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revision 1.79, Thu Nov 9 21:12:46 2006 UTC revision 1.87, Mon Jun 11 17:34:16 2007 UTC
# Line 186  Line 186 
186  using the L</StandardScript> or L</StandardSetup> methods, emergency tracing  using the L</StandardScript> or L</StandardSetup> methods, emergency tracing
187  will be configured automatically.  will be configured automatically.
188    
189    NOTE: to configure emergency tracing from the command line instead of the Debugging
190    Control Panel (see below), use the C<trace.pl> script.
191    
192  =head3 Debugging Control Panel  =head3 Debugging Control Panel
193    
194  The debugging control panel provides several tools to assist in development of  The debugging control panel provides several tools to assist in development of
# Line 445  Line 448 
448                            noAlias => [0, "do not expect aliases in CHANGE transactions"],                            noAlias => [0, "do not expect aliases in CHANGE transactions"],
449                            start => [' ', "start with this genome"],                            start => [' ', "start with this genome"],
450                            tblFiles => [0, "output TBL files containing the corrected IDs"] },                            tblFiles => [0, "output TBL files containing the corrected IDs"] },
451                          "command transactionDirectory IDfile",                          "<command> <transactionDirectory> <IDfile>",
452                        @ARGV);                        @ARGV);
453    
454    
# Line 457  Line 460 
460    
461      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
462    
463    Single and double hyphens are equivalent. So, you could also code the
464    above command as
465    
466        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
467    
468  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
469  parameters, and would find themselves in I<@parameters> after executing the  parameters, and would find themselves in I<@parameters> after executing the
470  above code fragment. The tracing would be set to level 2, and the categories  above code fragment. The tracing would be set to level 2, and the categories
# Line 491  Line 499 
499  the tracing key is taken from the C<Tracing> environment variable. If there  the tracing key is taken from the C<Tracing> environment variable. If there
500  is no value for that variable, the tracing key will be computed from the PID.  is no value for that variable, the tracing key will be computed from the PID.
501    
502  Finally, if the special option C<-h> is specified, the option names will  Finally, if the special option C<-help> is specified, the option
503  be traced at level 0 and the program will exit without processing.  names will be traced at level 0 and the program will exit without processing.
504  This provides a limited help capability. For example, if the user enters  This provides a limited help capability. For example, if the user enters
505    
506      TransactFeatures -h      TransactFeatures -help
507    
508  he would see the following output.  he would see the following output.
509    
510      TransactFeatures [options] command transactionDirectory IDfile      TransactFeatures [options] <command> <transactionDirectory> <IDfile>
511          -trace    tracing level (default E)          -trace    tracing level (default E)
512          -sql      trace SQL commands          -sql      trace SQL commands
513          -safe     use database transactions          -safe     use database transactions
# Line 571  Line 579 
579      my $tkey = EmergencyKey();      my $tkey = EmergencyKey();
580      # Add the tracing options.      # Add the tracing options.
581      if (! exists $options->{trace}) {      if (! exists $options->{trace}) {
582          $options->{trace} = ['E', "tracing level (E for emergency tracing)"];          $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
583      }      }
584      $options->{sql} = [0, "turn on SQL tracing"];      $options->{sql} = [0, "turn on SQL tracing"];
585      $options->{h} = [0, "display command-line options"];      $options->{help} = [0, "display command-line options"];
586      $options->{user} = [$tkey, "tracing key"];      $options->{user} = [$tkey, "tracing key"];
587      $options->{background} = [0, "spool standard and error output"];      $options->{background} = [0, "spool standard and error output"];
588      # Create a parsing hash from the options hash. The parsing hash      # Create a parsing hash from the options hash. The parsing hash
# Line 649  Line 657 
657      }      }
658      # Check for the "h" option. If it is specified, dump the command-line      # Check for the "h" option. If it is specified, dump the command-line
659      # options and exit the program.      # options and exit the program.
660      if ($retOptions->{h}) {      if ($retOptions->{help}) {
661          $0 =~ m#[/\\](\w+)(\.pl)?$#i;          $0 =~ m#[/\\](\w+)(\.pl)?$#i;
662          print "$1 [options] $parmHelp\n";          print "$1 [options] $parmHelp\n";
663          for my $key (sort keys %{$options}) {          for my $key (sort keys %{$options}) {
# Line 662  Line 670 
670          }          }
671          exit(0);          exit(0);
672      }      }
673        # Trace the options, if applicable.
674        if (T(3)) {
675            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
676            Trace("Selected options: " . join(", ", sort @parms) . ".");
677        }
678      # Return the parsed parameters.      # Return the parsed parameters.
679      return ($retOptions, @retParameters);      return ($retOptions, @retParameters);
680  }  }
# Line 1251  Line 1264 
1264              if (!$package) {              if (!$package) {
1265                  $category = "main";                  $category = "main";
1266              } else {              } else {
1267                  $category = $package;                  my @cats = split /::/, $package;
1268                    $category = $cats[$#cats];
1269              }              }
1270          }          }
1271          # Save the category name.          # Save the category name.
# Line 1281  Line 1295 
1295    
1296  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>
1297    
1298  In this case, the list @words will be treated as a command line. There are two options available,  In this case, the list @words will be treated as a command line and there are two options available,
1299  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
1300    
1301  C<< -logFile=error.log apple orange rutabaga >>  C<< -logFile=error.log apple orange rutabaga >>
# Line 1295  Line 1309 
1309  C<< apple orange rutabaga >>  C<< apple orange rutabaga >>
1310    
1311  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1312  support for quote characters.  support for quote characters. Options can be specified with single or double hyphens.
1313    
1314  =over 4  =over 4
1315    
# Line 1320  Line 1334 
1334      my ($optionTable, @inputList) = @_;      my ($optionTable, @inputList) = @_;
1335      # Process any options in the input list.      # Process any options in the input list.
1336      my %overrides = ();      my %overrides = ();
1337      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1338          # Get the current option.          # Get the current option.
1339          my $arg = shift @inputList;          my $arg = shift @inputList;
1340          # Pull out the option name.          # Pull out the option name.
1341          $arg =~ /^-([^=]*)/g;          $arg =~ /^--?([^=]*)/g;
1342          my $name = $1;          my $name = $1;
1343          # Check for an option value.          # Check for an option value.
1344          if ($arg =~ /\G=(.*)$/g) {          if ($arg =~ /\G=(.*)$/g) {
# Line 1759  Line 1773 
1773  sub Confess {  sub Confess {
1774      # Get the parameters.      # Get the parameters.
1775      my ($message) = @_;      my ($message) = @_;
1776        if (! defined($FIG_Config::no_tool_hdr)) {
1777            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
1778            my @lines = GetFile("$FIG_Config::common_runtime/tool_hdr");
1779            Trace("Tool header has " . scalar(@lines) . " lines.");
1780        }
1781      # Trace the call stack.      # Trace the call stack.
1782      Cluck($message);      Cluck($message);
1783      # Abort the program.      # Abort the program.
# Line 2104  Line 2123 
2123  C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>
2124    
2125  Perform standard tracing and debugging setup for scripts. The value returned is  Perform standard tracing and debugging setup for scripts. The value returned is
2126  the CGI object followed by a pre-built variable hash.  the CGI object followed by a pre-built variable hash. At the end of the script,
2127    the client should call L</ScriptFinish> to output the web page.
 The C<Trace> form parameter is used to determine whether or not tracing is active and  
 which trace modules (other than C<Tracer> itself) should be turned on. Specifying  
 the C<CGI> trace module will trace parameter and environment information. Parameters are  
 traced at level 3 and environment variables at level 4. To trace to a file instead of to  
 the web page, set C<TF> to 1. At the end of the script, the client should call  
 L</ScriptFinish> to output the web page.  
2128    
2129  In some situations, it is not practical to invoke tracing via form parameters. For this  This method calls L</ETracing> to configure tracing, which allows the tracing
2130  situation, you can turn on emergency tracing from the debugging control panel.  to be configured via the emergency tracing form on the debugging control panel.
2131  Tracing will then be turned on automatically for all programs that use the L</ETracing>  Tracing will then be turned on automatically for all programs that use the L</ETracing>
2132  method, which includes every program that uses this method or L</StandardSetup>.  method, which includes every program that uses this method or L</StandardSetup>.
2133    
# Line 2291  Line 2304 
2304  This method converts an emergency tracing destination to a real  This method converts an emergency tracing destination to a real
2305  tracing destination. The main difference is that if the  tracing destination. The main difference is that if the
2306  destination is C<FILE> or C<APPEND>, we convert it to file  destination is C<FILE> or C<APPEND>, we convert it to file
2307  output.  output. If the destination is C<DUAL>, we convert it to file
2308    and standard output.
2309    
2310  =over 4  =over 4
2311    
# Line 2315  Line 2329 
2329      # Get the parameters.      # Get the parameters.
2330      my ($tkey, $myDest) = @_;      my ($tkey, $myDest) = @_;
2331      # Declare the return variable.      # Declare the return variable.
2332      my $retVal;      my $retVal = $myDest;
2333      # Process according to the destination value.      # Process according to the destination value.
2334      if ($myDest eq 'FILE') {      if ($myDest eq 'FILE') {
2335          $retVal = ">" . EmergencyFileTarget($tkey);          $retVal = ">" . EmergencyFileTarget($tkey);
2336      } elsif ($myDest eq 'APPEND') {      } elsif ($myDest eq 'APPEND') {
2337          $retVal = ">>" . EmergencyFileTarget($tkey);          $retVal = ">>" . EmergencyFileTarget($tkey);
2338      } else {      } elsif ($myDest eq 'DUAL') {
2339          $retVal = $myDest;          $retVal = "+>" . EmergencyFileTarget($tkey);
2340      }      }
2341      # Return the result.      # Return the result.
2342      return $retVal;      return $retVal;
# Line 2332  Line 2346 
2346    
2347  C<< Emergency($key, $hours, $dest, $level, @modules); >>  C<< Emergency($key, $hours, $dest, $level, @modules); >>
2348    
2349  Turn on emergency tracing. This method can only be invoked over the web and is  Turn on emergency tracing. This method is normally invoked over the web from
2350  should not be called if debug mode is off. The caller specifies the duration of the  a debugging console, but it can also be called by the C<trace.pl> script.
2351  emergency in hours, the desired tracing destination, the trace level,  The caller specifies the duration of the emergency in hours, the desired tracing
2352  and a list of the trace modules to activate. For the length of the duration, when a  destination, the trace level, and a list of the trace modules to activate.
2353  program in an environment with the specified tracing key active invokes a Sprout  For the length of the duration, when a program in an environment with the
2354  CGI script, tracing will be turned on automatically. See L</TSetup> for more  specified tracing key active invokes a Sprout CGI script, tracing will be
2355  about tracing setup and L</ETracing> for more about emergency tracing.  turned on automatically. See L</TSetup> for more about tracing setup and
2356    L</ETracing> for more about emergency tracing.
2357    
2358  =over 4  =over 4
2359    
# Line 2974  Line 2989 
2989      my $line = <$handle>;      my $line = <$handle>;
2990      # Only proceed if we found something.      # Only proceed if we found something.
2991      if (defined $line) {      if (defined $line) {
2992          # Remove the new-line.          # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2993          chomp $line;          # upload control and have a nonstandard EOL combination.
2994          Trace("Line read: $line") if T(File => 4);          $line =~ s/(\r|\n)+$//;
2995            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2996            if (T(File => 4)) {
2997                my $escapedLine = $line;
2998                $escapedLine =~ s/\n/\\n/g;
2999                $escapedLine =~ s/\r/\\r/g;
3000                $escapedLine =~ s/\t/\\t/g;
3001                Trace("Line read: -->$escapedLine<--");
3002            }
3003          # If the line is empty, return a single empty string; otherwise, parse          # If the line is empty, return a single empty string; otherwise, parse
3004          # it into fields.          # it into fields.
3005          if ($line eq "") {          if ($line eq "") {
# Line 2994  Line 3017 
3017    
3018  =head3 PutLine  =head3 PutLine
3019    
3020  C<< Tracer::PutLine($handle, \@fields); >>  C<< Tracer::PutLine($handle, \@fields, $eol); >>
3021    
3022  Write a line of data to a tab-delimited file. The specified field values will be  Write a line of data to a tab-delimited file. The specified field values will be
3023  output in tab-separated form, with a trailing new-line.  output in tab-separated form, with a trailing new-line.
# Line 3009  Line 3032 
3032    
3033  List of field values.  List of field values.
3034    
3035    =item eol (optional)
3036    
3037    End-of-line character (default is "\n").
3038    
3039  =back  =back
3040    
3041  =cut  =cut
3042    
3043  sub PutLine {  sub PutLine {
3044      # Get the parameters.      # Get the parameters.
3045      my ($handle, $fields) = @_;      my ($handle, $fields, $eol) = @_;
3046      # Write the data.      # Write the data.
3047      print $handle join("\t", @{$fields}) . "\n";      print $handle join("\t", @{$fields}) . ($eol || "\n");
3048  }  }
3049    
3050  =head3 GenerateURL  =head3 GenerateURL
# Line 3154  Line 3181 
3181      return $retVal;      return $retVal;
3182  }  }
3183    
3184    
3185  1;  1;

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