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revision 1.23, Tue Sep 13 05:36:12 2005 UTC revision 1.55, Sun Jun 18 09:55:24 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 TICK);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup ScriptSetup ScriptFinish Insure ChDir);
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 Cwd;
28      use FIG_Config;      use FIG_Config;
29      use PageBuilder;      use PageBuilder;
30      use Digest::MD5;      use Digest::MD5;
31        use File::Basename;
32        use File::Path;
33        use File::stat;
34    
35  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
36    
# Line 72  Line 93 
93    
94  =over 4  =over 4
95    
96  =item 0 Error  =item Error 0
97    
98  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
99  application entirely.  application entirely.
100    
101  =item 1 Warning  =item Warning 1
102    
103  Message indicates something that is unexpected but that probably did not interfere  Message indicates something that is unexpected but that probably did not interfere
104  with program execution.  with program execution.
105    
106  =item 2 Notice  =item Notice 2
107    
108  Message indicates the beginning or end of a major task.  Message indicates the beginning or end of a major task.
109    
110  =item 3 Information  =item Information 3
111    
112  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
113  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.
114    
115  =item 4 Detail  =item Detail 4
116    
117  Message indicates a low-level loop iteration.  Message indicates a low-level loop iteration.
118    
# Line 157  Line 178 
178      # Presume category-based tracing until we learn otherwise.      # Presume category-based tracing until we learn otherwise.
179      $AllTrace = 0;      $AllTrace = 0;
180      # 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
181      # tracing.      # tracing. We must also clear away any pre-existing data.
182        %Categories = ( main => 1 );
183      for my $category (@categoryData) {      for my $category (@categoryData) {
184          if ($category eq '*') {          if ($category eq '*') {
185              $AllTrace = 1;              $AllTrace = 1;
# Line 188  Line 210 
210      $SetupCount++;      $SetupCount++;
211  }  }
212    
213    =head3 StandardSetup
214    
215    C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>
216    
217    This method performs standard command-line parsing and tracing setup. The return
218    values are a hash of the command-line options and a list of the positional
219    parameters. Tracing is automatically set up and the command-line options are
220    validated.
221    
222    This is a complex method that does a lot of grunt work. The parameters can
223    be more easily understood, however, once they are examined individually.
224    
225    The I<categories> parameter is the most obtuse. It is a reference to a list of
226    special-purpose tracing categories. Most tracing categories are PERL package
227    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
228    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
229    
230        ["Sprout", "SproutLoad", "ERDB"]
231    
232    This would cause trace messages in the specified three packages to appear in
233    the output. There are threer special tracing categories that are automatically
234    handled by this method. In other words, if you used L</TSetup> you would need
235    to include these categories manually, but if you use this method they are turned
236    on automatically.
237    
238    =over 4
239    
240    =item FIG
241    
242    Turns on trace messages inside the B<FIG> package.
243    
244    =item SQL
245    
246    Traces SQL commands and activity.
247    
248    =item Tracer
249    
250    Traces error messages and call stacks.
251    
252    =back
253    
254    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
255    The trace level is specified using the C<-trace> command-line option. For example,
256    the following command line for C<TransactFeatures> turns on SQL tracing and runs
257    all tracing at level 3.
258    
259        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
260    
261    Standard tracing is output to the standard output and echoed to the file
262    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
263    process ID. You can also specify the C<user> parameter to put a user ID
264    instead of a process ID in the trace file name. So, for example
265    
266    The default trace level is 2. To get all messages, specify a trace level of 4.
267    For a genome-by-genome update, use 3.
268    
269        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
270    
271    would send the trace output to C<traceBruce.log> in the temporary directory.
272    
273    The I<options> parameter is a reference to a hash containing the command-line
274    options, their default values, and an explanation of what they mean. Command-line
275    options may be in the form of switches or keywords. In the case of a switch, the
276    option value is 1 if it is specified and 0 if it is not specified. In the case
277    of a keyword, the value is separated from the option name by an equal sign. You
278    can see this last in the command-line example above.
279    
280    You can specify a different default trace level by setting C<$options->{trace}>
281    prior to calling this method.
282    
283    An example at this point would help. Consider, for example, the command-line utility
284    C<TransactFeatures>. It accepts a list of positional parameters plus the options
285    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
286    the following code.
287    
288        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
289                            { safe => [0, "use database transactions"],
290                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
291                              start => [' ', "start with this genome"],
292                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
293                            "command transactionDirectory IDfile",
294                          @ARGV);
295    
296    
297    The call to C<ParseCommand> specifies the default values for the options and
298    stores the actual options in a hash that is returned as C<$options>. The
299    positional parameters are returned in C<@parameters>.
300    
301    The following is a sample command line for C<TransactFeatures>.
302    
303        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
304    
305    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
306    parameters, and would find themselves in I<@parameters> after executing the
307    above code fragment. The tracing would be set to level 2, and the categories
308    would be C<FIG>, C<Tracer>, and <DocUtils>. C<FIG> and C<Tracer> are standard,
309    and C<DocUtils> was included because it came in within the first parameter
310    to this method. The I<$options> hash would be
311    
312        { trace => 2, sql => 0, safe => 0,
313          noAlias => 1, start => ' ', tblFiles => 0 }
314    
315    Use of C<StandardSetup> in this way provides a simple way of performing
316    standard tracing setup and command-line parsing. Note that the caller is
317    not even aware of the command-line switches C<-trace> and C<-sql>, which
318    are used by this method to control the tracing. If additional tracing features
319    need to be added in the future, they can be processed by this method without
320    upsetting the command-line utilities.
321    
322    If the C<background> option is specified on the command line, then the
323    standard and error outputs will be directed to files in the temporary
324    directory, using the same suffix as the trace file. So, if the command
325    line specified
326    
327        -user=Bruce -background
328    
329    then the trace output would go to C<traceBruce.log>, the standard output to
330    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
331    simplify starting a command in the background.
332    
333    Finally, if the special option C<-h> is specified, the option names will
334    be traced at level 0 and the program will exit without processing.
335    This provides a limited help capability. For example, if the user enters
336    
337        TransactFeatures -h
338    
339    he would see the following output.
340    
341        TransactFeatures [options] command transactionDirectory IDfile
342            -trace    tracing level (default 2)
343            -sql      trace SQL commands
344            -safe     use database transactions
345            -noAlias  do not expect aliases in CHANGE transactions
346            -start    start with this genome
347            -tblFiles output TBL files containing the corrected IDs
348    
349    The caller has the option of modifying the tracing scheme by placing a value
350    for C<trace> in the incoming options hash. The default value can be overridden,
351    or the tracing to the standard output can be turned off by suffixing a minus
352    sign to the trace level. So, for example,
353    
354        { trace => [0, "tracing level (default 0)"],
355           ...
356    
357    would set the default trace level to 0 instead of 2, while
358    
359        { trace => ["2-", "tracing level (default 2)"],
360           ...
361    
362    would leave the default at 2, but trace only to the log file, not to the
363    standard output.
364    
365    The parameters to this method are as follows.
366    
367    =over 4
368    
369    =item categories
370    
371    Reference to a list of tracing category names. These should be names of
372    packages whose internal workings will need to be debugged to get the
373    command working.
374    
375    =item options
376    
377    Reference to a hash containing the legal options for the current command mapped
378    to their default values and descriptions. The user can override the defaults
379    by specifying the options as command-line switches prefixed by a hyphen.
380    Tracing-related options may be added to this hash. If the C<-h> option is
381    specified on the command line, the option descriptions will be used to
382    explain the options. To turn off tracing to the standard output, add a
383    minus sign to the value for C<trace> (see above).
384    
385    =item parmHelp
386    
387    A string that vaguely describes the positional parameters. This is used
388    if the user specifies the C<-h> option.
389    
390    =item argv
391    
392    List of command line parameters, including the option switches, which must
393    precede the positional parameters and be prefixed by a hyphen.
394    
395    =item RETURN
396    
397    Returns a list. The first element of the list is the reference to a hash that
398    maps the command-line option switches to their values. These will either be the
399    default values or overrides specified on the command line. The remaining
400    elements of the list are the position parameters, in order.
401    
402    =back
403    
404    =cut
405    
406    sub StandardSetup {
407        # Get the parameters.
408        my ($categories, $options, $parmHelp, @argv) = @_;
409        # Add the tracing options.
410        if (! exists $options->{trace}) {
411            $options->{trace} = [2, "tracing level"];
412        }
413        $options->{sql} = [0, "turn on SQL tracing"];
414        $options->{h} = [0, "display command-line options"];
415        $options->{user} = [$$, "trace log file name suffix"];
416        $options->{background} = [0, "spool standard and error output"];
417        # Create a parsing hash from the options hash. The parsing hash
418        # contains the default values rather than the default value
419        # and the description. While we're at it, we'll memorize the
420        # length of the longest option name.
421        my $longestName = 0;
422        my %parseOptions = ();
423        for my $key (keys %{$options}) {
424            if (length $key > $longestName) {
425                $longestName = length $key;
426            }
427            $parseOptions{$key} = $options->{$key}->[0];
428        }
429        # Parse the command line.
430        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
431        # Get the logfile suffix.
432        my $suffix = $retOptions->{user};
433        # Check for background mode.
434        if ($retOptions->{background}) {
435            my $outFileName = "$FIG_Config::temp/out$suffix.log";
436            my $errFileName = "$FIG_Config::temp/err$suffix.log";
437            open STDOUT, ">$outFileName";
438            open STDERR, ">$errFileName";
439        }
440        # Now we want to set up tracing. First, we need to know if SQL is to
441        # be traced.
442        my @cats = @{$categories};
443        if ($retOptions->{sql}) {
444            push @cats, "SQL";
445        }
446        # Add the default categories.
447        push @cats, "Tracer", "FIG";
448        # Next, we create the category string by joining the categories.
449        my $cats = join(" ", @cats);
450        # Check to determine whether or not the caller wants to turn off tracing
451        # to the standard output.
452        my $traceLevel = $retOptions->{trace};
453        my $textOKFlag = 1;
454        if ($traceLevel =~ /^(.)-/) {
455            $traceLevel = $1;
456            $textOKFlag = 0;
457        }
458        # Now we set up the trace mode.
459        my $traceMode;
460        # Verify that we can open a file in the FIG temporary directory.
461        my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
462        if (open TESTTRACE, ">$traceFileName") {
463            # Here we can trace to a file.
464            $traceMode = ">$traceFileName";
465            if ($textOKFlag) {
466                # Echo to standard output if the text-OK flag is set.
467                $traceMode = "+$traceMode";
468            }
469            # Close the test file.
470            close TESTTRACE;
471        } else {
472            # Here we can't trace to a file. We trace to the standard output if it's
473            # okay, and the error log otherwise.
474            if ($textOKFlag) {
475                $traceMode = "TEXT";
476            } else {
477                $traceMode = "WARN";
478            }
479        }
480        # Now set up the tracing.
481        TSetup("$traceLevel $cats", $traceMode);
482        # Check for the "h" option. If it is specified, dump the command-line
483        # options and exit the program.
484        if ($retOptions->{h}) {
485            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
486            Trace("$1 [options] $parmHelp") if T(0);
487            for my $key (sort keys %{$options}) {
488                my $name = Pad($key, $longestName, 0, ' ');
489                my $desc = $options->{$key}->[1];
490                if ($options->{$key}->[0]) {
491                    $desc .= " (default " . $options->{$key}->[0] . ")";
492                }
493                Trace("  $name $desc") if T(0);
494            }
495            exit(0);
496        }
497        # Return the parsed parameters.
498        return ($retOptions, @retParameters);
499    }
500    
501  =head3 Setups  =head3 Setups
502    
503  C<< my $count = Tracer::Setups(); >>  C<< my $count = Tracer::Setups(); >>
# Line 348  Line 658 
658    
659  =head3 OpenDir  =head3 OpenDir
660    
661  C<< my @files = OpenDir($dirName, $filtered); >>  C<< my @files = OpenDir($dirName, $filtered, $flag); >>
662    
663  Open a directory and return all the file names. This function essentially performs  Open a directory and return all the file names. This function essentially performs
664  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
665  set to TRUE, all filenames beginning with a period (C<.>) will be filtered out of  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
666  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
667  for example,  filtered out of the return list. If the directory does not open and I<$flag> is not
668    set, an exception is thrown. So, for example,
669    
670      my @files = OpenDir("/Volumes/fig/contigs", 1);      my @files = OpenDir("/Volumes/fig/contigs", 1);
671    
672  is effectively the same as  is effectively the same as
673    
674      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
675      my @files = grep { $_ !~ /^\./ } readdir(TMP);      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
676    
677  Similarly, the following code  Similarly, the following code
678    
679      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs");      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
680    
681  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
682  automatically throws an error if the directory fails to open.  automatically returns an empty list if the directory fails to open.
683    
684  =over 4  =over 4
685    
# Line 381  Line 692 
692  TRUE if files whose names begin with a period (C<.>) should be automatically removed  TRUE if files whose names begin with a period (C<.>) should be automatically removed
693  from the list, else FALSE.  from the list, else FALSE.
694    
695    =item flag
696    
697    TRUE if a failure to open is okay, else FALSE
698    
699  =back  =back
700    
701  =cut  =cut
702  #: Return Type @;  #: Return Type @;
703  sub OpenDir {  sub OpenDir {
704      # Get the parameters.      # Get the parameters.
705      my ($dirName, $filtered) = @_;      my ($dirName, $filtered, $flag) = @_;
706      # Declare the return variable.      # Declare the return variable.
707      my @retVal;      my @retVal = ();
708      # Open the directory.      # Open the directory.
709      if (opendir(my $dirHandle, $dirName)) {      if (opendir(my $dirHandle, $dirName)) {
710          # The directory opened successfully. Get the appropriate list according to the          # The directory opened successfully. Get the appropriate list according to the
711          # strictures of the filter parameter.          # strictures of the filter parameter.
712          if ($filtered) {          if ($filtered) {
713              @retVal = grep { $_ !~ /^\./ } readdir $dirHandle;              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
714          } else {          } else {
715              @retVal = readdir $dirHandle;              @retVal = readdir $dirHandle;
716          }          }
717      } else {      } elsif (! $flag) {
718          # Here the directory would not open.          # Here the directory would not open and it's considered an error.
719          Confess("Could not open directory $dirName.");          Confess("Could not open directory $dirName.");
720      }      }
721      # Return the result.      # Return the result.
# Line 738  Line 1053 
1053          # Convert it to lower case before we hash it.          # Convert it to lower case before we hash it.
1054          $category = lc $category;          $category = lc $category;
1055          # Use the category and tracelevel to compute the result.          # Use the category and tracelevel to compute the result.
1056            if (ref $traceLevel) {
1057                Confess("Bad trace level.");
1058            } elsif (ref $TraceLevel) {
1059                Confess("Bad trace config.");
1060            }
1061          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
1062      }      }
1063      # Return the computed result.      # Return the computed result.
# Line 824  Line 1144 
1144    
1145  C<< my $codedString = Tracer::Escape($realString); >>  C<< my $codedString = Tracer::Escape($realString); >>
1146    
1147  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
1148  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
1149  doubled. The effect is to exactly reverse the effect of L</UnEscape>.  result is to reverse the effect of L</UnEscape>.
1150    
1151  =over 4  =over 4
1152    
# Line 850  Line 1170 
1170      # Loop through the parameter string, looking for sequences to escape.      # Loop through the parameter string, looking for sequences to escape.
1171      while (length $realString > 0) {      while (length $realString > 0) {
1172          # Look for the first sequence to escape.          # Look for the first sequence to escape.
1173          if ($realString =~ /^(.*?)([ \n\t\\])/) {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1174              # 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
1175              # 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.
1176              $retVal .= $1;              $retVal .= $1;
1177              # Strip the processed section off the real string.              # Strip the processed section off the real string.
1178              $realString = substr $realString, (length $2) + (length $1);              $realString = substr $realString, (length $2) + (length $1);
1179              # Encode the escape sequence.              # Get the matched character.
1180              my $char = $2;              my $char = $2;
1181              $char =~ tr/ \t\n/btn/;              # If we have a CR, we are done.
1182                if ($char ne "\r") {
1183                    # It's not a CR, so encode the escape sequence.
1184                    $char =~ tr/\t\n/tn/;
1185              $retVal .= "\\" . $char;              $retVal .= "\\" . $char;
1186                }
1187          } else {          } else {
1188              # 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
1189              # transferred unmodified.              # transferred unmodified.
# Line 875  Line 1199 
1199    
1200  C<< my $realString = Tracer::UnEscape($codedString); >>  C<< my $realString = Tracer::UnEscape($codedString); >>
1201    
1202  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
1203  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
1204    be deleted.
1205    
1206  =over 4  =over 4
1207    
# Line 896  Line 1221 
1221  sub UnEscape {  sub UnEscape {
1222      # Get the parameter.      # Get the parameter.
1223      my ($codedString) = @_;      my ($codedString) = @_;
     Tracer("Coded string is \"$codedString\".") if T(4);  
1224      # Initialize the return variable.      # Initialize the return variable.
1225      my $retVal = "";      my $retVal = "";
1226      # Only proceed if the incoming string is nonempty.      # Only proceed if the incoming string is nonempty.
1227      if (defined $codedString) {      if (defined $codedString) {
1228          # 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
1229          # translating because it causes problems with the escaped slash. ("\\b" becomes          # translating because it causes problems with the escaped slash. ("\\t" becomes
1230          # "\ " no matter what we do.)          # "\<tab>" no matter what we do.)
1231          while (length $codedString > 0) {          while (length $codedString > 0) {
1232              # Look for the first escape sequence.              # Look for the first escape sequence.
1233              if ($codedString =~ /^(.*?)\\(\\|b|n|t)/) {              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
1234                  # 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
1235                  # 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.
1236                  $retVal .= $1;                  $retVal .= $1;
1237                  $codedString = substr $codedString, (2 + length $1);                  $codedString = substr $codedString, (2 + length $1);
1238                  # Decode the escape sequence.                  # Get the escape value.
1239                  my $char = $2;                  my $char = $2;
1240                  $char =~ tr/\\btn/\\ \t\n/;                  # If we have a "\r", we are done.
1241                    if ($char ne 'r') {
1242                        # Here it's not an 'r', so we convert it.
1243                        $char =~ tr/\\tn/\\\t\n/;
1244                  $retVal .= $char;                  $retVal .= $char;
1245                    }
1246              } else {              } else {
1247                  # 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
1248                  # transferred unmodified.                  # transferred unmodified.
# Line 1020  Line 1348 
1348      return @inputList;      return @inputList;
1349  }  }
1350    
1351    =head3 Percent
1352    
1353    C<< my $percent = Tracer::Percent($number, $base); >>
1354    
1355    Returns the percent of the base represented by the given number. If the base
1356    is zero, returns zero.
1357    
1358    =over 4
1359    
1360    =item number
1361    
1362    Percent numerator.
1363    
1364    =item base
1365    
1366    Percent base.
1367    
1368    =item RETURN
1369    
1370    Returns the percentage of the base represented by the numerator.
1371    
1372    =back
1373    
1374    =cut
1375    
1376    sub Percent {
1377        # Get the parameters.
1378        my ($number, $base) = @_;
1379        # Declare the return variable.
1380        my $retVal = 0;
1381        # Compute the percent.
1382        if ($base != 0) {
1383            $retVal = $number * 100 / $base;
1384        }
1385        # Return the result.
1386        return $retVal;
1387    }
1388    
1389  =head3 GetFile  =head3 GetFile
1390    
1391  C<< my @fileContents = Tracer::GetFile($fileName); >>  C<< my @fileContents = Tracer::GetFile($fileName); >>
1392    
1393  Return the entire contents of a file.      or
1394    
1395    C<< my $fileContents = Tracer::GetFile($fileName); >>
1396    
1397    Return the entire contents of a file. In list context, line-ends are removed and
1398    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1399    
1400  =over 4  =over 4
1401    
# Line 1035  Line 1406 
1406  =item RETURN  =item RETURN
1407    
1408  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.
1409  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
1410    the file, an empty list will be returned.
1411    
1412  =back  =back
1413    
# Line 1151  Line 1523 
1523  C<< Assert($condition1, $condition2, ... $conditionN); >>  C<< Assert($condition1, $condition2, ... $conditionN); >>
1524    
1525  Return TRUE if all the conditions are true. This method can be used in conjunction with  Return TRUE if all the conditions are true. This method can be used in conjunction with
1526  the OR operator and the L</Confess> method, B<Assert> can function as a debugging assert.  the OR operator and the L</Confess> method as a debugging assert.
1527  So, for example  So, for example
1528    
1529  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
# Line 1272  Line 1644 
1644    
1645  =head3 AddToListMap  =head3 AddToListMap
1646    
1647  C<< Tracer::AddToListMap(\%hash, $key, $value); >>  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>
1648    
1649  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list
1650  is created for the key. Otherwise, the new value is pushed onto the list.  is created for the key. Otherwise, the new value is pushed onto the list.
# Line 1287  Line 1659 
1659    
1660  Key for which the value is to be added.  Key for which the value is to be added.
1661    
1662  =item value  =item value1, value2, ... valueN
1663    
1664  Value to add to the key's value list.  List of values to add to the key's value list.
1665    
1666  =back  =back
1667    
# Line 1297  Line 1669 
1669    
1670  sub AddToListMap {  sub AddToListMap {
1671      # Get the parameters.      # Get the parameters.
1672      my ($hash, $key, $value) = @_;      my ($hash, $key, @values) = @_;
1673      # Process according to whether or not the key already has a value.      # Process according to whether or not the key already has a value.
1674      if (! exists $hash->{$key}) {      if (! exists $hash->{$key}) {
1675          $hash->{$key} = [$value];          $hash->{$key} = [@values];
1676      } else {      } else {
1677          push @{$hash->{$key}}, $value;          push @{$hash->{$key}}, @values;
1678      }      }
1679  }  }
1680    
# Line 1364  Line 1736 
1736  sub Strip {  sub Strip {
1737      # Get a copy of the parameter string.      # Get a copy of the parameter string.
1738      my ($string) = @_;      my ($string) = @_;
1739      my $retVal = $string;      my $retVal = (defined $string ? $string : "");
1740      # Strip the line terminator characters.      # Strip the line terminator characters.
1741      $retVal =~ s/(\r|\n)+$//g;      $retVal =~ s/(\r|\n)+$//g;
1742      # Return the result.      # Return the result.
# Line 1432  Line 1804 
1804      return $retVal;      return $retVal;
1805  }  }
1806    
1807    =head3 EOF
1808    
1809    This is a constant that is lexically greater than any useful string.
1810    
1811    =cut
1812    
1813    sub EOF {
1814        return "\xFF\xFF\xFF\xFF\xFF";
1815    }
1816    
1817  =head3 TICK  =head3 TICK
1818    
1819  C<< my @results = TICK($commandString); >>  C<< my @results = TICK($commandString); >>
# Line 1473  Line 1855 
1855      return `$commandString`;      return `$commandString`;
1856  }  }
1857    
1858    =head3 ScriptSetup
1859    
1860    C<< my ($query, $varHash) = ScriptSetup(); >>
1861    
1862    Perform standard tracing and debugging setup for scripts. The value returned is
1863    the CGI object followed by a pre-built variable hash.
1864    
1865    The C<Trace> query parameter is used to determine whether or not tracing is active and
1866    which trace modules (other than C<Tracer> and C<FIG>) should be turned on. Specifying
1867    the C<CGI> trace module will trace parameter and environment information. Parameters are
1868    traced at level 3 and environment variables at level 4. At the end of the script, the
1869    client should call L</ScriptFinish> to output the web page.
1870    
1871    =cut
1872    
1873    sub ScriptSetup {
1874        # Get the CGI query object.
1875        my $query = CGI->new();
1876        # Check for tracing. Set it up if the user asked for it.
1877        if ($query->param('Trace')) {
1878            # Set up tracing to be queued for display at the bottom of the web page.
1879            TSetup($query->param('Trace') . " FIG Tracer", "QUEUE");
1880            # Trace the parameter and environment data.
1881            if (T(CGI => 3)) {
1882                # Here we want to trace the parameter data.
1883                my @names = $query->param;
1884                for my $parmName (sort @names) {
1885                    # Note we skip "Trace", which is for our use only.
1886                    if ($parmName ne 'Trace') {
1887                        my @values = $query->param($parmName);
1888                        Trace("CGI: $parmName = " . join(", ", @values));
1889                    }
1890                }
1891            }
1892            if (T(CGI => 4)) {
1893                # Here we want the environment data too.
1894                for my $envName (sort keys %ENV) {
1895                    Trace("ENV: $envName = $ENV{$envName}");
1896                }
1897            }
1898        } else {
1899            # Here tracing is to be turned off. All we allow is errors traced into the
1900            # error log.
1901            TSetup("0", "WARN");
1902        }
1903        # Create the variable hash.
1904        my $varHash = { DebugData => '' };
1905        # If we're in DEBUG mode, set up the debug mode data for forms.
1906        if (Tracer::DebugMode) {
1907            $varHash->{DebugData} = GetFile("Html/DebugFragment.html");
1908        }
1909        # Return the query object and variable hash.
1910        return ($query, $varHash);
1911    }
1912    
1913    =head3 ScriptFinish
1914    
1915    C<< ScriptFinish($webData, $varHash); >>
1916    
1917    Output a web page at the end of a script. Either the string to be output or the
1918    name of a template file can be specified. If the second parameter is omitted,
1919    it is assumed we have a string to be output; otherwise, it is assumed we have the
1920    name of a template file. The template should have the variable C<DebugData>
1921    specified in any form that invokes a standard script. If debugging mode is turned
1922    on, a form field will be put in that allows the user to enter tracing data.
1923    Trace messages will be placed immediately before the terminal C<BODY> tag in
1924    the output, formatted as a list.
1925    
1926    A typical standard script would loook like the following.
1927    
1928        BEGIN {
1929            # Print the HTML header.
1930            print "CONTENT-TYPE: text/html\n\n";
1931        }
1932        use Tracer;
1933        use CGI;
1934        use FIG;
1935        # ... more uses ...
1936    
1937        my ($query, $varHash) = ScriptSetup();
1938        eval {
1939            # ... get data from $query, put it in $varHash ...
1940        };
1941        if ($@) {
1942            Trace("Script Error: $@") if T(0);
1943        }
1944        ScriptFinish("Html/MyTemplate.html", $varHash);
1945    
1946    The idea here is that even if the script fails, you'll see trace messages and
1947    useful output.
1948    
1949    =over 4
1950    
1951    =item webData
1952    
1953    A string containing either the full web page to be written to the output or the
1954    name of a template file from which the page is to be constructed. If the name
1955    of a template file is specified, then the second parameter must be present;
1956    otherwise, it must be absent.
1957    
1958    =item varHash (optional)
1959    
1960    If specified, then a reference to a hash mapping variable names for a template
1961    to their values. The template file will be read into memory, and variable markers
1962    will be replaced by data in this hash reference.
1963    
1964    =back
1965    
1966    =cut
1967    
1968    sub ScriptFinish {
1969        # Get the parameters.
1970        my ($webData, $varHash) = @_;
1971        # Check for a template file situation.
1972        my $outputString;
1973        if (defined $varHash) {
1974            # Here we have a template file. We need to apply the variables to the template.
1975            $outputString = PageBuilder::Build("<$webData", $varHash, "Html");
1976        } else {
1977            # Here the user gave us a raw string.
1978            $outputString = $webData;
1979        }
1980        # Check for trace messages.
1981        if ($Destination eq "QUEUE") {
1982            # We have trace messages, so we want to put them at the end of the body. This
1983            # is either at the end of the whole string or at the beginning of the BODY
1984            # end-tag.
1985            my $pos = length $outputString;
1986            if ($outputString =~ m#</body>#gi) {
1987                $pos = (pos $outputString) - 7;
1988            }
1989            substr $outputString, $pos, 0, QTrace('Html');
1990        }
1991        # Write the output string.
1992        print $outputString;
1993    }
1994    
1995    =head3 Insure
1996    
1997    C<< Insure($dirName); >>
1998    
1999    Insure a directory is present.
2000    
2001    =over 4
2002    
2003    =item dirName
2004    
2005    Name of the directory to check. If it does not exist, it will be created.
2006    
2007    =back
2008    
2009    =cut
2010    
2011    sub Insure {
2012        my ($dirName) = @_;
2013        if (! -d $dirName) {
2014            Trace("Creating $dirName directory.") if T(2);
2015            eval { mkpath $dirName; };
2016            if ($@) {
2017                Confess("Error creating $dirName: $@");
2018            }
2019        }
2020    }
2021    
2022    =head3 ChDir
2023    
2024    C<< ChDir($dirName); >>
2025    
2026    Change to the specified directory.
2027    
2028    =over 4
2029    
2030    =item dirName
2031    
2032    Name of the directory to which we want to change.
2033    
2034    =back
2035    
2036    =cut
2037    
2038    sub ChDir {
2039        my ($dirName) = @_;
2040        if (! -d $dirName) {
2041            Confess("Cannot change to directory $dirName: no such directory.");
2042        } else {
2043            Trace("Changing to directory $dirName.") if T(4);
2044            my $okFlag = chdir $dirName;
2045            if (! $okFlag) {
2046                Confess("Error switching to directory $dirName.");
2047            }
2048        }
2049    }
2050    
2051    =head3 CommaFormat
2052    
2053    C<< my $formatted = Tracer::CommaFormat($number); >>
2054    
2055    Insert commas into a number.
2056    
2057    =over 4
2058    
2059    =item number
2060    
2061    A sequence of digits.
2062    
2063    =item RETURN
2064    
2065    Returns the same digits with commas strategically inserted.
2066    
2067    =back
2068    
2069    =cut
2070    
2071    sub CommaFormat {
2072        # Get the parameters.
2073        my ($number) = @_;
2074        # Pad the length up to a multiple of three.
2075        my $padded = "$number";
2076        $padded = " " . $padded while length($padded) % 3 != 0;
2077        # This is a fancy PERL trick. The parentheses in the SPLIT pattern
2078        # cause the delimiters to be included in the output stream. The
2079        # GREP removes the empty strings in between the delimiters.
2080        my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
2081        # Clean out the spaces.
2082        $retVal =~ s/ //g;
2083        # Return the result.
2084        return $retVal;
2085    }
2086    =head3 SetPermissions
2087    
2088    C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>
2089    
2090    Set the permissions for a directory and all the files and folders inside it.
2091    In addition, the group ownership will be changed to the specified value.
2092    
2093    This method is more vulnerable than most to permission and compatability
2094    problems, so it does internal error recovery.
2095    
2096    =over 4
2097    
2098    =item dirName
2099    
2100    Name of the directory to process.
2101    
2102    =item group
2103    
2104    Name of the group to be assigned.
2105    
2106    =item mask
2107    
2108    Permission mask. Bits that are C<1> in this mask will be ORed into the
2109    permission bits of any file or directory that does not already have them
2110    set to 1.
2111    
2112    =item otherMasks
2113    
2114    Map of search patterns to permission masks. If a directory name matches
2115    one of the patterns, that directory and all its members and subdirectories
2116    will be assigned the new pattern. For example, the following would
2117    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2118    
2119        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2120    
2121    The list is ordered, so the following would use 0777 for C<tmp1> and
2122    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2123    
2124        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2125                                                       '^tmp' => 0666);
2126    
2127    Note that the pattern matches are all case-insensitive, and only directory
2128    names are matched, not file names.
2129    
2130    =back
2131    
2132    =cut
2133    
2134    sub SetPermissions {
2135        # Get the parameters.
2136        my ($dirName, $group, $mask, @otherMasks) = @_;
2137        # Set up for error recovery.
2138        eval {
2139            # Switch to the specified directory.
2140            ChDir($dirName);
2141            # Get the group ID.
2142            my $gid = getgrnam($group);
2143            # Get the mask for tracing.
2144            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2145            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(2);
2146            my $fixCount = 0;
2147            my $lookCount = 0;
2148            # @dirs will be a stack of directories to be processed.
2149            my @dirs = (getcwd());
2150            while (scalar(@dirs) > 0) {
2151                # Get the current directory.
2152                my $dir = pop @dirs;
2153                # Check for a match to one of the specified directory names. To do
2154                # that, we need to pull the individual part of the name off of the
2155                # whole path.
2156                my $simpleName = $dir;
2157                if ($dir =~ m!/(.+)$!) {
2158                    $simpleName = $1;
2159                }
2160                # Search for a match.
2161                my $match = 0;
2162                my $i;
2163                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2164                    my $pattern = $otherMasks[$i];
2165                    if ($simpleName =~ /$pattern/i) {
2166                        $match = 1;
2167                    }
2168                }
2169                # Check for a match. Note we use $i-1 because the loop added 2
2170                # before terminating due to the match.
2171                if ($match && $otherMasks[$i-1] != $mask) {
2172                    # This directory matches one of the incoming patterns, and it's
2173                    # a different mask, so we process it recursively with that mask.
2174                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2175                } else {
2176                    # Here we can process normally. Get all of the non-hidden members.
2177                    my @submems = OpenDir($dir, 1);
2178                    for my $submem (@submems) {
2179                        # Get the full name.
2180                        my $thisMem = "$dir/$submem";
2181                        Trace("Checking member $thisMem.") if T(4);
2182                        $lookCount++;
2183                        if ($lookCount % 1000 == 0) {
2184                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(3);
2185                        }
2186                        # Fix the group.
2187                        chown -1, $gid, $thisMem;
2188                        # Insure this member is not a symlink.
2189                        if (! -l $thisMem) {
2190                            # Get its info.
2191                            my $fileInfo = stat $thisMem;
2192                            # Only proceed if we got the info. Otherwise, it's a hard link
2193                            # and we want to skip it anyway.
2194                            if ($fileInfo) {
2195                                my $fileMode = $fileInfo->mode;
2196                                if (($fileMode & $mask) == 0) {
2197                                    # Fix this member.
2198                                    $fileMode |= $mask;
2199                                    chmod $fileMode, $thisMem;
2200                                    $fixCount++;
2201                                }
2202                                # If it's a subdirectory, stack it.
2203                                if (-d $thisMem) {
2204                                    push @dirs, $thisMem;
2205                                }
2206                            }
2207                        }
2208                    }
2209                }
2210            }
2211            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(2);
2212        };
2213        # Check for an error.
2214        if ($@) {
2215            Confess("SetPermissions error: $@");
2216        }
2217    }
2218    
2219  1;  1;

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