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revision 1.79, Thu Nov 9 21:12:46 2006 UTC revision 1.91, Mon Aug 20 23:07:05 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 1172  Line 1185 
1185      # Get the timestamp.      # Get the timestamp.
1186      my $timeStamp = Now();      my $timeStamp = Now();
1187      # Format the message. Note we strip off any line terminators at the end.      # Format the message. Note we strip off any line terminators at the end.
1188      my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);      my $prefix = "[$timeStamp] <$LastCategory>: ";
1189        my $formatted = $prefix . Strip($message);
1190      # Process according to the destination.      # Process according to the destination.
1191      if ($Destination eq "TEXT") {      if ($Destination eq "TEXT") {
1192          # Write the message to the standard output.          # Write the message to the standard output.
# Line 1186  Line 1200 
1200      } elsif ($Destination eq "HTML") {      } elsif ($Destination eq "HTML") {
1201          # Convert the message to HTML and write it to the standard output.          # Convert the message to HTML and write it to the standard output.
1202          my $escapedMessage = CGI::escapeHTML($message);          my $escapedMessage = CGI::escapeHTML($message);
1203          print "<p>$formatted</p>\n";          print "<p>$timeStamp $LastCategory: $escapedMessage</p>\n";
1204      } elsif ($Destination eq "WARN") {      } elsif ($Destination eq "WARN") {
1205         # Emit the message as a warning.         # Emit the message as a warning.
1206         warn $message;         warn $message;
# Line 1251  Line 1265 
1265              if (!$package) {              if (!$package) {
1266                  $category = "main";                  $category = "main";
1267              } else {              } else {
1268                  $category = $package;                  my @cats = split /::/, $package;
1269                    $category = $cats[$#cats];
1270              }              }
1271          }          }
1272          # Save the category name.          # Save the category name.
# Line 1281  Line 1296 
1296    
1297  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>
1298    
1299  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,
1300  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
1301    
1302  C<< -logFile=error.log apple orange rutabaga >>  C<< -logFile=error.log apple orange rutabaga >>
# Line 1295  Line 1310 
1310  C<< apple orange rutabaga >>  C<< apple orange rutabaga >>
1311    
1312  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
1313  support for quote characters.  support for quote characters. Options can be specified with single or double hyphens.
1314    
1315  =over 4  =over 4
1316    
# Line 1320  Line 1335 
1335      my ($optionTable, @inputList) = @_;      my ($optionTable, @inputList) = @_;
1336      # Process any options in the input list.      # Process any options in the input list.
1337      my %overrides = ();      my %overrides = ();
1338      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1339          # Get the current option.          # Get the current option.
1340          my $arg = shift @inputList;          my $arg = shift @inputList;
1341          # Pull out the option name.          # Pull out the option name.
1342          $arg =~ /^-([^=]*)/g;          $arg =~ /^--?([^=]*)/g;
1343          my $name = $1;          my $name = $1;
1344          # Check for an option value.          # Check for an option value.
1345          if ($arg =~ /\G=(.*)$/g) {          if ($arg =~ /\G=(.*)$/g) {
# Line 1759  Line 1774 
1774  sub Confess {  sub Confess {
1775      # Get the parameters.      # Get the parameters.
1776      my ($message) = @_;      my ($message) = @_;
1777        if (! defined($FIG_Config::no_tool_hdr)) {
1778            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
1779            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
1780            # Only proceed if the tool header file is actually present.
1781            if (-f $toolHeaderFile) {
1782                my @lines = GetFile($toolHeaderFile);
1783                Trace("Tool header has " . scalar(@lines) . " lines.");
1784            }
1785        }
1786      # Trace the call stack.      # Trace the call stack.
1787      Cluck($message);      Cluck($message);
1788      # Abort the program.      # Abort the program.
# Line 2104  Line 2128 
2128  C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>  C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>
2129    
2130  Perform standard tracing and debugging setup for scripts. The value returned is  Perform standard tracing and debugging setup for scripts. The value returned is
2131  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,
2132    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.  
2133    
2134  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
2135  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.
2136  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>
2137  method, which includes every program that uses this method or L</StandardSetup>.  method, which includes every program that uses this method or L</StandardSetup>.
2138    
# Line 2291  Line 2309 
2309  This method converts an emergency tracing destination to a real  This method converts an emergency tracing destination to a real
2310  tracing destination. The main difference is that if the  tracing destination. The main difference is that if the
2311  destination is C<FILE> or C<APPEND>, we convert it to file  destination is C<FILE> or C<APPEND>, we convert it to file
2312  output.  output. If the destination is C<DUAL>, we convert it to file
2313    and standard output.
2314    
2315  =over 4  =over 4
2316    
# Line 2315  Line 2334 
2334      # Get the parameters.      # Get the parameters.
2335      my ($tkey, $myDest) = @_;      my ($tkey, $myDest) = @_;
2336      # Declare the return variable.      # Declare the return variable.
2337      my $retVal;      my $retVal = $myDest;
2338      # Process according to the destination value.      # Process according to the destination value.
2339      if ($myDest eq 'FILE') {      if ($myDest eq 'FILE') {
2340          $retVal = ">" . EmergencyFileTarget($tkey);          $retVal = ">" . EmergencyFileTarget($tkey);
2341      } elsif ($myDest eq 'APPEND') {      } elsif ($myDest eq 'APPEND') {
2342          $retVal = ">>" . EmergencyFileTarget($tkey);          $retVal = ">>" . EmergencyFileTarget($tkey);
2343      } else {      } elsif ($myDest eq 'DUAL') {
2344          $retVal = $myDest;          $retVal = "+>" . EmergencyFileTarget($tkey);
2345      }      }
2346      # Return the result.      # Return the result.
2347      return $retVal;      return $retVal;
# Line 2332  Line 2351 
2351    
2352  C<< Emergency($key, $hours, $dest, $level, @modules); >>  C<< Emergency($key, $hours, $dest, $level, @modules); >>
2353    
2354  Turn on emergency tracing. This method can only be invoked over the web and is  Turn on emergency tracing. This method is normally invoked over the web from
2355  should not be called if debug mode is off. The caller specifies the duration of the  a debugging console, but it can also be called by the C<trace.pl> script.
2356  emergency in hours, the desired tracing destination, the trace level,  The caller specifies the duration of the emergency in hours, the desired tracing
2357  and a list of the trace modules to activate. For the length of the duration, when a  destination, the trace level, and a list of the trace modules to activate.
2358  program in an environment with the specified tracing key active invokes a Sprout  For the length of the duration, when a program in an environment with the
2359  CGI script, tracing will be turned on automatically. See L</TSetup> for more  specified tracing key active invokes a Sprout CGI script, tracing will be
2360  about tracing setup and L</ETracing> for more about emergency tracing.  turned on automatically. See L</TSetup> for more about tracing setup and
2361    L</ETracing> for more about emergency tracing.
2362    
2363  =over 4  =over 4
2364    
# Line 2574  Line 2594 
2594    
2595  =head3 Insure  =head3 Insure
2596    
2597  C<< Insure($dirName); >>  C<< Insure($dirName, $chmod); >>
2598    
2599  Insure a directory is present.  Insure a directory is present.
2600    
# Line 2584  Line 2604 
2604    
2605  Name of the directory to check. If it does not exist, it will be created.  Name of the directory to check. If it does not exist, it will be created.
2606    
2607    =item chmod (optional)
2608    
2609    Security privileges to be given to the directory if it is created.
2610    
2611  =back  =back
2612    
2613  =cut  =cut
2614    
2615  sub Insure {  sub Insure {
2616      my ($dirName) = @_;      my ($dirName, $chmod) = @_;
2617      if (! -d $dirName) {      if (! -d $dirName) {
2618          Trace("Creating $dirName directory.") if T(File => 2);          Trace("Creating $dirName directory.") if T(2);
2619          eval { mkpath $dirName; };          eval {
2620                mkpath $dirName;
2621                # If we have permissions specified, set them here.
2622                if (defined($chmod)) {
2623                    chmod $chmod, $dirName;
2624                }
2625            };
2626          if ($@) {          if ($@) {
2627              Confess("Error creating $dirName: $@");              Confess("Error creating $dirName: $@");
2628          }          }
# Line 2974  Line 3004 
3004      my $line = <$handle>;      my $line = <$handle>;
3005      # Only proceed if we found something.      # Only proceed if we found something.
3006      if (defined $line) {      if (defined $line) {
3007          # Remove the new-line.          # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
3008          chomp $line;          # upload control and have a nonstandard EOL combination.
3009          Trace("Line read: $line") if T(File => 4);          $line =~ s/(\r|\n)+$//;
3010            # Here we do some fancy tracing to help in debugging complicated EOL marks.
3011            if (T(File => 4)) {
3012                my $escapedLine = $line;
3013                $escapedLine =~ s/\n/\\n/g;
3014                $escapedLine =~ s/\r/\\r/g;
3015                $escapedLine =~ s/\t/\\t/g;
3016                Trace("Line read: -->$escapedLine<--");
3017            }
3018          # If the line is empty, return a single empty string; otherwise, parse          # If the line is empty, return a single empty string; otherwise, parse
3019          # it into fields.          # it into fields.
3020          if ($line eq "") {          if ($line eq "") {
# Line 2994  Line 3032 
3032    
3033  =head3 PutLine  =head3 PutLine
3034    
3035  C<< Tracer::PutLine($handle, \@fields); >>  C<< Tracer::PutLine($handle, \@fields, $eol); >>
3036    
3037  Write a line of data to a tab-delimited file. The specified field values will be  Write a line of data to a tab-delimited file. The specified field values will be
3038  output in tab-separated form, with a trailing new-line.  output in tab-separated form, with a trailing new-line.
# Line 3009  Line 3047 
3047    
3048  List of field values.  List of field values.
3049    
3050    =item eol (optional)
3051    
3052    End-of-line character (default is "\n").
3053    
3054  =back  =back
3055    
3056  =cut  =cut
3057    
3058  sub PutLine {  sub PutLine {
3059      # Get the parameters.      # Get the parameters.
3060      my ($handle, $fields) = @_;      my ($handle, $fields, $eol) = @_;
3061      # Write the data.      # Write the data.
3062      print $handle join("\t", @{$fields}) . "\n";      print $handle join("\t", @{$fields}) . ($eol || "\n");
3063  }  }
3064    
3065  =head3 GenerateURL  =head3 GenerateURL
# Line 3154  Line 3196 
3196      return $retVal;      return $retVal;
3197  }  }
3198    
3199    
3200  1;  1;

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