get the input list in sort order.
2048      my ($message) = @_;      my @inputList = sort @_;
2049      if (! defined($FIG_Config::no_tool_hdr)) {      # Only proceed if the list has at least two elements.
2050          # Here we have a tool header. Display its length so that the user can adjust the line numbers.      if (@inputList > 1) {
2051          my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";          # Now we want to move through the list splicing out duplicates.
2052          # Only proceed if the tool header file is actually present.          my $i = 0;
2053          if (-f $toolHeaderFile) {          while ($i < @inputList) {
2054              my @lines = GetFile($toolHeaderFile);              # Get the current entry.
2055              Trace("Tool header has " . scalar(@lines) . " lines.");              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                # Now the element at position $dup1 is different from the element before it
2065                # at position $i. We push $i forward one position and start again.
2066                $i++;
2067      }      }
2068      # Trace the call stack.      }
2069      Cluck($message);      # Return the merged list.
2070      # Abort the program.      return @inputList;
     croak(">>> $message");  
2071  }  }
2072    
2073  =head3 Assert  =head3 Open
   
     Assert($condition1, $condition2, ... $conditionN);  
2074    
2075  Return TRUE if all the conditions are true. This method can be used in conjunction with      my $handle = Open($fileHandle, $fileSpec, $message);
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
2076    
2077      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");  Open a file.
2078    
2079  Will abort the program with a stack trace if the value of C<$recNum> is negative.  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  =cut      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
         }  
     }  
     return $retVal;  
 }  
2084    
2085  =head3 Cluck  would open for output appended to the specified file, and
2086    
2087      Cluck($message);      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2088    
2089  Trace the call stack. Note that for best results, you should qualify the call with a  would open a pipe that sorts the records written and removes duplicates. Note
2090  trace condition. For example,  the use of file handle syntax in the Open call. To use anonymous file handles,
2091    code as follows.
2092    
2093      Cluck("Starting record parse.") if T(3);      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2094    
2095  will only trace the stack if the trace level for the package is 3 or more.  The I<$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  =over 4      Could not open "/usr/spool/news/twitlog"
2102    
2103  =item message  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  Message to include in the trace.      Could not open "/usr/spool/news/twitlog": file not found.
2108    
2109  =back  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  =cut      Could not open "/usr/spool/news/twitlog": 6.
2113    
2114  sub Cluck {  =over 4
     # 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/);  
     }  
 }  
2115    
2116  =head3 Min  =item fileHandle
2117    
2118      my $min = Min($value1, $value2, ... $valueN);  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  Return the minimum argument. The arguments are treated as numbers.  =item fileSpec
2122    
2123  =over 4  File name and mode, as per the PERL C<open> function.
2124    
2125  =item $value1, $value2, ... $valueN  =item message (optional)
2126    
2127  List of numbers to compare.  Error message to use if the open fails. If omitted, a standard error message
2128    will be generated. In either case, the error information from the file system
2129    is appended to the message. To specify a conditional open that does not throw
2130    an error if it fails, use C<0>.
2131    
2132  =item RETURN  =item RETURN
2133    
2134  Returns the lowest number in the list.  Returns the name of the file handle assigned to the file, or C<undef> if the
2135    open failed.
2136    
2137  =back  =back
2138    
2139  =cut  =cut
2140    
2141  sub Min {  sub Open {
2142      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2143      my ($retVal, @values) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2144      # Loop through the remaining parameters, looking for the lowest.      # Attempt to open the file.
2145      for my $value (@values) {      my $rv = open $fileHandle, $fileSpec;
2146          if ($value < $retVal) {      # If the open failed, generate an error message.
2147              $retVal = $value;      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 minimum found.      # Return the file handle.
2162      return $retVal;      return $fileHandle;
2163  }  }
2164    
2165  =head3 Max  =head3 FindNamePart
2166    
2167      my $max = Max($value1, $value2, ... $valueN);      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2168    
2169  Return the maximum argument. The arguments are treated as numbers.  Extract the portion of a file specification that contains the file name.
2170    
2171    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        >>/usr/fig/myfile.txt
2178        </usr/fig/myfile.txt
2179        | sort -u > /usr/fig/myfile.txt
2180    
2181    If the method cannot find a file name using its normal methods, it will return the
2182    whole incoming string.
2183    
2184  =over 4  =over 4
2185    
2186  =item $value1, $value2, ... $valueN  =item fileSpec
2187    
2188  List of numbers to compare.  File specification string from which the file name is to be extracted.
2189    
2190  =item RETURN  =item RETURN
2191    
2192  Returns the highest number in the list.  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  =back
2198    
2199  =cut  =cut
2200    #: Return Type $;
2201  sub Max {  sub FindNamePart {
2202      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2203      my ($retVal, @values) = @_;      my ($fileSpec) = @_;
2204      # Loop through the remaining parameters, looking for the highest.      # Default to the whole input string.
2205      for my $value (@values) {      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2206          if ($value > $retVal) {      # Parse out the file name if we can.
2207              $retVal = $value;      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2208          }          $retVal = $2;
2209            $len = length $retVal;
2210            $pos = (length $fileSpec) - (length $3) - $len;
2211      }      }
2212      # Return the maximum found.      # Return the result.
2213      return $retVal;      return ($retVal, $pos, $len);
2214  }  }
2215    
2216  =head3 AddToListMap  =head3 OpenDir
2217    
2218      Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN);      my @files = OpenDir($dirName, $filtered, $flag);
2219    
2220  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Open a directory and return all the file names. This function essentially performs
2221  is created for the key. Otherwise, the new value is pushed onto the list.  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
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  =over 4      my @files = OpenDir("/Volumes/fig/contigs", 1);
2228    
2229  =item hash  is effectively the same as
2230    
2231  Reference to the target hash.      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2232        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2233    
2234  =item key  Similarly, the following code
2235    
2236  Key for which the value is to be added.      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2237    
2238  =item value1, value2, ... valueN  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2239    automatically returns an empty list if the directory fails to open.
2240    
2241  List of values to add to the key's value list.  =over 4
2242    
2243  =back  =item dirName
2244    
2245  =cut  Name of the directory to open.
2246    
2247  sub AddToListMap {  =item filtered
     # Get the parameters.  
     my ($hash, $key, @values) = @_;  
     # Process according to whether or not the key already has a value.  
     if (! exists $hash->{$key}) {  
         $hash->{$key} = [@values];  
     } else {  
         push @{$hash->{$key}}, @values;  
     }  
 }  
2248    
2249  =head3 DebugMode  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2250    from the list, else FALSE.
2251    
2252      if (Tracer::DebugMode) { ...code... }  =item flag
2253    
2254  Return TRUE if debug mode has been turned on, else abort.  TRUE if a failure to open is okay, else FALSE
2255    
2256  Certain CGI scripts are too dangerous to exist in the production  =back
 environment. This method provides a simple way to prevent them  
 from working unless they are explicitly turned on by creating a password  
 cookie via the B<SetPassword> script.  If debugging mode  
 is not turned on, an error will occur.  
2257    
2258  =cut  =cut
2259    #: Return Type @;
2260  sub DebugMode {  sub OpenDir {
2261        # Get the parameters.
2262        my ($dirName, $filtered, $flag) = @_;
2263      # Declare the return variable.      # Declare the return variable.
2264      my $retVal = 0;      my @retVal = ();
2265      # Check the debug configuration.      # Open the directory.
2266      my $password = CGI::cookie("DebugMode");      if (opendir(my $dirHandle, $dirName)) {
2267      my $encrypted = Digest::MD5::md5_hex($password);          # The directory opened successfully. Get the appropriate list according to the
2268      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {          # strictures of the filter parameter.
2269          $retVal = 1;          if ($filtered) {
2270                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2271      } else {      } else {
2272          # Here debug mode is off, so we generate an error.              @retVal = readdir $dirHandle;
         Confess("Cannot use this facility without logging in.");  
2273      }      }
2274      # Return the determination indicator.      } elsif (! $flag) {
2275      return $retVal;          # Here the directory would not open and it's considered an error.
2276            Confess("Could not open directory $dirName.");
2277        }
2278        # Return the result.
2279        return @retVal;
2280  }  }
2281    
 =head3 Strip  
2282    
2283      my $string = Tracer::Strip($line);  =head3 Insure
2284    
2285  Strip all line terminators off a string. This is necessary when dealing with files      Insure($dirName, $chmod);
2286  that may have been transferred back and forth several times among different  
2287  operating environments.  Insure a directory is present.
2288    
2289  =over 4  =over 4
2290    
2291  =item line  =item dirName
2292    
2293  Line of text to be stripped.  Name of the directory to check. If it does not exist, it will be created.
2294    
2295  =item RETURN  =item chmod (optional)
2296    
2297  The same line of text with all the line-ending characters chopped from the end.  Security privileges to be given to the directory if it is created.
2298    
2299  =back  =back
2300    
2301  =cut  =cut
2302    
2303  sub Strip {  sub Insure {
2304      # Get a copy of the parameter string.      my ($dirName, $chmod) = @_;
2305      my ($string) = @_;      if (! -d $dirName) {
2306      my $retVal = (defined $string ? $string : "");          Trace("Creating $dirName directory.") if T(2);
2307      # Strip the line terminator characters.          eval {
2308      $retVal =~ s/(\r|\n)+$//g;              mkpath $dirName;
2309      # Return the result.              # If we have permissions specified, set them here.
2310      return $retVal;              if (defined($chmod)) {
2311                    chmod $chmod, $dirName;
2312                }
2313            };
2314            if ($@) {
2315                Confess("Error creating $dirName: $@");
2316            }
2317        }
2318  }  }
2319    
2320  =head3 Pad  =head3 ChDir
2321    
2322      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);      ChDir($dirName);
2323    
2324  Pad a string to a specified length. The pad character will be a  Change to the specified directory.
 space, and the padding will be on the right side unless specified  
 in the third parameter.  
2325    
2326  =over 4  =over 4
2327    
2328  =item string  =item dirName
   
 String to be padded.  
   
 =item len  
   
 Desired length of the padded string.  
   
 =item left (optional)  
   
 TRUE if the string is to be left-padded; otherwise it will be padded on the right.  
   
 =item padChar (optional)  
   
 Character to use for padding. The default is a space.  
   
 =item RETURN  
2329    
2330  Returns a copy of the original string with the pad character added to the  Name of the directory to which we want to change.
 specified end so that it achieves the desired length.  
2331    
2332  =back  =back
2333    
2334  =cut  =cut
2335    
2336  sub Pad {  sub ChDir {
2337      # Get the parameters.      my ($dirName) = @_;
2338      my ($string, $len, $left, $padChar) = @_;      if (! -d $dirName) {
2339      # Compute the padding character.          Confess("Cannot change to directory $dirName: no such directory.");
     if (! defined $padChar) {  
         $padChar = " ";  
     }  
     # Compute the number of spaces needed.  
     my $needed = $len - length $string;  
     # Copy the string into the return variable.  
     my $retVal = $string;  
     # Only proceed if padding is needed.  
     if ($needed > 0) {  
         # Create the pad string.  
         my $pad = $padChar x $needed;  
         # Affix it to the return value.  
         if ($left) {  
             $retVal = $pad . $retVal;  
2340          } else {          } else {
2341              $retVal .= $pad;          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      }      }
     # Return the result.  
     return $retVal;  
2347  }  }
2348    
2349  =head3 EOF  =head3 SetPermissions
2350    
2351  This is a constant that is lexically greater than any useful string.      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2352    
2353  =cut  Set the permissions for a directory and all the files and folders inside it.
2354    In addition, the group ownership will be changed to the specified value.
2355    
2356  sub EOF {  This method is more vulnerable than most to permission and compatability
2357      return "\xFF\xFF\xFF\xFF\xFF";  problems, so it does internal error recovery.
 }  
2358    
2359  =head3 TICK  =over 4
2360    
2361      my @results = TICK($commandString);  =item dirName
2362    
2363  Perform a back-tick operation on a command. If this is a Windows environment, any leading  Name of the directory to process.
 dot-slash (C<./> will be removed. So, for example, if you were doing  
2364    
2365      `./protein.cgi`  =item group
2366    
2367  from inside a CGI script, it would work fine in Unix, but would issue an error message  Name of the group to be assigned.
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
2368    
2369      TICK("./protein.cgi")  =item mask
2370    
2371  it will work correctly in both environments.  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  =over 4  =item otherMasks
2376    
2377  =item commandString  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 command string to pass to the system.      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2383    
2384  =item RETURN  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  Returns the standard output from the specified command, as a list.      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2388                                                       '^tmp' => 0666);
2389    
2390    Note that the pattern matches are all case-insensitive, and only directory
2391    names are matched, not file names.
2392    
2393  =back  =back
2394    
2395  =cut  =cut
2396  #: Return Type @;  
2397  sub TICK {  sub SetPermissions {
2398      # Get the parameters.      # Get the parameters.
2399      my ($commandString) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2400      # Chop off the dot-slash if this is Windows.      # Set up for error recovery.
2401      if ($FIG_Config::win_mode) {      eval {
2402          $commandString =~ s!^\./!!;          # Switch to the specified directory.
2403            ChDir($dirName);
2404            # 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: $@");
2480      }      }
     # Activate the command and return the result.  
     return `$commandString`;  
2481  }  }
2482    
2483  =head3 ScriptSetup  =head3 GetLine
   
     my ($cgi, $varHash) = ScriptSetup($noTrace);  
2484    
2485  Perform standard tracing and debugging setup for scripts. The value returned is      my @data = Tracer::GetLine($handle);
 the CGI object followed by a pre-built variable hash. At the end of the script,  
 the client should call L</ScriptFinish> to output the web page.  
2486    
2487  This method calls L</ETracing> to configure tracing, which allows the tracing  Read a line of data from a tab-delimited file.
 to be configured via the emergency tracing form on the debugging control panel.  
 Tracing will then be turned on automatically for all programs that use the L</ETracing>  
 method, which includes every program that uses this method or L</StandardSetup>.  
2488    
2489  =over 4  =over 4
2490    
2491  =item noTrace (optional)  =item handle
2492    
2493  If specified, tracing will be suppressed. This is useful if the script wants to set up  Open file handle from which to read.
 tracing manually.  
2494    
2495  =item RETURN  =item RETURN
2496    
2497  Returns a two-element list consisting of a CGI query object and a variable hash for  Returns a list of the fields in the record read. The fields are presumed to be
2498  the output page.  tab-delimited. If we are at the end of the file, then an empty list will be
2499    returned. If an empty line is read, a single list item consisting of a null
2500    string will be returned.
2501    
2502  =back  =back
2503    
2504  =cut  =cut
2505    
2506  sub ScriptSetup {  sub GetLine {
2507      # Get the parameters.      # Get the parameters.
2508      my ($noTrace) = @_;      my ($handle) = @_;
2509      # Get the CGI query object.      # Declare the return variable.
2510      my $cgi = CGI->new();      my @retVal = ();
2511      # Set up tracing if it's not suppressed.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2512      ETracing($cgi) unless $noTrace;      # Read from the file.
2513      # Create the variable hash.      my $line = <$handle>;
2514      my $varHash = { results => '' };      # Only proceed if we found something.
2515      # Return the query object and variable hash.      if (defined $line) {
2516      return ($cgi, $varHash);          # 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            # If the line is empty, return a single empty string; otherwise, parse
2528            # it into fields.
2529            if ($line eq "") {
2530                push @retVal, "";
2531            } else {
2532                push @retVal, split /\t/,$line;
2533            }
2534        } else {
2535            # Trace the reason the read failed.
2536            Trace("End of file: $!") if T(File => 3);
2537        }
2538        # Return the result.
2539        return @retVal;
2540  }  }
2541    
2542  =head3 ETracing  =head3 PutLine
2543    
2544      ETracing($parameter);      Tracer::PutLine($handle, \@fields, $eol);
2545    
2546  Set up emergency tracing. Emergency tracing is tracing that is turned  Write a line of data to a tab-delimited file. The specified field values will be
2547  on automatically for any program that calls this method. The emergency  output in tab-separated form, with a trailing new-line.
 tracing parameters are stored in a a file identified by a tracing key.  
 If this method is called with a CGI object, then the tracing key is  
 taken from a cookie. If it is called with no parameters, then the tracing  
 key is taken from an environment variable. If it is called with a string,  
 the tracing key is that string.  
2548    
2549  =over 4  =over 4
2550    
2551  =item parameter  =item handle
2552    
2553  A parameter from which the tracing key is computed. If it is a scalar,  Output file handle.
2554  that scalar is used as the tracing key. If it is a CGI object, the  
2555  tracing key is taken from the C<IP> cookie. If it is omitted, the  =item fields
2556  tracing key is taken from the C<TRACING> environment variable. If it  
2557  is a CGI object and emergency tracing is not on, the C<Trace> and  List of field values.
2558  C<TF> parameters will be used to determine the type of tracing.  
2559    =item eol (optional)
2560    
2561    End-of-line character (default is "\n").
2562    
2563  =back  =back
2564    
2565  =cut  =cut
2566    
2567  sub ETracing {  sub PutLine {
2568      # Get the parameter.      # Get the parameters.
2569      my ($parameter) = @_;      my ($handle, $fields, $eol) = @_;
2570      # Check for CGI mode.      # Write the data.
2571      my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);      print $handle join("\t", @{$fields}) . ($eol || "\n");
     # Default to no tracing except errors.  
     my ($tracing, $dest) = ("0", "WARN");  
     # Check for emergency tracing.  
     my $tkey = EmergencyKey($parameter);  
     my $emergencyFile = EmergencyFileName($tkey);  
     if (-e $emergencyFile) {  
         # We have the file. Read in the data.  
         my @tracing = GetFile($emergencyFile);  
         # Pull off the time limit.  
         my $expire = shift @tracing;  
         # Convert it to seconds.  
         $expire *= 3600;  
         # Check the file data.  
         my $stat = stat($emergencyFile);  
         my ($now) = gettimeofday;  
         if ($now - $stat->mtime > $expire) {  
             # Delete the expired file.  
             unlink $emergencyFile;  
         } else {  
             # Emergency tracing is on. Pull off the destination and  
             # the trace level;  
             $dest = shift @tracing;  
             my $level = shift @tracing;  
             # Convert the destination to a real tracing destination.  
             # temp directory.  
             $dest = EmergencyTracingDest($tkey, $dest);  
             # Insure Tracer is specified.  
             my %moduleHash = map { $_ => 1 } @tracing;  
             $moduleHash{Tracer} = 1;  
             # Set the trace parameter.  
             $tracing = join(" ", $level, sort keys %moduleHash);  
         }  
     } elsif (defined $cgi) {  
         # There's no emergency tracing, but we have a CGI object, so check  
         # for tracing from the form parameters.  
         if ($cgi->param('Trace')) {  
             # Here the user has requested tracing via a form.  
             $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");  
             $tracing = $cgi->param('Trace') . " Tracer";  
         }  
     }  
     # Setup the tracing we've determined from all the stuff above.  
     TSetup($tracing, $dest);  
     # If we're a web script, trace the parameter and environment data.  
     if (defined $cgi) {  
         TraceParms($cgi);  
     }  
2572  }  }
2573    
 =head3 EmergencyFileName  
   
     my $fileName = Tracer::EmergencyFileName($tkey);  
2574    
2575  Return the emergency tracing file name. This is the file that specifies  =head3 PrintLine
 the tracing information.  
2576    
2577  =over 4      Tracer::PrintLine($line);
2578    
2579  =item tkey  Print a line of text with a trailing new-line.
2580    
2581  Tracing key for the current program.  =over 4
2582    
2583  =item RETURN  =item line
2584    
2585  Returns the name of the file to contain the emergency tracing information.  Line of text to print.
2586    
2587  =back  =back
2588    
2589  =cut  =cut
2590    
2591  sub EmergencyFileName {  sub PrintLine {
2592      # Get the parameters.      # Get the parameters.
2593      my ($tkey) = @_;      my ($line) = @_;
2594      # Compute the emergency tracing file name.      # Print the line.
2595      return "$FIG_Config::temp/Emergency$tkey.txt";      print "$line\n";
2596  }  }
2597    
 =head3 EmergencyFileTarget  
2598    
2599      my $fileName = Tracer::EmergencyFileTarget($tkey);  =head2 Other Useful Methods
2600    
2601  Return the emergency tracing target file name. This is the file that receives  =head3 ParseParm
2602  the tracing output for file-based tracing.  
2603        my $listValue = Tracer::ParseParm($string);
2604    
2605    Convert a parameter into a list reference. If the parameter is undefined,
2606    an undefined value will be returned. Otherwise, it will be parsed as a
2607    comma-separated list of values.
2608    
2609  =over 4  =over 4
2610    
2611  =item tkey  =item string
2612    
2613  Tracing key for the current program.  Incoming string.
2614    
2615  =item RETURN  =item RETURN
2616    
2617  Returns the name of the file to contain the trace output.  Returns a reference to a list of values, or C<undef> if the incoming value
2618    was undefined.
2619    
2620  =back  =back
2621    
2622  =cut  =cut
2623    
2624  sub EmergencyFileTarget {  sub ParseParm {
2625      # Get the parameters.      # Get the parameters.
2626      my ($tkey) = @_;      my ($string) = @_;
2627      # Compute the emergency tracing file name.      # Declare the return variable.
2628      return "$FIG_Config::temp/trace$tkey.log";      my $retVal;
2629        # Check for data.
2630        if (defined $string) {
2631            # We have some, so split it into a list.
2632            $retVal = [ split /\s*,\s*/, $string];
2633        }
2634        # Return the result.
2635        return $retVal;
2636  }  }
2637    
2638  =head3 EmergencyTracingDest  =head3 Now
2639    
2640      my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);      my $string = Tracer::Now();
2641    
2642  This method converts an emergency tracing destination to a real  Return a displayable time stamp containing the local time. Whatever format this
2643  tracing destination. The main difference is that if the  method produces must be parseable by L</ParseDate>.
 destination is C<FILE> or C<APPEND>, we convert it to file  
 output. If the destination is C<DUAL>, we convert it to file  
 and standard output.  
2644    
2645  =over 4  =cut
2646    
2647  =item tkey  sub Now {
2648        return DisplayTime(time);
2649    }
2650    
2651  Tracing key for this environment.  =head3 DisplayTime
2652    
2653  =item myDest      my $string = Tracer::DisplayTime($time);
2654    
2655  Destination from the emergency tracing file.  Convert a time value to a displayable time stamp. Whatever format this
2656    method produces must be parseable by L</ParseDate>.
2657    
2658    =over 4
2659    
2660    =item time
2661    
2662    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 a destination that can be passed into L</TSetup>.  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 EmergencyTracingDest {  sub DisplayTime {
2673      # Get the parameters.      my ($time) = @_;
2674      my ($tkey, $myDest) = @_;      my $retVal = "(n/a)";
2675      # Declare the return variable.      if (defined $time) {
2676      my $retVal = $myDest;          my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2677      # Process according to the destination value.          $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2678      if ($myDest eq 'FILE') {                    _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
         $retVal = ">" . EmergencyFileTarget($tkey);  
     } elsif ($myDest eq 'APPEND') {  
         $retVal = ">>" . EmergencyFileTarget($tkey);  
     } elsif ($myDest eq 'DUAL') {  
         $retVal = "+>" . EmergencyFileTarget($tkey);  
2679      }      }
     # Return the result.  
2680      return $retVal;      return $retVal;
2681  }  }
2682    
2683  =head3 Emergency  # Pad a number to 2 digits.
2684    sub _p2 {
2685      Emergency($key, $hours, $dest, $level, @modules);      my ($value) = @_;
2686        $value = "0$value" if ($value < 10);
2687  Turn on emergency tracing. This method is normally invoked over the web from      return $value;
2688  a debugging console, but it can also be called by the C<trace.pl> script.  }
 The caller specifies the duration of the emergency in hours, the desired tracing  
 destination, the trace level, and a list of the trace modules to activate.  
 For the length of the duration, when a program in an environment with the  
 specified tracing key active invokes a Sprout CGI script, tracing will be  
 turned on automatically. See L</TSetup> for more about tracing setup and  
 L</ETracing> for more about emergency tracing.  
   
 =over 4  
   
 =item tkey  
   
 The tracing key. This is used to identify the control file and the trace file.  
2689    
2690  =item hours  =head3 Escape
2691    
2692  Number of hours to keep emergency tracing alive.      my $codedString = Tracer::Escape($realString);
2693    
2694  =item dest  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 destination. If no path information is specified for a file  =over 4
 destination, it is put in the FIG temporary directory.  
2699    
2700  =item level  =item realString
2701    
2702  Tracing level. A higher level means more trace messages.  String to escape.
2703    
2704  =item modules  =item RETURN
2705    
2706  A list of the tracing modules to activate.  Escaped equivalent of the real string.
2707    
2708  =back  =back
2709    
2710  =cut  =cut
2711    
2712  sub Emergency {  sub Escape {
2713      # Get the parameters.      # Get the parameter.
2714      my ($tkey, $hours, $dest, $level, @modules) = @_;      my ($realString) = @_;
2715      # Create the emergency file.      # Initialize the return variable.
2716      my $specFile = EmergencyFileName($tkey);      my $retVal = "";
2717      my $outHandle = Open(undef, ">$specFile");      # Loop through the parameter string, looking for sequences to escape.
2718      print $outHandle join("\n", $hours, $dest, $level, @modules, "");      while (length $realString > 0) {
2719            # Look for the first sequence to escape.
2720            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2721                # 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 {
2735                # 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.
2742        return $retVal;
2743  }  }
2744    
2745  =head3 EmergencyKey  =head3 UnEscape
2746    
2747      my $tkey = EmergencyKey($parameter);      my $realString = Tracer::UnEscape($codedString);
2748    
2749  Return the Key to be used for emergency tracing. This could be an IP address,  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2750   a session ID, or a user name, depending on the environment.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2751    be deleted.
2752    
2753  =over 4  =over 4
2754    
2755  =item parameter  =item codedString
2756    
2757  Parameter defining the method for finding the tracing key. If it is a scalar,  String to un-escape.
 then it is presumed to be the tracing key itself. If it is a CGI object, then  
 the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is  
 taken from the C<TRACING> environment variable.  
2758    
2759  =item RETURN  =item RETURN
2760    
2761  Returns the key to be used for labels in emergency tracing.  Returns a copy of the original string with the escape sequences converted to their actual
2762    values.
2763    
2764  =back  =back
2765    
2766  =cut  =cut
2767    
2768  sub EmergencyKey {  sub UnEscape {
2769      # Get the parameters.      # Get the parameter.
2770      my ($parameter) = @_;      my ($codedString) = @_;
2771      # Declare the return variable.      # Initialize the return variable.
2772      my $retVal;      my $retVal = "";
2773      # Determine the parameter type.      # Only proceed if the incoming string is nonempty.
2774      if (! defined $parameter) {      if (defined $codedString) {
2775          # Here we're supposed to check the environment.          # Loop through the parameter string, looking for escape sequences. We can't do
2776          $retVal = $ENV{TRACING};          # 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 {      } else {
2794          my $ptype = ref $parameter;                  # Here there are no more escape sequences. The rest of the string is
2795          if ($ptype eq 'CGI') {                  # transferred unmodified.
2796              # Here we were invoked from a web page. Look for a cookie.                  $retVal .= $codedString;
2797              $retVal = $parameter->cookie('IP');                  $codedString = "";
         } elsif (! $ptype) {  
             # Here the key was passed in.  
             $retVal = $parameter;  
2798          }          }
2799      }      }
     # If no luck finding a key, use the PID.  
     if (! defined $retVal) {  
         $retVal = $$;  
2800      }      }
2801      # Return the result.      # Return the result.
2802      return $retVal;      return $retVal;
2803  }  }
2804    
2805    =head3 Percent
2806    
2807  =head3 TraceParms      my $percent = Tracer::Percent($number, $base);
   
     Tracer::TraceParms($cgi);  
2808    
2809  Trace the CGI parameters at trace level CGI => 3 and the environment variables  Returns the percent of the base represented by the given number. If the base
2810  at level CGI => 4.  is zero, returns zero.
2811    
2812  =over 4  =over 4
2813    
2814  =item cgi  =item number
2815    
2816  CGI query object containing the parameters to trace.  Percent numerator.
2817    
2818    =item base
2819    
2820    Percent base.
2821    
2822    =item RETURN
2823    
2824    Returns the percentage of the base represented by the numerator.
2825    
2826  =back  =back
2827    
2828  =cut  =cut
2829    
2830  sub TraceParms {  sub Percent {
2831      # Get the parameters.      # Get the parameters.
2832      my ($cgi) = @_;      my ($number, $base) = @_;
2833      if (T(CGI => 3)) {      # Declare the return variable.
2834          # Here we want to trace the parameter data.      my $retVal = 0;
2835          my @names = $cgi->param;      # Compute the percent.
2836          for my $parmName (sort @names) {      if ($base != 0) {
2837              # Note we skip the Trace parameters, which are for our use only.          $retVal = $number * 100 / $base;
             if ($parmName ne 'Trace' && $parmName ne 'TF') {  
                 my @values = $cgi->param($parmName);  
                 Trace("CGI: $parmName = " . join(", ", @values));  
             }  
         }  
         # Display the request method.  
         my $method = $cgi->request_method();  
         Trace("Method: $method");  
     }  
     if (T(CGI => 4)) {  
         # Here we want the environment data too.  
         for my $envName (sort keys %ENV) {  
             Trace("ENV: $envName = $ENV{$envName}");  
         }  
2838      }      }
2839        # Return the result.
2840        return $retVal;
2841  }  }
2842    
2843  =head3 ScriptFinish  =head3 Constrain
   
     ScriptFinish($webData, $varHash);  
   
 Output a web page at the end of a script. Either the string to be output or the  
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
   
 A typical standard script would loook like the following.  
   
     BEGIN {  
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
2844    
2845      my ($cgi, $varHash) = ScriptSetup();      my $constrained = Constrain($value, $min, $max);
     eval {  
         # ... get data from $cgi, put it in $varHash ...  
     };  
     if ($@) {  
         Trace("Script Error: $@") if T(0);  
     }  
     ScriptFinish("Html/MyTemplate.html", $varHash);  
2846    
2847  The idea here is that even if the script fails, you'll see trace messages and  Modify a numeric value to bring it to a point in between a maximum and a minimum.
 useful output.  
2848    
2849  =over 4  =over 4
2850    
2851  =item webData  =item value
2852    
2853  A string containing either the full web page to be written to the output or the  Value to constrain.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
2854    
2855  =item varHash (optional)  =item min (optional)
2856    
2857  If specified, then a reference to a hash mapping variable names for a template  Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
2858    
2859  =back  =item max (optional)
2860    
2861  =cut  Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
2862    
2863  sub ScriptFinish {  =item RETURN
2864      # Get the parameters.  
2865      my ($webData, $varHash) = @_;  Returns the incoming value, constrained according to the other parameters.
2866      # Check for a template file situation.  
2867      my $outputString;  =back
2868      if (defined $varHash) {  
2869          # Here we have a template file. We need to determine the template type.  =cut
2870          my $template;  
2871          if ($FIG_Config::template_url && $webData =~ /\.php$/) {  sub Constrain {
2872              $template = "$FIG_Config::template_url/$webData";      # Get the parameters.
2873          } else {      my ($value, $min, $max) = @_;
2874              $template = "<<$webData";      # Declare the return variable.
2875          }      my $retVal = $value;
2876          $outputString = PageBuilder::Build($template, $varHash, "Html");      # Apply the minimum constraint.
2877      } else {      if (defined $min && $retVal < $min) {
2878          # Here the user gave us a raw string.          $retVal = $min;
2879          $outputString = $webData;      }
2880      }      # Apply the maximum constraint.
2881      # Check for trace messages.      if (defined $max && $retVal > $max) {
2882      if ($Destination ne "NONE" && $TraceLevel > 0) {          $retVal = $max;
         # We have trace messages, so we want to put them at the end of the body. This  
         # is either at the end of the whole string or at the beginning of the BODY  
         # end-tag.  
         my $pos = length $outputString;  
         if ($outputString =~ m#</body>#gi) {  
             $pos = (pos $outputString) - 7;  
         }  
         # If the trace messages were queued, we unroll them. Otherwise, we display the  
         # destination.  
         my $traceHtml;  
         if ($Destination eq "QUEUE") {  
             $traceHtml = QTrace('Html');  
         } elsif ($Destination =~ /^>>(.+)$/) {  
             # Here the tracing output it to a file. We code it as a hyperlink so the user  
             # can copy the file name into the clipboard easily.  
             my $actualDest = $1;  
             $traceHtml = "<p>Tracing output to $actualDest.</p>\n";  
         } else {  
             # Here we have one of the special destinations.  
             $traceHtml = "<P>Tracing output type is $Destination.</p>\n";  
         }  
         substr $outputString, $pos, 0, $traceHtml;  
2883      }      }
2884      # Write the output string.      # Return the result.
2885      print $outputString;      return $retVal;
2886  }  }
2887    
2888  =head3 Insure  =head3 Min
2889    
2890      Insure($dirName, $chmod);      my $min = Min($value1, $value2, ... $valueN);
2891    
2892  Insure a directory is present.  Return the minimum argument. The arguments are treated as numbers.
2893    
2894  =over 4  =over 4
2895    
2896  =item dirName  =item $value1, $value2, ... $valueN
2897    
2898  Name of the directory to check. If it does not exist, it will be created.  List of numbers to compare.
2899    
2900  =item chmod (optional)  =item RETURN
2901    
2902  Security privileges to be given to the directory if it is created.  Returns the lowest number in the list.
2903    
2904  =back  =back
2905    
2906  =cut  =cut
2907    
2908  sub Insure {  sub Min {
2909      my ($dirName, $chmod) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
2910      if (! -d $dirName) {      my ($retVal, @values) = @_;
2911          Trace("Creating $dirName directory.") if T(2);      # Loop through the remaining parameters, looking for the lowest.
2912          eval {      for my $value (@values) {
2913              mkpath $dirName;          if ($value < $retVal) {
2914              # If we have permissions specified, set them here.              $retVal = $value;
             if (defined($chmod)) {  
                 chmod $chmod, $dirName;  
             }  
         };  
         if ($@) {  
             Confess("Error creating $dirName: $@");  
2915          }          }
2916      }      }
2917        # Return the minimum found.
2918        return $retVal;
2919  }  }
2920    
2921  =head3 ChDir  =head3 Max
2922    
2923      ChDir($dirName);      my $max = Max($value1, $value2, ... $valueN);
2924    
2925  Change to the specified directory.  Return the maximum argument. The arguments are treated as numbers.
2926    
2927  =over 4  =over 4
2928    
2929  =item dirName  =item $value1, $value2, ... $valueN
2930    
2931  Name of the directory to which we want to change.  List of numbers to compare.
2932    
2933    =item RETURN
2934    
2935    Returns the highest number in the list.
2936    
2937  =back  =back
2938    
2939  =cut  =cut
2940    
2941  sub ChDir {  sub Max {
2942      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
2943      if (! -d $dirName) {      my ($retVal, @values) = @_;
2944          Confess("Cannot change to directory $dirName: no such directory.");      # Loop through the remaining parameters, looking for the highest.
2945      } else {      for my $value (@values) {
2946          Trace("Changing to directory $dirName.") if T(File => 4);          if ($value > $retVal) {
2947          my $okFlag = chdir $dirName;              $retVal = $value;
         if (! $okFlag) {  
             Confess("Error switching to directory $dirName.");  
2948          }          }
2949      }      }
2950        # Return the maximum found.
2951        return $retVal;
2952  }  }
2953    
 =head3 SendSMS  
   
     my $msgID = Tracer::SendSMS($phoneNumber, $msg);  
   
 Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  
 user name, password, and API ID for the relevant account in the hash reference variable  
 I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For  
 example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID  
 is C<2561022>, then the FIG_Config file must contain  
2954    
2955      $phone =  { user => 'BruceTheHumanPet',  =head3 Strip
                 password => 'silly',  
                 api_id => '2561022' };  
2956    
2957  The original purpose of this method was to insure Bruce would be notified immediately when the      my $string = Tracer::Strip($line);
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
2958    
2959  The message ID will be returned if successful, and C<undef> if an error occurs.  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 phoneNumber  =item line
   
 Phone number to receive the message, in international format. A United States phone number  
 would be prefixed by "1". A British phone number would be prefixed by "44".  
   
 =item msg  
2966    
2967  Message to send to the specified phone.  Line of text to be stripped.
2968    
2969  =item RETURN  =item RETURN
2970    
2971  Returns the message ID if successful, and C<undef> if the message could not be sent.  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 SendSMS {  sub Strip {
2978      # Get the parameters.      # Get a copy of the parameter string.
2979      my ($phoneNumber, $msg) = @_;      my ($string) = @_;
2980      # Declare the return variable. If we do not change it, C<undef> will be returned.      my $retVal = (defined $string ? $string : "");
2981      my $retVal;      # Strip the line terminator characters.
2982      # Only proceed if we have phone support.      $retVal =~ s/(\r|\n)+$//g;
     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);  
             }  
         }  
     }  
2983      # Return the result.      # Return the result.
2984      return $retVal;      return $retVal;
2985  }  }
2986    
2987  =head3 CommaFormat  =head3 Pad
2988    
2989      my $formatted = Tracer::CommaFormat($number);      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
2990    
2991  Insert commas into a number.  Pad a string to a specified length. The pad character will be a
2992    space, and the padding will be on the right side unless specified
2993    in the third parameter.
2994    
2995  =over 4  =over 4
2996    
2997  =item number  =item string
2998    
2999  A sequence of digits.  String to be padded.
3000    
3001    =item len
3002    
3003    Desired length of the padded string.
3004    
3005    =item left (optional)
3006    
3007    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3008    
3009    =item padChar (optional)
3010    
3011    Character to use for padding. The default is a space.
3012    
3013  =item RETURN  =item RETURN
3014    
3015  Returns the same digits with commas strategically inserted.  Returns a copy of the original string with the pad character added to the
3016    specified end so that it achieves the desired length.
3017    
3018  =back  =back
3019    
3020  =cut  =cut
3021    
3022  sub CommaFormat {  sub Pad {
3023      # Get the parameters.      # Get the parameters.
3024      my ($number) = @_;      my ($string, $len, $left, $padChar) = @_;
3025      # Pad the length up to a multiple of three.      # Compute the padding character.
3026      my $padded = "$number";      if (! defined $padChar) {
3027      $padded = " " . $padded while length($padded) % 3 != 0;          $padChar = " ";
3028      # This is a fancy PERL trick. The parentheses in the SPLIT pattern      }
3029      # cause the delimiters to be included in the output stream. The      # Compute the number of spaces needed.
3030      # GREP removes the empty strings in between the delimiters.      my $needed = $len - length $string;
3031      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));      # Copy the string into the return variable.
3032      # Clean out the spaces.      my $retVal = $string;
3033      $retVal =~ s/ //g;      # Only proceed if padding is needed.
3034        if ($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 $retVal;
3046  }  }
 =head3 SetPermissions  
3047    
3048      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);  =head3 EOF
3049    
3050  Set the permissions for a directory and all the files and folders inside it.  This is a constant that is lexically greater than any useful string.
 In addition, the group ownership will be changed to the specified value.  
3051    
3052  This method is more vulnerable than most to permission and compatability  =cut
3053  problems, so it does internal error recovery.  
3054    sub EOF {
3055        return "\xFF\xFF\xFF\xFF\xFF";
3056    }
3057    
3058    =head3 TICK
3059    
3060        my @results = TICK($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  =over 4
3075    
3076  =item dirName  =item commandString
3077    
3078  Name of the directory to process.  The command string to pass to the system.
3079    
3080  =item group  =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    
 Name of the group to be assigned.  
3099    
3100  =item mask  =head3 CommaFormat
3101    
3102  Permission mask. Bits that are C<1> in this mask will be ORed into the      my $formatted = Tracer::CommaFormat($number);
 permission bits of any file or directory that does not already have them  
 set to 1.  
3103    
3104  =item otherMasks  Insert commas into a number.
3105    
3106  Map of search patterns to permission masks. If a directory name matches  =over 4
 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>.  
3107    
3108      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  =item number
3109    
3110  The list is ordered, so the following would use 0777 for C<tmp1> and  A sequence of digits.
 0666 for C<tmp>, C<tmp2>, or C<tmp3>.  
3111    
3112      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  =item RETURN
                                                    '^tmp' => 0666);  
3113    
3114  Note that the pattern matches are all case-insensitive, and only directory  Returns the same digits with commas strategically inserted.
 names are matched, not file names.  
3115    
3116  =back  =back
3117    
3118  =cut  =cut
3119    
3120  sub SetPermissions {  sub CommaFormat {
3121      # Get the parameters.      # Get the parameters.
3122      my ($dirName, $group, $mask, @otherMasks) = @_;      my ($number) = @_;
3123      # Set up for error recovery.      # Pad the length up to a multiple of three.
3124      eval {      my $padded = "$number";
3125          # Switch to the specified directory.      $padded = " " . $padded while length($padded) % 3 != 0;
3126          ChDir($dirName);      # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3127          # Get the group ID.      # cause the delimiters to be included in the output stream. The
3128          my $gid = getgrnam($group);      # GREP removes the empty strings in between the delimiters.
3129          # Get the mask for tracing.      my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3130          my $traceMask = sprintf("%04o", $mask) . "($mask)";      # Clean out the spaces.
3131          Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);      $retVal =~ s/ //g;
3132          my $fixCount = 0;      # Return the result.
3133          my $lookCount = 0;      return $retVal;
         # @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: $@");  
     }  
3134  }  }
3135    
3136    
3137  =head3 CompareLists  =head3 CompareLists
3138    
3139      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
# Line 2976  Line 3201 
3201      return ($inserted, $deleted);      return ($inserted, $deleted);
3202  }  }
3203    
 =head3 GetLine  
   
     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  
   
     Tracer::PutLine($handle, \@fields, $eol);  
   
 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.  
   
 =item eol (optional)  
   
 End-of-line character (default is "\n").  
   
 =back  
   
 =cut  
   
 sub PutLine {  
     # Get the parameters.  
     my ($handle, $fields, $eol) = @_;  
     # Write the data.  
     print $handle join("\t", @{$fields}) . ($eol || "\n");  
 }  
   
3204  =head3 GenerateURL  =head3 GenerateURL
3205    
3206      my $queryUrl = Tracer::GenerateURL($page, %parameters);      my $queryUrl = Tracer::GenerateURL($page, %parameters);
# Line 3201  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;

Legend:
Removed from v.1.92  
changed lines
  Added in v.1.98

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3