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revision 1.14, Tue Jul 26 20:12:33 2005 UTC revision 1.39, Fri Feb 24 19:45:29 2006 UTC
# Line 1  Line 1 
1    #
2    # Copyright (c) 2003-2006 University of Chicago and Fellowship
3    # for Interpretations of Genomes. All Rights Reserved.
4    #
5    # This file is part of the SEED Toolkit.
6    #
7    # The SEED Toolkit is free software. You can redistribute
8    # it and/or modify it under the terms of the SEED Toolkit
9    # Public License.
10    #
11    # You should have received a copy of the SEED Toolkit Public License
12    # along with this program; if not write to the University of Chicago
13    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14    # Genomes at veronika@thefig.info or download a copy from
15    # http://www.theseed.org/LICENSE.TXT.
16    #
17    
18  package Tracer;  package Tracer;
19    
20      require Exporter;      require Exporter;
21      @ISA = ('Exporter');      @ISA = ('Exporter');
22      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup ScriptSetup ScriptFinish Insure);
23      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);
24      use strict;      use strict;
25      use Carp qw(longmess croak);      use Carp qw(longmess croak);
26      use CGI;      use CGI;
27      use FIG_Config;      use FIG_Config;
28      use PageBuilder;      use PageBuilder;
29        use Digest::MD5;
30        use File::Basename;
31        use File::Path;
32    
33  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
34    
# Line 71  Line 91 
91    
92  =over 4  =over 4
93    
94  =item 0 Error  =item Error 0
95    
96  Message indicates an error that may lead to incorrect results or that has stopped the  Message indicates an error that may lead to incorrect results or that has stopped the
97  application entirely.  application entirely.
98    
99  =item 1 Warning  =item Warning 1
100    
101  Message indicates something that is unexpected but that probably did not interfere  Message indicates something that is unexpected but that probably did not interfere
102  with program execution.  with program execution.
103    
104  =item 2 Notice  =item Notice 2
105    
106  Message indicates the beginning or end of a major task.  Message indicates the beginning or end of a major task.
107    
108  =item 3 Information  =item Information 3
109    
110  Message indicates a subtask. In the FIG system, a subtask generally relates to a single  Message indicates a subtask. In the FIG system, a subtask generally relates to a single
111  genome. This would be a big loop that is not expected to execute more than 500 times or so.  genome. This would be a big loop that is not expected to execute more than 500 times or so.
112    
113  =item 4 Detail  =item Detail 4
114    
115  Message indicates a low-level loop iteration.  Message indicates a low-level loop iteration.
116    
# Line 156  Line 176 
176      # Presume category-based tracing until we learn otherwise.      # Presume category-based tracing until we learn otherwise.
177      $AllTrace = 0;      $AllTrace = 0;
178      # Build the category hash. Note that if we find a "*", we turn on non-category      # Build the category hash. Note that if we find a "*", we turn on non-category
179      # tracing.      # tracing. We must also clear away any pre-existing data.
180        %Categories = ( main => 1 );
181      for my $category (@categoryData) {      for my $category (@categoryData) {
182          if ($category eq '*') {          if ($category eq '*') {
183              $AllTrace = 1;              $AllTrace = 1;
# Line 187  Line 208 
208      $SetupCount++;      $SetupCount++;
209  }  }
210    
211    =head3 StandardSetup
212    
213    C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>
214    
215    This method performs standard command-line parsing and tracing setup. The return
216    values are a hash of the command-line options and a list of the positional
217    parameters. Tracing is automatically set up and the command-line options are
218    validated.
219    
220    This is a complex method that does a lot of grunt work. The parameters can
221    be more easily understood, however, once they are examined individually.
222    
223    The I<categories> parameter is the most obtuse. It is a reference to a list of
224    special-purpose tracing categories. Most tracing categories are PERL package
225    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
226    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
227    
228        ["Sprout", "SproutLoad", "ERDB"]
229    
230    This would cause trace messages in the specified three packages to appear in
231    the output. There are threer special tracing categories that are automatically
232    handled by this method. In other words, if you used L</TSetup> you would need
233    to include these categories manually, but if you use this method they are turned
234    on automatically.
235    
236    =over 4
237    
238    =item FIG
239    
240    Turns on trace messages inside the B<FIG> package.
241    
242    =item SQL
243    
244    Traces SQL commands and activity.
245    
246    =item Tracer
247    
248    Traces error messages and call stacks.
249    
250    =back
251    
252    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
253    The trace level is specified using the C<-trace> command-line option. For example,
254    the following command line for C<TransactFeatures> turns on SQL tracing and runs
255    all tracing at level 3.
256    
257        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
258    
259    Standard tracing is output to the standard output and echoed to the file
260    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
261    process ID. You can also specify the C<user> parameter to put a user ID
262    instead of a process ID in the trace file name. So, for example
263    
264    The default trace level is 2. To get all messages, specify a trace level of 4.
265    For a genome-by-genome update, use 3.
266    
267        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
268    
269    would send the trace output to C<traceBruce.log> in the temporary directory.
270    
271    The I<options> parameter is a reference to a hash containing the command-line
272    options, their default values, and an explanation of what they mean. Command-line
273    options may be in the form of switches or keywords. In the case of a switch, the
274    option value is 1 if it is specified and 0 if it is not specified. In the case
275    of a keyword, the value is separated from the option name by an equal sign. You
276    can see this last in the command-line example above.
277    
278    An example at this point would help. Consider, for example, the command-line utility
279    C<TransactFeatures>. It accepts a list of positional parameters plus the options
280    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
281    the following code.
282    
283        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
284                            { safe => [0, "use database transactions"],
285                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
286                              start => [' ', "start with this genome"],
287                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
288                            "command transactionDirectory IDfile",
289                          @ARGV);
290    
291    
292    The call to C<ParseCommand> specifies the default values for the options and
293    stores the actual options in a hash that is returned as C<$options>. The
294    positional parameters are returned in C<@parameters>.
295    
296    The following is a sample command line for C<TransactFeatures>.
297    
298        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
299    
300    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
301    parameters, and would find themselves in I<@parameters> after executing the
302    above code fragment. The tracing would be set to level 2, and the categories
303    would be C<FIG>, C<Tracer>, and <DocUtils>. C<FIG> and C<Tracer> are standard,
304    and C<DocUtils> was included because it came in within the first parameter
305    to this method. The I<$options> hash would be
306    
307        { trace => 2, sql => 0, safe => 0,
308          noAlias => 1, start => ' ', tblFiles => 0 }
309    
310    Use of C<StandardSetup> in this way provides a simple way of performing
311    standard tracing setup and command-line parsing. Note that the caller is
312    not even aware of the command-line switches C<-trace> and C<-sql>, which
313    are used by this method to control the tracing. If additional tracing features
314    need to be added in the future, they can be processed by this method without
315    upsetting the command-line utilities.
316    
317    Finally, if the special option C<-h> is specified, the option names will
318    be traced at level 0 and the program will exit without processing.
319    This provides a limited help capability. For example, if the user enters
320    
321        TransactFeatures -h
322    
323    he would see the following output.
324    
325        TransactFeatures [options] command transactionDirectory IDfile
326            -trace    tracing level (default 2)
327            -sql      trace SQL commands
328            -safe     use database transactions
329            -noAlias  do not expect aliases in CHANGE transactions
330            -start    start with this genome
331            -tblFiles output TBL files containing the corrected IDs
332    
333    The parameters to this method are as follows.
334    
335    =over 4
336    
337    =item categories
338    
339    Reference to a list of tracing category names. These should be names of
340    packages whose internal workings will need to be debugged to get the
341    command working.
342    
343    =item options
344    
345    Reference to a hash containing the legal options for the current command mapped
346    to their default values and descriptions. The user can override the defaults
347    by specifying the options as command-line switches prefixed by a hyphen.
348    Tracing-related options may be added to this hash. If the C<-h> option is
349    specified on the command line, the option descriptions will be used to
350    explain the options.
351    
352    =item parmHelp
353    
354    A string that vaguely describes the positional parameters. This is used
355    if the user specifies the C<-h> option.
356    
357    =item ARGV
358    
359    List of command line parameters, including the option switches, which must
360    precede the positional parameters and be prefixed by a hyphen.
361    
362    =item RETURN
363    
364    Returns a list. The first element of the list is the reference to a hash that
365    maps the command-line option switches to their values. These will either be the
366    default values or overrides specified on the command line. The remaining
367    elements of the list are the position parameters, in order.
368    
369    =back
370    
371    =cut
372    
373    sub StandardSetup {
374        # Get the parameters.
375        my ($categories, $options, $parmHelp, @argv) = @_;
376        # Add the tracing options.
377        $options->{trace} = [2, "tracing level"];
378        $options->{sql} = [0, "turn on SQL tracing"];
379        $options->{h} = [0, "display command-line options"];
380        $options->{user} = [$$, "trace log file name suffix"];
381        # Create a parsing hash from the options hash. The parsing hash
382        # contains the default values rather than the default value
383        # and the description. While we're at it, we'll memorize the
384        # length of the longest option name.
385        my $longestName = 0;
386        my %parseOptions = ();
387        for my $key (keys %{$options}) {
388            if (length $key > $longestName) {
389                $longestName = length $key;
390            }
391            $parseOptions{$key} = $options->{$key}->[0];
392        }
393        # Parse the command line.
394        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
395        # Now we want to set up tracing. First, we need to know if SQL is to
396        # be traced.
397        my @cats = @{$categories};
398        if ($retOptions->{sql}) {
399            push @cats, "SQL";
400        }
401        # Add the default categories.
402        push @cats, "Tracer", "FIG";
403        # Next, we create the category string by prefixing the trace level
404        # and joining the categories.
405        my $cats = join(" ", $parseOptions{trace}, @cats);
406        # Now set up the tracing.
407        my $suffix = $retOptions->{user};
408        TSetup($cats, "+>$FIG_Config::temp/trace$suffix.log");
409        # Check for the "h" option. If it is specified, dump the command-line
410        # options and exit the program.
411        if ($retOptions->{h}) {
412            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
413            Trace("$1 [options] $parmHelp") if T(0);
414            for my $key (sort keys %{$options}) {
415                my $name = Pad($key, $longestName, 0, ' ');
416                my $desc = $options->{$key}->[1];
417                if ($options->{$key}->[0]) {
418                    $desc .= " (default " . $options->{$key}->[0] . ")";
419                }
420                Trace("  $name $desc") if T(0);
421            }
422            exit(0);
423        }
424        # Return the parsed parameters.
425        return ($retOptions, @retParameters);
426    }
427    
428  =head3 Setups  =head3 Setups
429    
430  C<< my $count = Tracer::Setups(); >>  C<< my $count = Tracer::Setups(); >>
# Line 347  Line 585 
585    
586  =head3 OpenDir  =head3 OpenDir
587    
588  C<< my @files = OpenDir($dirName, $filtered); >>  C<< my @files = OpenDir($dirName, $filtered, $flag); >>
589    
590  Open a directory and return all the file names. This function essentially performs  Open a directory and return all the file names. This function essentially performs
591  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
592  set to TRUE, all filenames beginning with a period (C<.>) will be filtered out of  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
593  the return list. If the directory does not open, an exception is thrown. So,  or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
594  for example,  filtered out of the return list. If the directory does not open and I<$flag> is not
595    set, an exception is thrown. So, for example,
596    
597      my @files = OpenDir("/Volumes/fig/contigs", 1);      my @files = OpenDir("/Volumes/fig/contigs", 1);
598    
599  is effectively the same as  is effectively the same as
600    
601      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
602      my @files = grep { $_ !~ /^\./ } readdir(TMP);      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
603    
604  Similarly, the following code  Similarly, the following code
605    
606      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs");      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
607    
608  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
609  automatically throws an error if the directory fails to open.  automatically returns an empty list if the directory fails to open.
610    
611  =over 4  =over 4
612    
# Line 380  Line 619 
619  TRUE if files whose names begin with a period (C<.>) should be automatically removed  TRUE if files whose names begin with a period (C<.>) should be automatically removed
620  from the list, else FALSE.  from the list, else FALSE.
621    
622    =item flag
623    
624    TRUE if a failure to open is okay, else FALSE
625    
626  =back  =back
627    
628  =cut  =cut
629  #: Return Type @;  #: Return Type @;
630  sub OpenDir {  sub OpenDir {
631      # Get the parameters.      # Get the parameters.
632      my ($dirName, $filtered) = @_;      my ($dirName, $filtered, $flag) = @_;
633      # Declare the return variable.      # Declare the return variable.
634      my @retVal;      my @retVal = ();
635      # Open the directory.      # Open the directory.
636      if (opendir(my $dirHandle, $dirName)) {      if (opendir(my $dirHandle, $dirName)) {
637          # The directory opened successfully. Get the appropriate list according to the          # The directory opened successfully. Get the appropriate list according to the
638          # strictures of the filter parameter.          # strictures of the filter parameter.
639          if ($filtered) {          if ($filtered) {
640              @retVal = grep { $_ !~ /^\./ } readdir $dirHandle;              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
641          } else {          } else {
642              @retVal = readdir $dirHandle;              @retVal = readdir $dirHandle;
643          }          }
644      } else {      } elsif (! $flag) {
645          # Here the directory would not open.          # Here the directory would not open and it's considered an error.
646          Confess("Could not open directory $dirName.");          Confess("Could not open directory $dirName.");
647      }      }
648      # Return the result.      # Return the result.
# Line 737  Line 980 
980          # Convert it to lower case before we hash it.          # Convert it to lower case before we hash it.
981          $category = lc $category;          $category = lc $category;
982          # Use the category and tracelevel to compute the result.          # Use the category and tracelevel to compute the result.
983            if (ref $traceLevel) {
984                Confess("Bad trace level.");
985            } elsif (ref $TraceLevel) {
986                Confess("Bad trace config.");
987            }
988          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
989      }      }
990      # Return the computed result.      # Return the computed result.
# Line 823  Line 1071 
1071    
1072  C<< my $codedString = Tracer::Escape($realString); >>  C<< my $codedString = Tracer::Escape($realString); >>
1073    
1074  Escape a string for use in a command length. Spaces will be replaced by C<\b>,  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines
1075  tabs replaced by C<\t>, new-lines replaced by C<\n>, and backslashes will be  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
1076  doubled. The effect is to exactly reverse the effect of L</UnEscape>.  result is to reverse the effect of L</UnEscape>.
1077    
1078  =over 4  =over 4
1079    
# Line 849  Line 1097 
1097      # Loop through the parameter string, looking for sequences to escape.      # Loop through the parameter string, looking for sequences to escape.
1098      while (length $realString > 0) {      while (length $realString > 0) {
1099          # Look for the first sequence to escape.          # Look for the first sequence to escape.
1100          if ($realString =~ /^(.*?)([ \n\t\\])/) {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1101              # Here we found it. The text preceding the sequence is in $1. The sequence              # Here we found it. The text preceding the sequence is in $1. The sequence
1102              # itself is in $2. First, move the clear text to the return variable.              # itself is in $2. First, move the clear text to the return variable.
1103              $retVal .= $1;              $retVal .= $1;
1104              # Strip the processed section off the real string.              # Strip the processed section off the real string.
1105              $realString = substr $realString, (length $2) + (length $1);              $realString = substr $realString, (length $2) + (length $1);
1106              # Encode the escape sequence.              # Get the matched character.
1107              my $char = $2;              my $char = $2;
1108              $char =~ tr/ \t\n/btn/;              # If we have a CR, we are done.
1109                if ($char ne "\r") {
1110                    # It's not a CR, so encode the escape sequence.
1111                    $char =~ tr/\t\n/tn/;
1112              $retVal .= "\\" . $char;              $retVal .= "\\" . $char;
1113                }
1114          } else {          } else {
1115              # Here there are no more escape sequences. The rest of the string is              # Here there are no more escape sequences. The rest of the string is
1116              # transferred unmodified.              # transferred unmodified.
# Line 874  Line 1126 
1126    
1127  C<< my $realString = Tracer::UnEscape($codedString); >>  C<< my $realString = Tracer::UnEscape($codedString); >>
1128    
1129  Replace escape sequences with their actual equivalents. C<\b> will be replaced by a space,  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
1130  C<\t> by a tab, C<\n> by a new-line character, and C<\\> by a back-slash.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
1131    be deleted.
1132    
1133  =over 4  =over 4
1134    
# Line 900  Line 1153 
1153      # Only proceed if the incoming string is nonempty.      # Only proceed if the incoming string is nonempty.
1154      if (defined $codedString) {      if (defined $codedString) {
1155          # Loop through the parameter string, looking for escape sequences. We can't do          # Loop through the parameter string, looking for escape sequences. We can't do
1156          # translating because it causes problems with the escaped slash. ("\\b" becomes          # translating because it causes problems with the escaped slash. ("\\t" becomes
1157          # "\ " no matter what we do.)          # "\<tab>" no matter what we do.)
1158          while (length $codedString > 0) {          while (length $codedString > 0) {
1159              # Look for the first escape sequence.              # Look for the first escape sequence.
1160              if ($codedString =~ /^(.*?)\\(\\|b|n|t)/) {              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
1161                  # Here we found it. The text preceding the sequence is in $1. The sequence                  # Here we found it. The text preceding the sequence is in $1. The sequence
1162                  # itself is in $2. First, move the clear text to the return variable.                  # itself is in $2. First, move the clear text to the return variable.
1163                  $retVal .= $1;                  $retVal .= $1;
1164                  $codedString = substr $codedString, (2 + length $1);                  $codedString = substr $codedString, (2 + length $1);
1165                  # Decode the escape sequence.                  # Get the escape value.
1166                  my $char = $2;                  my $char = $2;
1167                  $char =~ tr/\\btn/\\ \t\n/;                  # If we have a "\r", we are done.
1168                    if ($char ne 'r') {
1169                        # Here it's not an 'r', so we convert it.
1170                        $char =~ tr/\\tn/\\\t\n/;
1171                  $retVal .= $char;                  $retVal .= $char;
1172                    }
1173              } else {              } else {
1174                  # Here there are no more escape sequences. The rest of the string is                  # Here there are no more escape sequences. The rest of the string is
1175                  # transferred unmodified.                  # transferred unmodified.
# Line 1022  Line 1279 
1279    
1280  C<< my @fileContents = Tracer::GetFile($fileName); >>  C<< my @fileContents = Tracer::GetFile($fileName); >>
1281    
1282  Return the entire contents of a file.      or
1283    
1284    C<< my $fileContents = Tracer::GetFile($fileName); >>
1285    
1286    Return the entire contents of a file. In list context, line-ends are removed and
1287    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1288    
1289  =over 4  =over 4
1290    
# Line 1033  Line 1295 
1295  =item RETURN  =item RETURN
1296    
1297  In a list context, returns the entire file as a list with the line terminators removed.  In a list context, returns the entire file as a list with the line terminators removed.
1298  In a scalar context, returns the entire file as a string.  In a scalar context, returns the entire file as a string. If an error occurs opening
1299    the file, an empty list will be returned.
1300    
1301  =back  =back
1302    
# Line 1048  Line 1311 
1311      my $ok = open INPUTFILE, "<$fileName";      my $ok = open INPUTFILE, "<$fileName";
1312      if (!$ok) {      if (!$ok) {
1313          # If we had an error, trace it. We will automatically return a null value.          # If we had an error, trace it. We will automatically return a null value.
1314          Trace("Could not open \"$fileName\" for input.") if T(0);          Trace("Could not open \"$fileName\" for input: $!") if T(0);
1315      } else {      } else {
1316          # Read the whole file into the return variable, stripping off any terminator          # Read the whole file into the return variable, stripping off any terminator
1317          # characters.          # characters.
# Line 1117  Line 1380 
1380    
1381  C<< Confess($message); >>  C<< Confess($message); >>
1382    
1383  Trace the call stack and abort the program with the specified message. The stack  Trace the call stack and abort the program with the specified message. When used with
 trace will only appear if the trace level for this package is 1 or more. When used with  
1384  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
1385  So, for example  So, for example
1386    
# Line 1140  Line 1402 
1402      # Get the parameters.      # Get the parameters.
1403      my ($message) = @_;      my ($message) = @_;
1404      # Trace the call stack.      # Trace the call stack.
1405      Cluck($message) if T(1);      Cluck($message);
1406      # Abort the program.      # Abort the program.
1407      croak(">>> $message");      croak(">>> $message");
1408  }  }
# Line 1150  Line 1412 
1412  C<< Assert($condition1, $condition2, ... $conditionN); >>  C<< Assert($condition1, $condition2, ... $conditionN); >>
1413    
1414  Return TRUE if all the conditions are true. This method can be used in conjunction with  Return TRUE if all the conditions are true. This method can be used in conjunction with
1415  the OR operator and the L</Confess> method, B<Assert> can function as a debugging assert.  the OR operator and the L</Confess> method as a debugging assert.
1416  So, for example  So, for example
1417    
1418  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
# Line 1309  Line 1571 
1571    
1572  C<< if (Tracer::DebugMode) { ...code... } >>  C<< if (Tracer::DebugMode) { ...code... } >>
1573    
1574  Return TRUE if debug mode has been turned on in FIG_Config, else output  Return TRUE if debug mode has been turned on, else output an error
1575  an error page and return FALSE.  page and return FALSE.
1576    
1577  Certain CGI scripts are too dangerous to exist in the production  Certain CGI scripts are too dangerous to exist in the production
1578  environment. This method provides a simple way to prevent them  environment. This method provides a simple way to prevent them
1579  from working unless they are explicitly turned on in the configuration  from working unless they are explicitly turned on by creating a password
1580  file by setting C<$FIG_Config::debug_mode> to 1. If debugging mode  cookie via the B<SetPassword> script.  If debugging mode
1581  is not turned on, an error web page will be output.  is not turned on, an error web page will be output directing the
1582    user to enter in the correct password.
1583    
1584  =cut  =cut
1585    
1586  sub DebugMode {  sub DebugMode {
1587      # Declare the return variable.      # Declare the return variable.
1588      my $retVal;      my $retVal = 0;
1589      # Check the debug configuration.      # Check the debug configuration.
1590      if ($FIG_Config::debug_mode) {      my $password = CGI::cookie("DebugMode");
1591        my $encrypted = Digest::MD5::md5_hex($password);
1592        if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1593          $retVal = 1;          $retVal = 1;
1594      } else {      } else {
1595          # Here debug mode is off, so we generate an error page.          # Here debug mode is off, so we generate an error page.
# Line 1360  Line 1625 
1625  sub Strip {  sub Strip {
1626      # Get a copy of the parameter string.      # Get a copy of the parameter string.
1627      my ($string) = @_;      my ($string) = @_;
1628      my $retVal = $string;      my $retVal = (defined $string ? $string : "");
1629      # Strip the line terminator characters.      # Strip the line terminator characters.
1630      $retVal =~ s/(\r|\n)+$//g;      $retVal =~ s/(\r|\n)+$//g;
1631      # Return the result.      # Return the result.
# Line 1391  Line 1656 
1656    
1657  =item padChar (optional)  =item padChar (optional)
1658    
1659    Character to use for padding. The default is a space.
1660    
1661  =item RETURN  =item RETURN
1662    
1663  Returns a copy of the original string with the spaces added to the specified end so  Returns a copy of the original string with the pad character added to the
1664  that it achieves the desired length.  specified end so that it achieves the desired length.
1665    
1666  =back  =back
1667    
# Line 1426  Line 1693 
1693      return $retVal;      return $retVal;
1694  }  }
1695    
1696    =head3 EOF
1697    
1698    This is a constant that is lexically greater than any useful string.
1699    
1700    =cut
1701    
1702    sub EOF {
1703        return "\xFF\xFF\xFF\xFF\xFF";
1704    }
1705    
1706    =head3 TICK
1707    
1708    C<< my @results = TICK($commandString); >>
1709    
1710    Perform a back-tick operation on a command. If this is a Windows environment, any leading
1711    dot-slash (C<./> will be removed. So, for example, if you were doing
1712    
1713        `./protein.cgi`
1714    
1715    from inside a CGI script, it would work fine in Unix, but would issue an error message
1716    in Windows complaining that C<'.'> is not a valid command. If instead you code
1717    
1718        TICK("./protein.cgi")
1719    
1720    it will work correctly in both environments.
1721    
1722    =over 4
1723    
1724    =item commandString
1725    
1726    The command string to pass to the system.
1727    
1728    =item RETURN
1729    
1730    Returns the standard output from the specified command, as a list.
1731    
1732    =back
1733    
1734    =cut
1735    #: Return Type @;
1736    sub TICK {
1737        # Get the parameters.
1738        my ($commandString) = @_;
1739        # Chop off the dot-slash if this is Windows.
1740        if ($FIG_Config::win_mode) {
1741            $commandString =~ s!^\./!!;
1742        }
1743        # Activate the command and return the result.
1744        return `$commandString`;
1745    }
1746    
1747    =head3 ScriptSetup
1748    
1749    C<< my ($query, $varHash) = ScriptSetup(); >>
1750    
1751    Perform standard tracing and debugging setup for scripts. The value returned is
1752    the CGI object followed by a pre-built variable hash.
1753    
1754    The C<Trace> query parameter is used to determine whether or not tracing is active and
1755    which trace modules (other than C<Tracer> and C<FIG>) should be turned on. Specifying
1756    the C<CGI> trace module will trace parameter and environment information. Parameters are
1757    traced at level 3 and environment variables at level 4. At the end of the script, the
1758    client should call L</ScriptFinish> to output the web page.
1759    
1760    =cut
1761    
1762    sub ScriptSetup {
1763        # Get the CGI query object.
1764        my $query = CGI->new();
1765        # Check for tracing. Set it up if the user asked for it.
1766        if ($query->param('Trace')) {
1767            # Set up tracing to be queued for display at the bottom of the web page.
1768            TSetup($query->param('Trace') . " FIG Tracer", "QUEUE");
1769            # Trace the parameter and environment data.
1770            if (T(CGI => 3)) {
1771                # Here we want to trace the parameter data.
1772                my @names = $query->param;
1773                for my $parmName (sort @names) {
1774                    # Note we skip "Trace", which is for our use only.
1775                    if ($parmName ne 'Trace') {
1776                        my @values = $query->param($parmName);
1777                        Trace("CGI: $parmName = " . join(", ", @values));
1778                    }
1779                }
1780            }
1781            if (T(CGI => 4)) {
1782                # Here we want the environment data too.
1783                for my $envName (sort keys %ENV) {
1784                    Trace("ENV: $envName = $ENV{$envName}");
1785                }
1786            }
1787        } else {
1788            # Here tracing is to be turned off. All we allow is errors traced into the
1789            # error log.
1790            TSetup("0", "WARN");
1791        }
1792        # Create the variable hash.
1793        my $varHash = { DebugData => '' };
1794        # If we're in DEBUG mode, set up the debug mode data for forms.
1795        if (Tracer::DebugMode) {
1796            $varHash->{DebugData} = GetFile("Html/DebugFragment.html");
1797        }
1798        # Return the query object and variable hash.
1799        return ($query, $varHash);
1800    }
1801    
1802    =head3 ScriptFinish
1803    
1804    C<< ScriptFinish($webData, $varHash); >>
1805    
1806    Output a web page at the end of a script. Either the string to be output or the
1807    name of a template file can be specified. If the second parameter is omitted,
1808    it is assumed we have a string to be output; otherwise, it is assumed we have the
1809    name of a template file. The template should have the variable C<DebugData>
1810    specified in any form that invokes a standard script. If debugging mode is turned
1811    on, a form field will be put in that allows the user to enter tracing data.
1812    Trace messages will be placed immediately before the terminal C<BODY> tag in
1813    the output, formatted as a list.
1814    
1815    A typical standard script would loook like the following.
1816    
1817        BEGIN {
1818            # Print the HTML header.
1819            print "CONTENT-TYPE: text/html\n\n";
1820        }
1821        use Tracer;
1822        use CGI;
1823        use FIG;
1824        # ... more uses ...
1825    
1826        my ($query, $varHash) = ScriptSetup();
1827        eval {
1828            # ... get data from $query, put it in $varHash ...
1829        };
1830        if ($@) {
1831            Trace("Script Error: $@") if T(0);
1832        }
1833        ScriptFinish("Html/MyTemplate.html", $varHash);
1834    
1835    The idea here is that even if the script fails, you'll see trace messages and
1836    useful output.
1837    
1838    =over 4
1839    
1840    =item webData
1841    
1842    A string containing either the full web page to be written to the output or the
1843    name of a template file from which the page is to be constructed. If the name
1844    of a template file is specified, then the second parameter must be present;
1845    otherwise, it must be absent.
1846    
1847    =item varHash (optional)
1848    
1849    If specified, then a reference to a hash mapping variable names for a template
1850    to their values. The template file will be read into memory, and variable markers
1851    will be replaced by data in this hash reference.
1852    
1853    =back
1854    
1855    =cut
1856    
1857    sub ScriptFinish {
1858        # Get the parameters.
1859        my ($webData, $varHash) = @_;
1860        # Check for a template file situation.
1861        my $outputString;
1862        if (defined $varHash) {
1863            # Here we have a template file. We need to apply the variables to the template.
1864            $outputString = PageBuilder::Build("<$webData", $varHash, "Html");
1865        } else {
1866            # Here the user gave us a raw string.
1867            $outputString = $webData;
1868        }
1869        # Check for trace messages.
1870        if ($Destination eq "QUEUE") {
1871            # We have trace messages, so we want to put them at the end of the body. This
1872            # is either at the end of the whole string or at the beginning of the BODY
1873            # end-tag.
1874            my $pos = length $outputString;
1875            if ($outputString =~ m#</body>#gi) {
1876                $pos = (pos $outputString) - 7;
1877            }
1878            substr $outputString, $pos, 0, QTrace('Html');
1879        }
1880        # Write the output string.
1881        print $outputString;
1882    }
1883    
1884    =head3 Insure
1885    
1886    C<< Insure($dirName); >>
1887    
1888    Insure a directory is present.
1889    
1890    =over 4
1891    
1892    =item dirName
1893    
1894    Name of the directory to check. If it does not exist, it will be created.
1895    
1896    =back
1897    
1898    =cut
1899    
1900    sub Insure {
1901        my ($dirName) = @_;
1902        if (! -d $dirName) {
1903            Trace("Creating $dirName directory.") if T(2);
1904            mkpath $dirName;
1905        }
1906    }
1907    
1908  1;  1;

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