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# 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 Assert);      @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);      @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;
29        use PageBuilder;
30        use Digest::MD5;
31        use File::Basename;
32        use File::Path;
33        use File::stat;
34        use LWP::UserAgent;
35        use Time::HiRes 'gettimeofday';
36        use URI::Escape;
37    
38  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
39    
# Line 18  Line 45 
45  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace
46  level is less than or equal to this package's trace level and whose category is activated will  level is less than or equal to this package's trace level and whose category is activated will
47  be written. Thus, a higher trace level on a message indicates that the message  be written. Thus, a higher trace level on a message indicates that the message
48  is less likely to be seen. A higher trace level passed to B<Setup> means more trace messages will  is less likely to be seen. A higher trace level passed to B<TSetup> means more trace messages will
49  appear. To generate a trace message, use the following syntax.  appear. To generate a trace message, use the following syntax.
50    
51  C<< Trace($message) if T(errors => 4); >>  C<< Trace($message) if T(errors => 4); >>
52    
53  This statement will produce a trace message if the trace level is 4 or more and the C<errors>  This statement will produce a trace message if the trace level is 4 or more and the C<errors>
54  category is active. Note that the special category C<root> is always active, so  category is active. Note that the special category C<main> is always active, so
55    
56  C<< Trace($message) if T(root => 4); >>  C<< Trace($message) if T(main => 4); >>
57    
58  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
59    
# Line 36  Line 63 
63    
64  C<< Trace($message) if T(2); >>  C<< Trace($message) if T(2); >>
65    
66  To set up tracing, you call the C</Setup> method. The method takes as input a trace level, a list  To set up tracing, you call the L</TSetup> method. The method takes as input a trace level, a list
67  of category names, and a set of options. The trace level and list of category names are  of category names, and a set of options. The trace level and list of category names are
68  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
69    
70  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>
71    
72  sets the trace level to 3, activated the C<errors>, C<Sprout>, and C<ERDB> categories, and  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
73  specifies that messages should be output as HTML paragraphs. The idea is to make it easier to  specifies that messages should be output as HTML paragraphs.
74  input tracing configuration on a web form.  
75    To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
76    level 3 and writes the output to the standard error output. This sort of thing might be
77    useful in a CGI environment.
78    
79    C<< TSetup('3 *', 'WARN'); >>
80    
81  In addition to HTML and file output for trace messages, you can specify that the trace messages  In addition to HTML and file output for trace messages, you can specify that the trace messages
82  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
# Line 52  Line 84 
84  the page output, they can be gathered together and displayed at the end of the page. This makes  the page output, they can be gathered together and displayed at the end of the page. This makes
85  it easier to debug page formatting problems.  it easier to debug page formatting problems.
86    
87    Finally, you can specify that all trace messages be emitted as warnings.
88    
89  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
90  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
91  Thus, debugging information is available and easily retrieved even when the application is  Thus, debugging information is available and easily retrieved even when the application is
92  being used out in the field.  being used out in the field.
93    
94    There is no hard and fast rule on how to use trace levels. The following is therefore only
95    a suggestion.
96    
97    =over 4
98    
99    =item Error 0
100    
101    Message indicates an error that may lead to incorrect results or that has stopped the
102    application entirely.
103    
104    =item Warning 1
105    
106    Message indicates something that is unexpected but that probably did not interfere
107    with program execution.
108    
109    =item Notice 2
110    
111    Message indicates the beginning or end of a major task.
112    
113    =item Information 3
114    
115    Message indicates a subtask. In the FIG system, a subtask generally relates to a single
116    genome. This would be a big loop that is not expected to execute more than 500 times or so.
117    
118    =item Detail 4
119    
120    Message indicates a low-level loop iteration.
121    
122    =back
123    
124  =cut  =cut
125    
126  # Declare the configuration variables.  # Declare the configuration variables.
127    
128  my $Destination = "NONE";       # Description of where to send the trace output.  my $Destination = "NONE";       # Description of where to send the trace output.
129  my %Categories = ( root => 1 );  my $TeeFlag = 0;            # TRUE if output is going to a file and to the
130                                # standard output
131    my %Categories = ( main => 1 );
132                                                          # hash of active category names                                                          # hash of active category names
133  my $TraceLevel = 0;                     # trace level; a higher trace level produces more  my $TraceLevel = 0;                     # trace level; a higher trace level produces more
134                                                          # messages                                                          # messages
135  my @Queue = ();                         # queued list of trace messages.  my @Queue = ();                         # queued list of trace messages.
136    my $LastCategory = "main";  # name of the last category interrogated
137    my $SetupCount = 0;         # number of times TSetup called
138    my $AllTrace = 0;           # TRUE if we are tracing all categories.
139    
140  =head2 Public Methods  =head2 Public Methods
141    
# Line 88  Line 157 
157    
158  The destination for the trace output. To send the trace output to a file, specify the file  The destination for the trace output. To send the trace output to a file, specify the file
159  name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended  name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
160  to the file. Otherwise the file is cleared before tracing begins. In addition to sending  to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
161  the trace messages to a file, you can specify XX special destinations. C<HTML> will  symbol with a C<+> to echo output to a file AND to the standard output. In addition to
162    sending the trace messages to a file, you can specify a special destination. C<HTML> will
163  cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>  cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
164  will cause tracing to the standard output as ordinary text. C<QUEUE> will cause trace messages  will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
165  to be stored in a queue for later retrieval by the L</QTrace> method. C<NONE> will cause  messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
166  tracing to be suppressed.  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
167    cause trace messages to be emitted as warnings using the B<warn> directive.  C<NONE> will
168    cause tracing to be suppressed.
169    
170  =back  =back
171    
# Line 106  Line 178 
178          my @categoryData = split /\s+/, $categoryList;          my @categoryData = split /\s+/, $categoryList;
179          # Extract the trace level.          # Extract the trace level.
180          $TraceLevel = shift @categoryData;          $TraceLevel = shift @categoryData;
181          # Build the category hash.      # Presume category-based tracing until we learn otherwise.
182        $AllTrace = 0;
183        # Build the category hash. Note that if we find a "*", we turn on non-category
184        # tracing. We must also clear away any pre-existing data.
185        %Categories = ( main => 1 );
186          for my $category (@categoryData) {          for my $category (@categoryData) {
187                  $Categories{$category} = 1;          if ($category eq '*') {
188                $AllTrace = 1;
189            } else {
190                $Categories{lc $category} = 1;
191            }
192          }          }
193          # Now we need to process the destination information. The most important special          # Now we need to process the destination information. The most important special
194          # case is the single ">", which requires we clear the file first. After doing      # cases are the single ">", which requires we clear the file first, and the
195          # so, we tack on another ">" sign so that future trace messages are appended.      # "+" prefix which indicates a double echo.
196        if ($target =~ m/^\+?>>?/) {
197            if ($target =~ m/^\+/) {
198                $TeeFlag = 1;
199                $target = substr($target, 1);
200            }
201          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
202                  open TRACEFILE, $target;                  open TRACEFILE, $target;
203                  print TRACEFILE Now() . " Tracing initialized.\n";                  print TRACEFILE Now() . " Tracing initialized.\n";
204                  close TRACEFILE;                  close TRACEFILE;
205                  $Destination = ">$target";                  $Destination = ">$target";
206          } else {          } else {
207                $Destination = $target;
208            }
209        } else {
210                  $Destination = uc($target);                  $Destination = uc($target);
211          }          }
212        # Increment the setup counter.
213        $SetupCount++;
214    }
215    
216    =head3 StandardSetup
217    
218    C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>
219    
220    This method performs standard command-line parsing and tracing setup. The return
221    values are a hash of the command-line options and a list of the positional
222    parameters. Tracing is automatically set up and the command-line options are
223    validated.
224    
225    This is a complex method that does a lot of grunt work. The parameters can
226    be more easily understood, however, once they are examined individually.
227    
228    The I<categories> parameter is the most obtuse. It is a reference to a list of
229    special-purpose tracing categories. Most tracing categories are PERL package
230    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
231    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
232    
233        ["Sprout", "SproutLoad", "ERDB"]
234    
235    This would cause trace messages in the specified three packages to appear in
236    the output. There are threer special tracing categories that are automatically
237    handled by this method. In other words, if you used L</TSetup> you would need
238    to include these categories manually, but if you use this method they are turned
239    on automatically.
240    
241    =over 4
242    
243    =item FIG
244    
245    Turns on trace messages inside the B<FIG> package.
246    
247    =item SQL
248    
249    Traces SQL commands and activity.
250    
251    =item Tracer
252    
253    Traces error messages and call stacks.
254    
255    =back
256    
257    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
258    The trace level is specified using the C<-trace> command-line option. For example,
259    the following command line for C<TransactFeatures> turns on SQL tracing and runs
260    all tracing at level 3.
261    
262        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
263    
264    Standard tracing is output to the standard output and echoed to the file
265    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
266    process ID. You can also specify the C<user> parameter to put a user ID
267    instead of a process ID in the trace file name. So, for example
268    
269    The default trace level is 2. To get all messages, specify a trace level of 4.
270    For a genome-by-genome update, use 3.
271    
272        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
273    
274    would send the trace output to C<traceBruce.log> in the temporary directory.
275    
276    The I<options> parameter is a reference to a hash containing the command-line
277    options, their default values, and an explanation of what they mean. Command-line
278    options may be in the form of switches or keywords. In the case of a switch, the
279    option value is 1 if it is specified and 0 if it is not specified. In the case
280    of a keyword, the value is separated from the option name by an equal sign. You
281    can see this last in the command-line example above.
282    
283    You can specify a different default trace level by setting C<$options->{trace}>
284    prior to calling this method.
285    
286    An example at this point would help. Consider, for example, the command-line utility
287    C<TransactFeatures>. It accepts a list of positional parameters plus the options
288    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
289    the following code.
290    
291        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
292                            { safe => [0, "use database transactions"],
293                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
294                              start => [' ', "start with this genome"],
295                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
296                            "command transactionDirectory IDfile",
297                          @ARGV);
298    
299    
300    The call to C<ParseCommand> specifies the default values for the options and
301    stores the actual options in a hash that is returned as C<$options>. The
302    positional parameters are returned in C<@parameters>.
303    
304    The following is a sample command line for C<TransactFeatures>.
305    
306        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
307    
308    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
309    parameters, and would find themselves in I<@parameters> after executing the
310    above code fragment. The tracing would be set to level 2, and the categories
311    would be C<FIG>, C<Tracer>, and <DocUtils>. C<FIG> and C<Tracer> are standard,
312    and C<DocUtils> was included because it came in within the first parameter
313    to this method. The I<$options> hash would be
314    
315        { trace => 2, sql => 0, safe => 0,
316          noAlias => 1, start => ' ', tblFiles => 0 }
317    
318    Use of C<StandardSetup> in this way provides a simple way of performing
319    standard tracing setup and command-line parsing. Note that the caller is
320    not even aware of the command-line switches C<-trace> and C<-sql>, which
321    are used by this method to control the tracing. If additional tracing features
322    need to be added in the future, they can be processed by this method without
323    upsetting the command-line utilities.
324    
325    If the C<background> option is specified on the command line, then the
326    standard and error outputs will be directed to files in the temporary
327    directory, using the same suffix as the trace file. So, if the command
328    line specified
329    
330        -user=Bruce -background
331    
332    then the trace output would go to C<traceBruce.log>, the standard output to
333    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
334    simplify starting a command in the background.
335    
336    Finally, if the special option C<-h> is specified, the option names will
337    be traced at level 0 and the program will exit without processing.
338    This provides a limited help capability. For example, if the user enters
339    
340        TransactFeatures -h
341    
342    he would see the following output.
343    
344        TransactFeatures [options] command transactionDirectory IDfile
345            -trace    tracing level (default 2)
346            -sql      trace SQL commands
347            -safe     use database transactions
348            -noAlias  do not expect aliases in CHANGE transactions
349            -start    start with this genome
350            -tblFiles output TBL files containing the corrected IDs
351    
352    The caller has the option of modifying the tracing scheme by placing a value
353    for C<trace> in the incoming options hash. The default value can be overridden,
354    or the tracing to the standard output can be turned off by suffixing a minus
355    sign to the trace level. So, for example,
356    
357        { trace => [0, "tracing level (default 0)"],
358           ...
359    
360    would set the default trace level to 0 instead of 2, while
361    
362        { trace => ["2-", "tracing level (default 2)"],
363           ...
364    
365    would leave the default at 2, but trace only to the log file, not to the
366    standard output.
367    
368    The parameters to this method are as follows.
369    
370    =over 4
371    
372    =item categories
373    
374    Reference to a list of tracing category names. These should be names of
375    packages whose internal workings will need to be debugged to get the
376    command working.
377    
378    =item options
379    
380    Reference to a hash containing the legal options for the current command mapped
381    to their default values and descriptions. The user can override the defaults
382    by specifying the options as command-line switches prefixed by a hyphen.
383    Tracing-related options may be added to this hash. If the C<-h> option is
384    specified on the command line, the option descriptions will be used to
385    explain the options. To turn off tracing to the standard output, add a
386    minus sign to the value for C<trace> (see above).
387    
388    =item parmHelp
389    
390    A string that vaguely describes the positional parameters. This is used
391    if the user specifies the C<-h> option.
392    
393    =item argv
394    
395    List of command line parameters, including the option switches, which must
396    precede the positional parameters and be prefixed by a hyphen.
397    
398    =item RETURN
399    
400    Returns a list. The first element of the list is the reference to a hash that
401    maps the command-line option switches to their values. These will either be the
402    default values or overrides specified on the command line. The remaining
403    elements of the list are the position parameters, in order.
404    
405    =back
406    
407    =cut
408    
409    sub StandardSetup {
410        # Get the parameters.
411        my ($categories, $options, $parmHelp, @argv) = @_;
412        # Add the tracing options.
413        if (! exists $options->{trace}) {
414            $options->{trace} = [2, "tracing level"];
415        }
416        $options->{sql} = [0, "turn on SQL tracing"];
417        $options->{h} = [0, "display command-line options"];
418        $options->{user} = [$$, "trace log file name suffix"];
419        $options->{background} = [0, "spool standard and error output"];
420        # Create a parsing hash from the options hash. The parsing hash
421        # contains the default values rather than the default value
422        # and the description. While we're at it, we'll memorize the
423        # length of the longest option name.
424        my $longestName = 0;
425        my %parseOptions = ();
426        for my $key (keys %{$options}) {
427            if (length $key > $longestName) {
428                $longestName = length $key;
429            }
430            $parseOptions{$key} = $options->{$key}->[0];
431        }
432        # Parse the command line.
433        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
434        # Get the logfile suffix.
435        my $suffix = $retOptions->{user};
436        # Check for background mode.
437        if ($retOptions->{background}) {
438            my $outFileName = "$FIG_Config::temp/out$suffix.log";
439            my $errFileName = "$FIG_Config::temp/err$suffix.log";
440            open STDOUT, ">$outFileName";
441            open STDERR, ">$errFileName";
442        }
443        # Now we want to set up tracing. First, we need to know if SQL is to
444        # be traced.
445        my @cats = @{$categories};
446        if ($retOptions->{sql}) {
447            push @cats, "SQL";
448        }
449        # Add the default categories.
450        push @cats, "Tracer", "FIG";
451        # Next, we create the category string by joining the categories.
452        my $cats = join(" ", @cats);
453        # Check to determine whether or not the caller wants to turn off tracing
454        # to the standard output.
455        my $traceLevel = $retOptions->{trace};
456        my $textOKFlag = 1;
457        if ($traceLevel =~ /^(.)-/) {
458            $traceLevel = $1;
459            $textOKFlag = 0;
460        }
461        # Now we set up the trace mode.
462        my $traceMode;
463        # Verify that we can open a file in the FIG temporary directory.
464        my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
465        if (open TESTTRACE, ">$traceFileName") {
466            # Here we can trace to a file.
467            $traceMode = ">$traceFileName";
468            if ($textOKFlag) {
469                # Echo to standard output if the text-OK flag is set.
470                $traceMode = "+$traceMode";
471            }
472            # Close the test file.
473            close TESTTRACE;
474        } else {
475            # Here we can't trace to a file. We trace to the standard output if it's
476            # okay, and the error log otherwise.
477            if ($textOKFlag) {
478                $traceMode = "TEXT";
479            } else {
480                $traceMode = "WARN";
481            }
482        }
483        # Now set up the tracing.
484        TSetup("$traceLevel $cats", $traceMode);
485        # Check for the "h" option. If it is specified, dump the command-line
486        # options and exit the program.
487        if ($retOptions->{h}) {
488            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
489            Trace("$1 [options] $parmHelp") if T(0);
490            for my $key (sort keys %{$options}) {
491                my $name = Pad($key, $longestName, 0, ' ');
492                my $desc = $options->{$key}->[1];
493                if ($options->{$key}->[0]) {
494                    $desc .= " (default " . $options->{$key}->[0] . ")";
495                }
496                Trace("  $name $desc") if T(0);
497            }
498            exit(0);
499        }
500        # Return the parsed parameters.
501        return ($retOptions, @retParameters);
502    }
503    
504    =head3 Setups
505    
506    C<< my $count = Tracer::Setups(); >>
507    
508    Return the number of times L</TSetup> has been called.
509    
510    This method allows for the creation of conditional tracing setups where, for example, we
511    may want to set up tracing if nobody else has done it before us.
512    
513    =cut
514    
515    sub Setups {
516        return $SetupCount;
517    }
518    
519    =head3 Open
520    
521    C<< my $handle = Open($fileHandle, $fileSpec, $message); >>
522    
523    Open a file.
524    
525    The I<$fileSpec> is essentially the second argument of the PERL C<open>
526    function. The mode is specified using Unix-like shell information. So, for
527    example,
528    
529        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
530    
531    would open for output appended to the specified file, and
532    
533        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
534    
535    would open a pipe that sorts the records written and removes duplicates. Note
536    the use of file handle syntax in the Open call. To use anonymous file handles,
537    code as follows.
538    
539        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
540    
541    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
542    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
543    failed open will throw an exception and the third parameter will be used to construct
544    an error message. If the parameter is omitted, a standard message is constructed
545    using the file spec.
546    
547        Could not open "/usr/spool/news/twitlog"
548    
549    Note that the mode characters are automatically cleaned from the file name.
550    The actual error message from the file system will be captured and appended to the
551    message in any case.
552    
553        Could not open "/usr/spool/news/twitlog": file not found.
554    
555    In some versions of PERL the only error message we get is a number, which
556    corresponds to the C++ C<errno> value.
557    
558        Could not open "/usr/spool/news/twitlog": 6.
559    
560    =over 4
561    
562    =item fileHandle
563    
564    File handle. If this parameter is C<undef>, a file handle will be generated
565    and returned as the value of this method.
566    
567    =item fileSpec
568    
569    File name and mode, as per the PERL C<open> function.
570    
571    =item message (optional)
572    
573    Error message to use if the open fails. If omitted, a standard error message
574    will be generated. In either case, the error information from the file system
575    is appended to the message. To specify a conditional open that does not throw
576    an error if it fails, use C<0>.
577    
578    =item RETURN
579    
580    Returns the name of the file handle assigned to the file, or C<undef> if the
581    open failed.
582    
583    =back
584    
585    =cut
586    
587    sub Open {
588        # Get the parameters.
589        my ($fileHandle, $fileSpec, $message) = @_;
590        # Attempt to open the file.
591        my $rv = open $fileHandle, $fileSpec;
592        # If the open failed, generate an error message.
593        if (! $rv) {
594            # Save the system error message.
595            my $sysMessage = $!;
596            # See if we need a default message.
597            if (!$message) {
598                # Clean any obvious mode characters and leading spaces from the
599                # filename.
600                my ($fileName) = FindNamePart($fileSpec);
601                $message = "Could not open \"$fileName\"";
602            }
603            # Terminate with an error using the supplied message and the
604            # error message from the file system.
605            Confess("$message: $!");
606        }
607        # Return the file handle.
608        return $fileHandle;
609    }
610    
611    =head3 FindNamePart
612    
613    C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>
614    
615    Extract the portion of a file specification that contains the file name.
616    
617    A file specification is the string passed to an C<open> call. It specifies the file
618    mode and name. In a truly complex situation, it can specify a pipe sequence. This
619    method assumes that the file name is whatever follows the first angle bracket
620    sequence.  So, for example, in the following strings the file name is
621    C</usr/fig/myfile.txt>.
622    
623        >>/usr/fig/myfile.txt
624        </usr/fig/myfile.txt
625        | sort -u > /usr/fig/myfile.txt
626    
627    If the method cannot find a file name using its normal methods, it will return the
628    whole incoming string.
629    
630    =over 4
631    
632    =item fileSpec
633    
634    File specification string from which the file name is to be extracted.
635    
636    =item RETURN
637    
638    Returns a three-element list. The first element contains the file name portion of
639    the specified string, or the whole string if a file name cannot be found via normal
640    methods. The second element contains the start position of the file name portion and
641    the third element contains the length.
642    
643    =back
644    
645    =cut
646    #: Return Type $;
647    sub FindNamePart {
648        # Get the parameters.
649        my ($fileSpec) = @_;
650        # Default to the whole input string.
651        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
652        # Parse out the file name if we can.
653        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
654            $retVal = $2;
655            $len = length $retVal;
656            $pos = (length $fileSpec) - (length $3) - $len;
657        }
658        # Return the result.
659        return ($retVal, $pos, $len);
660    }
661    
662    =head3 OpenDir
663    
664    C<< my @files = OpenDir($dirName, $filtered, $flag); >>
665    
666    Open a directory and return all the file names. This function essentially performs
667    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
668    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
669    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
670    filtered out of the return list. If the directory does not open and I<$flag> is not
671    set, an exception is thrown. So, for example,
672    
673        my @files = OpenDir("/Volumes/fig/contigs", 1);
674    
675    is effectively the same as
676    
677        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
678        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
679    
680    Similarly, the following code
681    
682        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
683    
684    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
685    automatically returns an empty list if the directory fails to open.
686    
687    =over 4
688    
689    =item dirName
690    
691    Name of the directory to open.
692    
693    =item filtered
694    
695    TRUE if files whose names begin with a period (C<.>) should be automatically removed
696    from the list, else FALSE.
697    
698    =item flag
699    
700    TRUE if a failure to open is okay, else FALSE
701    
702    =back
703    
704    =cut
705    #: Return Type @;
706    sub OpenDir {
707        # Get the parameters.
708        my ($dirName, $filtered, $flag) = @_;
709        # Declare the return variable.
710        my @retVal = ();
711        # Open the directory.
712        if (opendir(my $dirHandle, $dirName)) {
713            # The directory opened successfully. Get the appropriate list according to the
714            # strictures of the filter parameter.
715            if ($filtered) {
716                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
717            } else {
718                @retVal = readdir $dirHandle;
719            }
720        } elsif (! $flag) {
721            # Here the directory would not open and it's considered an error.
722            Confess("Could not open directory $dirName.");
723        }
724        # Return the result.
725        return @retVal;
726    }
727    
728    =head3 SetLevel
729    
730    C<< Tracer::SetLevel($newLevel); >>
731    
732    Modify the trace level. A higher trace level will cause more messages to appear.
733    
734    =over 4
735    
736    =item newLevel
737    
738    Proposed new trace level.
739    
740    =back
741    
742    =cut
743    
744    sub SetLevel {
745        $TraceLevel = $_[0];
746  }  }
747    
748  =head3 Now  =head3 Now
# Line 168  Line 790 
790          open STDERR, '>', $fileName;          open STDERR, '>', $fileName;
791  }  }
792    
793    =head3 ReadOptions
794    
795    C<< my %options = Tracer::ReadOptions($fileName); >>
796    
797    Read a set of options from a file. Each option is encoded in a line of text that has the
798    format
799    
800    I<optionName>C<=>I<optionValue>C<; >I<comment>
801    
802    The option name must consist entirely of letters, digits, and the punctuation characters
803    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
804    character is a semi-colon will be ignored. The return hash will map each option name to
805    the corresponding option value.
806    
807    =over 4
808    
809    =item fileName
810    
811    Name of the file containing the option data.
812    
813    =item RETURN
814    
815    Returns a hash mapping the option names specified in the file to their corresponding option
816    value.
817    
818    =back
819    
820    =cut
821    
822    sub ReadOptions {
823        # Get the parameters.
824        my ($fileName) = @_;
825        # Open the file.
826        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
827        # Count the number of records read.
828        my ($records, $comments) = 0;
829        # Create the return hash.
830        my %retVal = ();
831        # Loop through the file, accumulating key-value pairs.
832        while (my $line = <CONFIGFILE>) {
833            # Denote we've read a line.
834            $records++;
835            # Determine the line type.
836            if ($line =~ /^\s*[\n\r]/) {
837                # A blank line is a comment.
838                $comments++;
839            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
840                # Here we have an option assignment.
841                retVal{$1} = $2;
842            } elsif ($line =~ /^\s*;/) {
843                # Here we have a text comment.
844                $comments++;
845            } else {
846                # Here we have an invalid line.
847                Trace("Invalid option statement in record $records.") if T(0);
848            }
849        }
850        # Return the hash created.
851        return %retVal;
852    }
853    
854  =head3 GetOptions  =head3 GetOptions
855    
856  C<< Tracer::GetOptions(\%defaults, \%options); >>  C<< Tracer::GetOptions(\%defaults, \%options); >>
# Line 285  Line 968 
968          my ($message) = @_;          my ($message) = @_;
969          # Get the timestamp.          # Get the timestamp.
970          my $timeStamp = Now();          my $timeStamp = Now();
971        # Format the message. Note we strip off any line terminators at the end.
972        my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);
973          # Process according to the destination.          # Process according to the destination.
974          if ($Destination eq "TEXT") {          if ($Destination eq "TEXT") {
975                  # Write the message to the standard output.                  # Write the message to the standard output.
976                  print "$timeStamp $message\n";          print "$formatted\n";
977        } elsif ($Destination eq "ERROR") {
978            # Write the message to the error output.
979            print STDERR "$formatted\n";
980          } elsif ($Destination eq "QUEUE") {          } elsif ($Destination eq "QUEUE") {
981                  # Push the message into the queue.                  # Push the message into the queue.
982                  push @Queue, "$timeStamp $message";          push @Queue, "$formatted";
983          } elsif ($Destination eq "HTML") {          } elsif ($Destination eq "HTML") {
984                  # Convert the message to HTML and write it to the standard output.                  # Convert the message to HTML and write it to the standard output.
985                  my $escapedMessage = CGI::escapeHTML($message);                  my $escapedMessage = CGI::escapeHTML($message);
986                  print "<p>$timeStamp $message</p>\n";          print "<p>$formatted</p>\n";
987        } elsif ($Destination eq "WARN") {
988           # Emit the message as a warning.
989           warn $message;
990          } elsif ($Destination =~ m/^>>/) {          } elsif ($Destination =~ m/^>>/) {
991                  # Write the trace message to an output file.                  # Write the trace message to an output file.
992                  open TRACING, $Destination;          (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
993                  print TRACING "$timeStamp $message\n";          print TRACING "$formatted\n";
994                  close TRACING;                  close TRACING;
995            # If the Tee flag is on, echo it to the standard output.
996            if ($TeeFlag) {
997                print "$formatted\n";
998            }
999          }          }
1000  }  }
1001    
# Line 343  Line 1038 
1038                  my ($category, $traceLevel) = @_;                  my ($category, $traceLevel) = @_;
1039                  if (!defined $traceLevel) {                  if (!defined $traceLevel) {
1040                          # Here we have no category, so we need to get the calling package.                          # Here we have no category, so we need to get the calling package.
1041                # The calling package is normally the first parameter. If it is
1042                # omitted, the first parameter will be the tracelevel. So, the
1043                # first thing we do is shift the so-called category into the
1044                # $traceLevel variable where it belongs.
1045                          $traceLevel = $category;                          $traceLevel = $category;
1046                          my ($package, $fileName, $line) = caller;                          my ($package, $fileName, $line) = caller;
1047                          # If there is no calling package, we default to "root".              # If there is no calling package, we default to "main".
1048                          if (!$package) {                          if (!$package) {
1049                                  $category = "root";                  $category = "main";
1050                          } else {                          } else {
1051                                  $category = $package;                                  $category = $package;
1052                          }                          }
1053                  }                  }
1054                  # Use the package and tracelevel to compute the result.          # Save the category name.
1055                  $retVal = ($traceLevel <= $TraceLevel && exists $Categories{$category});          $LastCategory = $category;
1056            # Convert it to lower case before we hash it.
1057            $category = lc $category;
1058            # Use the category and tracelevel to compute the result.
1059            if (ref $traceLevel) {
1060                Confess("Bad trace level.");
1061            } elsif (ref $TraceLevel) {
1062                Confess("Bad trace config.");
1063            }
1064            $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
1065          }          }
1066          # Return the computed result.          # Return the computed result.
1067          return $retVal;          return $retVal;
# Line 435  Line 1143 
1143          return ($optionTable, @retVal);          return ($optionTable, @retVal);
1144  }  }
1145    
1146  =head3 UnEscape  =head3 Escape
1147    
1148  C<< my $realString = Tracer::UnEscape($codedString); >>  C<< my $codedString = Tracer::Escape($realString); >>
1149    
1150  Replace escape sequences with their actual equivalents. C<\b> will be replaced by a space,  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines
1151  C<\t> by a tab, C<\n> by a new-line character, and C<\\> by a back-slash.  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
1152    result is to reverse the effect of L</UnEscape>.
1153    
1154  =over 4  =over 4
1155    
1156  =item codedString  =item realString
1157    
1158  String to un-escape.  String to escape.
1159    
1160  =item RETURN  =item RETURN
1161    
1162  Returns a copy of the original string with the escape sequences converted to their actual  Escaped equivalent of the real string.
 values.  
1163    
1164  =back  =back
1165    
1166  =cut  =cut
1167    
1168  sub UnEscape {  sub Escape {
1169          # Get the parameter.          # Get the parameter.
1170          my ($codedString) = @_;      my ($realString) = @_;
1171          # Initialize the return variable.          # Initialize the return variable.
1172          my $retVal = "";          my $retVal = "";
1173          # Loop through the parameter string, looking for escape sequences. We can't do      # Loop through the parameter string, looking for sequences to escape.
1174          # translating because it causes problems with the escaped slash. ("\\b" becomes      while (length $realString > 0) {
1175          # "\ " no matter what we do.)          # Look for the first sequence to escape.
1176          while (length $codedString > 0) {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
                 # Look for the first escape sequence.  
                 if ($codedString =~ /^(.*?)\\(\\|b|n|t)/) {  
1177                          # 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
1178                          # 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.
1179                          $retVal .= $1;                          $retVal .= $1;
1180                          $codedString = substr $codedString, (2 + length $1);              # Strip the processed section off the real string.
1181                          # Decode the escape sequence.              $realString = substr $realString, (length $2) + (length $1);
1182                # Get the matched character.
1183                          my $char = $2;                          my $char = $2;
1184                          $char =~ tr/\\btn/\\ \t\n/;              # If we have a CR, we are done.
1185                          $retVal .= $char;              if ($char ne "\r") {
1186                    # It's not a CR, so encode the escape sequence.
1187                    $char =~ tr/\t\n/tn/;
1188                    $retVal .= "\\" . $char;
1189                }
1190                  } else {                  } else {
1191                          # 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
1192                          # transferred unmodified.                          # transferred unmodified.
1193                          $retVal .= $codedString;              $retVal .= $realString;
1194                          $codedString = "";              $realString = "";
1195                  }                  }
1196          }          }
1197          # Return the result.          # Return the result.
1198          return $retVal;          return $retVal;
1199  }  }
1200    
1201  =head3 ParseRecord  =head3 UnEscape
1202    
1203  C<< my @fields = Tracer::ParseRecord($line); >>  C<< my $realString = Tracer::UnEscape($codedString); >>
1204    
1205  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
1206  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
1207  These will automatically be converted.  be deleted.
1208    
1209  =over 4  =over 4
1210    
1211  =item line  =item codedString
1212    
1213  Line of data containing the tab-delimited fields.  String to un-escape.
1214    
1215  =item RETURN  =item RETURN
1216    
1217  Returns a list of the fields found in the data line.  Returns a copy of the original string with the escape sequences converted to their actual
1218    values.
1219    
1220  =back  =back
1221    
1222  =cut  =cut
1223    
1224  sub ParseRecord {  sub UnEscape {
1225        # Get the parameter.
1226        my ($codedString) = @_;
1227        # Initialize the return variable.
1228        my $retVal = "";
1229        # Only proceed if the incoming string is nonempty.
1230        if (defined $codedString) {
1231            # Loop through the parameter string, looking for escape sequences. We can't do
1232            # translating because it causes problems with the escaped slash. ("\\t" becomes
1233            # "\<tab>" no matter what we do.)
1234            while (length $codedString > 0) {
1235                # Look for the first escape sequence.
1236                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
1237                    # Here we found it. The text preceding the sequence is in $1. The sequence
1238                    # itself is in $2. First, move the clear text to the return variable.
1239                    $retVal .= $1;
1240                    $codedString = substr $codedString, (2 + length $1);
1241                    # Get the escape value.
1242                    my $char = $2;
1243                    # If we have a "\r", we are done.
1244                    if ($char ne 'r') {
1245                        # Here it's not an 'r', so we convert it.
1246                        $char =~ tr/\\tn/\\\t\n/;
1247                        $retVal .= $char;
1248                    }
1249                } else {
1250                    # Here there are no more escape sequences. The rest of the string is
1251                    # transferred unmodified.
1252                    $retVal .= $codedString;
1253                    $codedString = "";
1254                }
1255            }
1256        }
1257        # Return the result.
1258        return $retVal;
1259    }
1260    
1261    =head3 ParseRecord
1262    
1263    C<< my @fields = Tracer::ParseRecord($line); >>
1264    
1265    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1266    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1267    These will automatically be converted.
1268    
1269    =over 4
1270    
1271    =item line
1272    
1273    Line of data containing the tab-delimited fields.
1274    
1275    =item RETURN
1276    
1277    Returns a list of the fields found in the data line.
1278    
1279    =back
1280    
1281    =cut
1282    
1283    sub ParseRecord {
1284          # Get the parameter.          # Get the parameter.
1285          my ($line) = @_;          my ($line) = @_;
1286          # Remove the trailing new-line, if any.          # Remove the trailing new-line, if any.
# Line 580  Line 1351 
1351          return @inputList;          return @inputList;
1352  }  }
1353    
1354    =head3 Percent
1355    
1356    C<< my $percent = Tracer::Percent($number, $base); >>
1357    
1358    Returns the percent of the base represented by the given number. If the base
1359    is zero, returns zero.
1360    
1361    =over 4
1362    
1363    =item number
1364    
1365    Percent numerator.
1366    
1367    =item base
1368    
1369    Percent base.
1370    
1371    =item RETURN
1372    
1373    Returns the percentage of the base represented by the numerator.
1374    
1375    =back
1376    
1377    =cut
1378    
1379    sub Percent {
1380        # Get the parameters.
1381        my ($number, $base) = @_;
1382        # Declare the return variable.
1383        my $retVal = 0;
1384        # Compute the percent.
1385        if ($base != 0) {
1386            $retVal = $number * 100 / $base;
1387        }
1388        # Return the result.
1389        return $retVal;
1390    }
1391    
1392  =head3 GetFile  =head3 GetFile
1393    
1394    C<< my @fileContents = Tracer::GetFile($fileName); >>
1395    
1396        or
1397    
1398  C<< my $fileContents = Tracer::GetFile($fileName); >>  C<< my $fileContents = Tracer::GetFile($fileName); >>
1399    
1400  Return the entire contents of a file.  Return the entire contents of a file. In list context, line-ends are removed and
1401    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1402    
1403  =over 4  =over 4
1404    
# Line 594  Line 1408 
1408    
1409  =item RETURN  =item RETURN
1410    
1411  Returns the entire file as a single string. If an error occurs, will return  In a list context, returns the entire file as a list with the line terminators removed.
1412  an empty string.  In a scalar context, returns the entire file as a string. If an error occurs opening
1413    the file, an empty list will be returned.
1414    
1415  =back  =back
1416    
# Line 605  Line 1420 
1420          # Get the parameters.          # Get the parameters.
1421          my ($fileName) = @_;          my ($fileName) = @_;
1422          # Declare the return variable.          # Declare the return variable.
1423          my $retVal = "";      my @retVal = ();
1424          # Open the file for input.          # Open the file for input.
1425          my $ok = open INPUTFILE, "<$fileName";      my $handle = Open(undef, "<$fileName");
1426          if (!$ok) {      # Read the whole file into the return variable, stripping off any terminator
1427                  # If we had an error, trace it. We will automatically return a null string.      # characters.
1428                  Trace(0, "Could not open \"$fileName\" for input.");      my $lineCount = 0;
1429          } else {      while (my $line = <$handle>) {
1430                  # Read the whole file into the return variable.          $lineCount++;
1431                  while (<INPUTFILE>) {          $line = Strip($line);
1432                          $retVal .= $_;          push @retVal, $line;
1433                  }                  }
1434                  # Close it.                  # Close it.
1435                  close INPUTFILE;      close $handle;
1436        my $actualLines = @retVal;
1437        # Return the file's contents in the desired format.
1438        if (wantarray) {
1439            return @retVal;
1440        } else {
1441            return join "\n", @retVal;
1442        }
1443    }
1444    
1445    =head3 PutFile
1446    
1447    C<< Tracer::PutFile($fileName, \@lines); >>
1448    
1449    Write out a file from a list of lines of text.
1450    
1451    =over 4
1452    
1453    =item fileName
1454    
1455    Name of the output file.
1456    
1457    =item lines
1458    
1459    Reference to a list of text lines. The lines will be written to the file in order, with trailing
1460    new-line characters. Alternatively, may be a string, in which case the string will be written without
1461    modification.
1462    
1463    =back
1464    
1465    =cut
1466    
1467    sub PutFile {
1468        # Get the parameters.
1469        my ($fileName, $lines) = @_;
1470        # Open the output file.
1471        my $handle = Open(undef, ">$fileName");
1472        if (ref $lines ne 'ARRAY') {
1473            # Here we have a scalar, so we write it raw.
1474            print $handle $lines;
1475        } else {
1476            # Write the lines one at a time.
1477            for my $line (@{$lines}) {
1478                print $handle "$line\n";
1479          }          }
1480          # Return the file's contents.      }
1481          return $retVal;      # Close the output file.
1482        close $handle;
1483  }  }
1484    
1485  =head3 QTrace  =head3 QTrace
# Line 644  Line 1503 
1503          my ($format) = @_;          my ($format) = @_;
1504          # Create the return variable.          # Create the return variable.
1505          my $retVal = "";          my $retVal = "";
1506        # Only proceed if there is an actual queue.
1507        if (@Queue) {
1508          # Process according to the format.          # Process according to the format.
1509          if ($format =~ m/^HTML$/i) {          if ($format =~ m/^HTML$/i) {
1510                  # Convert the queue into an HTML list.                  # Convert the queue into an HTML list.
# Line 659  Line 1520 
1520          }          }
1521          # Clear the queue.          # Clear the queue.
1522          @Queue = ();          @Queue = ();
1523        }
1524          # Return the formatted list.          # Return the formatted list.
1525          return $retVal;          return $retVal;
1526  }  }
# Line 667  Line 1529 
1529    
1530  C<< Confess($message); >>  C<< Confess($message); >>
1531    
1532  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
1533  trace will only appear if the trace level for this package is 1 or more. When used with  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
1534  the OR operator, this method can function as a debugging assert. So, for example  So, for example
1535    
1536  C<< ($recNum >= 0) || Confess("Invalid record number $recNum."); >>  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
1537    
1538  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Will abort the program with a stack trace if the value of C<$recNum> is negative.
1539    
# Line 689  Line 1551 
1551          # Get the parameters.          # Get the parameters.
1552          my ($message) = @_;          my ($message) = @_;
1553          # Trace the call stack.          # Trace the call stack.
1554          Cluck($message) if T(1);      Cluck($message);
1555          # Abort the program.          # Abort the program.
1556          die $message;      croak(">>> $message");
1557    }
1558    
1559    =head3 Assert
1560    
1561    C<< Assert($condition1, $condition2, ... $conditionN); >>
1562    
1563    Return TRUE if all the conditions are true. This method can be used in conjunction with
1564    the OR operator and the L</Confess> method as a debugging assert.
1565    So, for example
1566    
1567    C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
1568    
1569    Will abort the program with a stack trace if the value of C<$recNum> is negative.
1570    
1571    =cut
1572    sub Assert {
1573        my $retVal = 1;
1574        LOOP: for my $condition (@_) {
1575            if (! $condition) {
1576                $retVal = 0;
1577                last LOOP;
1578            }
1579        }
1580        return $retVal;
1581  }  }
1582    
1583  =head3 Cluck  =head3 Cluck
# Line 718  Line 1604 
1604  sub Cluck {  sub Cluck {
1605          # Get the parameters.          # Get the parameters.
1606          my ($message) = @_;          my ($message) = @_;
1607        # Trace what's happening.
1608        Trace("Stack trace for event: $message");
1609          my $confession = longmess($message);          my $confession = longmess($message);
1610          # Convert the confession to a series of trace messages.      # Convert the confession to a series of trace messages. Note we skip any
1611        # messages relating to calls into Tracer.
1612          for my $line (split /\s*\n/, $confession) {          for my $line (split /\s*\n/, $confession) {
1613                  Trace($line);          Trace($line) if ($line !~ /Tracer\.pm/);
1614        }
1615    }
1616    
1617    =head3 Min
1618    
1619    C<< my $min = Min($value1, $value2, ... $valueN); >>
1620    
1621    Return the minimum argument. The arguments are treated as numbers.
1622    
1623    =over 4
1624    
1625    =item $value1, $value2, ... $valueN
1626    
1627    List of numbers to compare.
1628    
1629    =item RETURN
1630    
1631    Returns the lowest number in the list.
1632    
1633    =back
1634    
1635    =cut
1636    
1637    sub Min {
1638        # Get the parameters. Note that we prime the return value with the first parameter.
1639        my ($retVal, @values) = @_;
1640        # Loop through the remaining parameters, looking for the lowest.
1641        for my $value (@values) {
1642            if ($value < $retVal) {
1643                $retVal = $value;
1644            }
1645        }
1646        # Return the minimum found.
1647        return $retVal;
1648    }
1649    
1650    =head3 Max
1651    
1652    C<< my $max = Max($value1, $value2, ... $valueN); >>
1653    
1654    Return the maximum argument. The arguments are treated as numbers.
1655    
1656    =over 4
1657    
1658    =item $value1, $value2, ... $valueN
1659    
1660    List of numbers to compare.
1661    
1662    =item RETURN
1663    
1664    Returns the highest number in the list.
1665    
1666    =back
1667    
1668    =cut
1669    
1670    sub Max {
1671        # Get the parameters. Note that we prime the return value with the first parameter.
1672        my ($retVal, @values) = @_;
1673        # Loop through the remaining parameters, looking for the highest.
1674        for my $value (@values) {
1675            if ($value > $retVal) {
1676                $retVal = $value;
1677            }
1678        }
1679        # Return the maximum found.
1680        return $retVal;
1681    }
1682    
1683    =head3 AddToListMap
1684    
1685    C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>
1686    
1687    Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list
1688    is created for the key. Otherwise, the new value is pushed onto the list.
1689    
1690    =over 4
1691    
1692    =item hash
1693    
1694    Reference to the target hash.
1695    
1696    =item key
1697    
1698    Key for which the value is to be added.
1699    
1700    =item value1, value2, ... valueN
1701    
1702    List of values to add to the key's value list.
1703    
1704    =back
1705    
1706    =cut
1707    
1708    sub AddToListMap {
1709        # Get the parameters.
1710        my ($hash, $key, @values) = @_;
1711        # Process according to whether or not the key already has a value.
1712        if (! exists $hash->{$key}) {
1713            $hash->{$key} = [@values];
1714        } else {
1715            push @{$hash->{$key}}, @values;
1716        }
1717    }
1718    
1719    =head3 DebugMode
1720    
1721    C<< if (Tracer::DebugMode) { ...code... } >>
1722    
1723    Return TRUE if debug mode has been turned on, else output an error
1724    page and return FALSE.
1725    
1726    Certain CGI scripts are too dangerous to exist in the production
1727    environment. This method provides a simple way to prevent them
1728    from working unless they are explicitly turned on by creating a password
1729    cookie via the B<SetPassword> script.  If debugging mode
1730    is not turned on, an error web page will be output directing the
1731    user to enter in the correct password.
1732    
1733    =cut
1734    
1735    sub DebugMode {
1736        # Declare the return variable.
1737        my $retVal = 0;
1738        # Check the debug configuration.
1739        my $password = CGI::cookie("DebugMode");
1740        my $encrypted = Digest::MD5::md5_hex($password);
1741        if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1742            $retVal = 1;
1743        } else {
1744            # Here debug mode is off, so we generate an error page.
1745            my $pageString = PageBuilder::Build("<<Html/ErrorPage.html", {}, "Html");
1746            print $pageString;
1747        }
1748        # Return the determination indicator.
1749        return $retVal;
1750    }
1751    
1752    =head3 Strip
1753    
1754    C<< my $string = Tracer::Strip($line); >>
1755    
1756    Strip all line terminators off a string. This is necessary when dealing with files
1757    that may have been transferred back and forth several times among different
1758    operating environments.
1759    
1760    =over 4
1761    
1762    =item line
1763    
1764    Line of text to be stripped.
1765    
1766    =item RETURN
1767    
1768    The same line of text with all the line-ending characters chopped from the end.
1769    
1770    =back
1771    
1772    =cut
1773    
1774    sub Strip {
1775        # Get a copy of the parameter string.
1776        my ($string) = @_;
1777        my $retVal = (defined $string ? $string : "");
1778        # Strip the line terminator characters.
1779        $retVal =~ s/(\r|\n)+$//g;
1780        # Return the result.
1781        return $retVal;
1782    }
1783    
1784    =head3 Pad
1785    
1786    C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>
1787    
1788    Pad a string to a specified length. The pad character will be a
1789    space, and the padding will be on the right side unless specified
1790    in the third parameter.
1791    
1792    =over 4
1793    
1794    =item string
1795    
1796    String to be padded.
1797    
1798    =item len
1799    
1800    Desired length of the padded string.
1801    
1802    =item left (optional)
1803    
1804    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
1805    
1806    =item padChar (optional)
1807    
1808    Character to use for padding. The default is a space.
1809    
1810    =item RETURN
1811    
1812    Returns a copy of the original string with the pad character added to the
1813    specified end so that it achieves the desired length.
1814    
1815    =back
1816    
1817    =cut
1818    
1819    sub Pad {
1820        # Get the parameters.
1821        my ($string, $len, $left, $padChar) = @_;
1822        # Compute the padding character.
1823        if (! defined $padChar) {
1824            $padChar = " ";
1825        }
1826        # Compute the number of spaces needed.
1827        my $needed = $len - length $string;
1828        # Copy the string into the return variable.
1829        my $retVal = $string;
1830        # Only proceed if padding is needed.
1831        if ($needed > 0) {
1832            # Create the pad string.
1833            my $pad = $padChar x $needed;
1834            # Affix it to the return value.
1835            if ($left) {
1836                $retVal = $pad . $retVal;
1837            } else {
1838                $retVal .= $pad;
1839            }
1840        }
1841        # Return the result.
1842        return $retVal;
1843    }
1844    
1845    =head3 EOF
1846    
1847    This is a constant that is lexically greater than any useful string.
1848    
1849    =cut
1850    
1851    sub EOF {
1852        return "\xFF\xFF\xFF\xFF\xFF";
1853    }
1854    
1855    =head3 TICK
1856    
1857    C<< my @results = TICK($commandString); >>
1858    
1859    Perform a back-tick operation on a command. If this is a Windows environment, any leading
1860    dot-slash (C<./> will be removed. So, for example, if you were doing
1861    
1862        `./protein.cgi`
1863    
1864    from inside a CGI script, it would work fine in Unix, but would issue an error message
1865    in Windows complaining that C<'.'> is not a valid command. If instead you code
1866    
1867        TICK("./protein.cgi")
1868    
1869    it will work correctly in both environments.
1870    
1871    =over 4
1872    
1873    =item commandString
1874    
1875    The command string to pass to the system.
1876    
1877    =item RETURN
1878    
1879    Returns the standard output from the specified command, as a list.
1880    
1881    =back
1882    
1883    =cut
1884    #: Return Type @;
1885    sub TICK {
1886        # Get the parameters.
1887        my ($commandString) = @_;
1888        # Chop off the dot-slash if this is Windows.
1889        if ($FIG_Config::win_mode) {
1890            $commandString =~ s!^\./!!;
1891        }
1892        # Activate the command and return the result.
1893        return `$commandString`;
1894    }
1895    
1896    =head3 ScriptSetup
1897    
1898    C<< my ($query, $varHash) = ScriptSetup(); >>
1899    
1900    Perform standard tracing and debugging setup for scripts. The value returned is
1901    the CGI object followed by a pre-built variable hash.
1902    
1903    The C<Trace> query parameter is used to determine whether or not tracing is active and
1904    which trace modules (other than C<Tracer> and C<FIG>) should be turned on. Specifying
1905    the C<CGI> trace module will trace parameter and environment information. Parameters are
1906    traced at level 3 and environment variables at level 4. At the end of the script, the
1907    client should call L</ScriptFinish> to output the web page.
1908    
1909    =cut
1910    
1911    sub ScriptSetup {
1912        # Get the CGI query object.
1913        my $query = CGI->new();
1914        # Check for tracing. Set it up if the user asked for it.
1915        if ($query->param('Trace')) {
1916            # Set up tracing.
1917            my $ttype = ($query->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1918            TSetup($query->param('Trace') . " FIG Tracer", $ttype);
1919            # Trace the parameter and environment data.
1920            TraceParms($query);
1921        } else {
1922            # Here tracing is to be turned off. All we allow is errors traced into the
1923            # error log.
1924            TSetup("0", "WARN");
1925        }
1926        # Create the variable hash.
1927        my $varHash = { DebugData => '' };
1928        # Return the query object and variable hash.
1929        return ($query, $varHash);
1930    }
1931    
1932    =head3 TraceParms
1933    
1934    C<< Tracer::TraceParms($query); >>
1935    
1936    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1937    at level CGI => 4.
1938    
1939    =over 4
1940    
1941    =item query
1942    
1943    CGI query object containing the parameters to trace.
1944    
1945    =back
1946    
1947    =cut
1948    
1949    sub TraceParms {
1950        # Get the parameters.
1951        my ($query) = @_;
1952        if (T(CGI => 3)) {
1953            # Here we want to trace the parameter data.
1954            my @names = $query->param;
1955            for my $parmName (sort @names) {
1956                # Note we skip "Trace", which is for our use only.
1957                if ($parmName ne 'Trace') {
1958                    my @values = $query->param($parmName);
1959                    Trace("CGI: $parmName = " . join(", ", @values));
1960                }
1961            }
1962            # Now output a GET-style URL for this query.
1963            my $getURL = $query->url(-relative => 1, -query => 1);
1964            # Strip out the Trace parameters.
1965            $getURL =~ s/Trace=\d[^;&]+[;&]//;
1966            $getURL =~ s/TF=\d[;&]//;
1967            # Output the URL.
1968            Trace("URL: ../FIG/$getURL");
1969            # Display the request method.
1970            my $method = $query->request_method();
1971            Trace("Method: $method");
1972        }
1973        if (T(CGI => 4)) {
1974            # Here we want the environment data too.
1975            for my $envName (sort keys %ENV) {
1976                Trace("ENV: $envName = $ENV{$envName}");
1977            }
1978        }
1979    }
1980    
1981    =head3 ScriptFinish
1982    
1983    C<< ScriptFinish($webData, $varHash); >>
1984    
1985    Output a web page at the end of a script. Either the string to be output or the
1986    name of a template file can be specified. If the second parameter is omitted,
1987    it is assumed we have a string to be output; otherwise, it is assumed we have the
1988    name of a template file. The template should have the variable C<DebugData>
1989    specified in any form that invokes a standard script. If debugging mode is turned
1990    on, a form field will be put in that allows the user to enter tracing data.
1991    Trace messages will be placed immediately before the terminal C<BODY> tag in
1992    the output, formatted as a list.
1993    
1994    A typical standard script would loook like the following.
1995    
1996        BEGIN {
1997            # Print the HTML header.
1998            print "CONTENT-TYPE: text/html\n\n";
1999        }
2000        use Tracer;
2001        use CGI;
2002        use FIG;
2003        # ... more uses ...
2004    
2005        my ($query, $varHash) = ScriptSetup();
2006        eval {
2007            # ... get data from $query, put it in $varHash ...
2008        };
2009        if ($@) {
2010            Trace("Script Error: $@") if T(0);
2011        }
2012        ScriptFinish("Html/MyTemplate.html", $varHash);
2013    
2014    The idea here is that even if the script fails, you'll see trace messages and
2015    useful output.
2016    
2017    =over 4
2018    
2019    =item webData
2020    
2021    A string containing either the full web page to be written to the output or the
2022    name of a template file from which the page is to be constructed. If the name
2023    of a template file is specified, then the second parameter must be present;
2024    otherwise, it must be absent.
2025    
2026    =item varHash (optional)
2027    
2028    If specified, then a reference to a hash mapping variable names for a template
2029    to their values. The template file will be read into memory, and variable markers
2030    will be replaced by data in this hash reference.
2031    
2032    =back
2033    
2034    =cut
2035    
2036    sub ScriptFinish {
2037        # Get the parameters.
2038        my ($webData, $varHash) = @_;
2039        # Check for a template file situation.
2040        my $outputString;
2041        if (defined $varHash) {
2042            # Here we have a template file. We need to determine the template type.
2043            my $template;
2044            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
2045                $template = "$FIG_Config::template_url/$webData";
2046            } else {
2047                $template = "<<$webData";
2048            }
2049            $outputString = PageBuilder::Build($template, $varHash, "Html");
2050        } else {
2051            # Here the user gave us a raw string.
2052            $outputString = $webData;
2053        }
2054        # Check for trace messages.
2055        if ($Destination eq "QUEUE") {
2056            # We have trace messages, so we want to put them at the end of the body. This
2057            # is either at the end of the whole string or at the beginning of the BODY
2058            # end-tag.
2059            my $pos = length $outputString;
2060            if ($outputString =~ m#</body>#gi) {
2061                $pos = (pos $outputString) - 7;
2062            }
2063            substr $outputString, $pos, 0, QTrace('Html');
2064        }
2065        # Write the output string.
2066        print $outputString;
2067    }
2068    
2069    =head3 Insure
2070    
2071    C<< Insure($dirName); >>
2072    
2073    Insure a directory is present.
2074    
2075    =over 4
2076    
2077    =item dirName
2078    
2079    Name of the directory to check. If it does not exist, it will be created.
2080    
2081    =back
2082    
2083    =cut
2084    
2085    sub Insure {
2086        my ($dirName) = @_;
2087        if (! -d $dirName) {
2088            Trace("Creating $dirName directory.") if T(2);
2089            eval { mkpath $dirName; };
2090            if ($@) {
2091                Confess("Error creating $dirName: $@");
2092            }
2093        }
2094    }
2095    
2096    =head3 ChDir
2097    
2098    C<< ChDir($dirName); >>
2099    
2100    Change to the specified directory.
2101    
2102    =over 4
2103    
2104    =item dirName
2105    
2106    Name of the directory to which we want to change.
2107    
2108    =back
2109    
2110    =cut
2111    
2112    sub ChDir {
2113        my ($dirName) = @_;
2114        if (! -d $dirName) {
2115            Confess("Cannot change to directory $dirName: no such directory.");
2116        } else {
2117            Trace("Changing to directory $dirName.") if T(4);
2118            my $okFlag = chdir $dirName;
2119            if (! $okFlag) {
2120                Confess("Error switching to directory $dirName.");
2121            }
2122        }
2123    }
2124    
2125    =head3 SendSMS
2126    
2127    C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>
2128    
2129    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
2130    user name, password, and API ID for the relevant account in the hash reference variable
2131    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
2132    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
2133    is C<2561022>, then the FIG_Config file must contain
2134    
2135        $phone =  { user => 'BruceTheHumanPet',
2136                    password => 'silly',
2137                    api_id => '2561022' };
2138    
2139    The original purpose of this method was to insure Bruce would be notified immediately when the
2140    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
2141    when you call this method.
2142    
2143    The message ID will be returned if successful, and C<undef> if an error occurs.
2144    
2145    =over 4
2146    
2147    =item phoneNumber
2148    
2149    Phone number to receive the message, in international format. A United States phone number
2150    would be prefixed by "1". A British phone number would be prefixed by "44".
2151    
2152    =item msg
2153    
2154    Message to send to the specified phone.
2155    
2156    =item RETURN
2157    
2158    Returns the message ID if successful, and C<undef> if the message could not be sent.
2159    
2160    =back
2161    
2162    =cut
2163    
2164    sub SendSMS {
2165        # Get the parameters.
2166        my ($phoneNumber, $msg) = @_;
2167        # Declare the return variable. If we do not change it, C<undef> will be returned.
2168        my $retVal;
2169        # Only proceed if we have phone support.
2170        if (! defined $FIG_Config::phone) {
2171            Trace("Phone support not present in FIG_Config.") if T(1);
2172        } else {
2173            # Get the phone data.
2174            my $parms = $FIG_Config::phone;
2175            # Get the Clickatell URL.
2176            my $url = "http://api.clickatell.com/http/";
2177            # Create the user agent.
2178            my $ua = LWP::UserAgent->new;
2179            # Request a Clickatell session.
2180            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
2181                                         password => $parms->{password},
2182                                         api_id => $parms->{api_id},
2183                                         to => $phoneNumber,
2184                                         text => $msg});
2185            # Check for an error.
2186            if (! $resp->is_success) {
2187                Trace("Alert failed.") if T(1);
2188            } else {
2189                # Get the message ID.
2190                my $rstring = $resp->content;
2191                if ($rstring =~ /^ID:\s+(.*)$/) {
2192                    $retVal = $1;
2193                } else {
2194                    Trace("Phone attempt failed with $rstring") if T(1);
2195                }
2196            }
2197        }
2198        # Return the result.
2199        return $retVal;
2200    }
2201    
2202    =head3 CommaFormat
2203    
2204    C<< my $formatted = Tracer::CommaFormat($number); >>
2205    
2206    Insert commas into a number.
2207    
2208    =over 4
2209    
2210    =item number
2211    
2212    A sequence of digits.
2213    
2214    =item RETURN
2215    
2216    Returns the same digits with commas strategically inserted.
2217    
2218    =back
2219    
2220    =cut
2221    
2222    sub CommaFormat {
2223        # Get the parameters.
2224        my ($number) = @_;
2225        # Pad the length up to a multiple of three.
2226        my $padded = "$number";
2227        $padded = " " . $padded while length($padded) % 3 != 0;
2228        # This is a fancy PERL trick. The parentheses in the SPLIT pattern
2229        # cause the delimiters to be included in the output stream. The
2230        # GREP removes the empty strings in between the delimiters.
2231        my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
2232        # Clean out the spaces.
2233        $retVal =~ s/ //g;
2234        # Return the result.
2235        return $retVal;
2236    }
2237    =head3 SetPermissions
2238    
2239    C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>
2240    
2241    Set the permissions for a directory and all the files and folders inside it.
2242    In addition, the group ownership will be changed to the specified value.
2243    
2244    This method is more vulnerable than most to permission and compatability
2245    problems, so it does internal error recovery.
2246    
2247    =over 4
2248    
2249    =item dirName
2250    
2251    Name of the directory to process.
2252    
2253    =item group
2254    
2255    Name of the group to be assigned.
2256    
2257    =item mask
2258    
2259    Permission mask. Bits that are C<1> in this mask will be ORed into the
2260    permission bits of any file or directory that does not already have them
2261    set to 1.
2262    
2263    =item otherMasks
2264    
2265    Map of search patterns to permission masks. If a directory name matches
2266    one of the patterns, that directory and all its members and subdirectories
2267    will be assigned the new pattern. For example, the following would
2268    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2269    
2270        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2271    
2272    The list is ordered, so the following would use 0777 for C<tmp1> and
2273    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2274    
2275        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2276                                                       '^tmp' => 0666);
2277    
2278    Note that the pattern matches are all case-insensitive, and only directory
2279    names are matched, not file names.
2280    
2281    =back
2282    
2283    =cut
2284    
2285    sub SetPermissions {
2286        # Get the parameters.
2287        my ($dirName, $group, $mask, @otherMasks) = @_;
2288        # Set up for error recovery.
2289        eval {
2290            # Switch to the specified directory.
2291            ChDir($dirName);
2292            # Get the group ID.
2293            my $gid = getgrnam($group);
2294            # Get the mask for tracing.
2295            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2296            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(2);
2297            my $fixCount = 0;
2298            my $lookCount = 0;
2299            # @dirs will be a stack of directories to be processed.
2300            my @dirs = (getcwd());
2301            while (scalar(@dirs) > 0) {
2302                # Get the current directory.
2303                my $dir = pop @dirs;
2304                # Check for a match to one of the specified directory names. To do
2305                # that, we need to pull the individual part of the name off of the
2306                # whole path.
2307                my $simpleName = $dir;
2308                if ($dir =~ m!/([^/]+)$!) {
2309                    $simpleName = $1;
2310                }
2311                Trace("Simple directory name for $dir is $simpleName.") if T(4);
2312                # Search for a match.
2313                my $match = 0;
2314                my $i;
2315                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2316                    my $pattern = $otherMasks[$i];
2317                    if ($simpleName =~ /$pattern/i) {
2318                        $match = 1;
2319                    }
2320                }
2321                # Check for a match. Note we use $i-1 because the loop added 2
2322                # before terminating due to the match.
2323                if ($match && $otherMasks[$i-1] != $mask) {
2324                    # This directory matches one of the incoming patterns, and it's
2325                    # a different mask, so we process it recursively with that mask.
2326                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2327                } else {
2328                    # Here we can process normally. Get all of the non-hidden members.
2329                    my @submems = OpenDir($dir, 1);
2330                    for my $submem (@submems) {
2331                        # Get the full name.
2332                        my $thisMem = "$dir/$submem";
2333                        Trace("Checking member $thisMem.") if T(4);
2334                        $lookCount++;
2335                        if ($lookCount % 1000 == 0) {
2336                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(3);
2337                        }
2338                        # Fix the group.
2339                        chown -1, $gid, $thisMem;
2340                        # Insure this member is not a symlink.
2341                        if (! -l $thisMem) {
2342                            # Get its info.
2343                            my $fileInfo = stat $thisMem;
2344                            # Only proceed if we got the info. Otherwise, it's a hard link
2345                            # and we want to skip it anyway.
2346                            if ($fileInfo) {
2347                                my $fileMode = $fileInfo->mode;
2348                                if (($fileMode & $mask) != $mask) {
2349                                    # Fix this member.
2350                                    $fileMode |= $mask;
2351                                    chmod $fileMode, $thisMem;
2352                                    $fixCount++;
2353                                }
2354                                # If it's a subdirectory, stack it.
2355                                if (-d $thisMem) {
2356                                    push @dirs, $thisMem;
2357                                }
2358                            }
2359                        }
2360                    }
2361                }
2362            }
2363            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(2);
2364        };
2365        # Check for an error.
2366        if ($@) {
2367            Confess("SetPermissions error: $@");
2368        }
2369    }
2370    
2371    =head3 CompareLists
2372    
2373    C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>
2374    
2375    Compare two lists of tuples, and return a hash analyzing the differences. The lists
2376    are presumed to be sorted alphabetically by the value in the $keyIndex column.
2377    The return value contains a list of items that are only in the new list
2378    (inserted) and only in the old list (deleted).
2379    
2380    =over 4
2381    
2382    =item newList
2383    
2384    Reference to a list of new tuples.
2385    
2386    =item oldList
2387    
2388    Reference to a list of old tuples.
2389    
2390    =item keyIndex (optional)
2391    
2392    Index into each tuple of its key field. The default is 0.
2393    
2394    =item RETURN
2395    
2396    Returns a 2-tuple consisting of a reference to the list of items that are only in the new
2397    list (inserted) followed by a reference to the list of items that are only in the old
2398    list (deleted).
2399    
2400    =back
2401    
2402    =cut
2403    
2404    sub CompareLists {
2405        # Get the parameters.
2406        my ($newList, $oldList, $keyIndex) = @_;
2407        if (! defined $keyIndex) {
2408            $keyIndex = 0;
2409        }
2410        # Declare the return variables.
2411        my ($inserted, $deleted) = ([], []);
2412        # Loop through the two lists simultaneously.
2413        my ($newI, $oldI) = (0, 0);
2414        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
2415        while ($newI < $newN || $oldI < $oldN) {
2416            # Get the current object in each list. Note that if one
2417            # of the lists is past the end, we'll get undef.
2418            my $newItem = $newList->[$newI];
2419            my $oldItem = $oldList->[$oldI];
2420            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
2421                # The old item is not in the new list, so mark it deleted.
2422                push @{$deleted}, $oldItem;
2423                $oldI++;
2424            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
2425                # The new item is not in the old list, so mark it inserted.
2426                push @{$inserted}, $newItem;
2427                $newI++;
2428            } else {
2429                # The item is in both lists, so push forward.
2430                $oldI++;
2431                $newI++;
2432            }
2433        }
2434        # Return the result.
2435        return ($inserted, $deleted);
2436          }          }
2437    
2438    =head3 GetLine
2439    
2440    C<< my @data = Tracer::GetLine($handle); >>
2441    
2442    Read a line of data from a tab-delimited file.
2443    
2444    =over 4
2445    
2446    =item handle
2447    
2448    Open file handle from which to read.
2449    
2450    =item RETURN
2451    
2452    Returns a list of the fields in the record read. The fields are presumed to be
2453    tab-delimited. If we are at the end of the file, then an empty list will be
2454    returned. If an empty line is read, a single list item consisting of a null
2455    string will be returned.
2456    
2457    =back
2458    
2459    =cut
2460    
2461    sub GetLine {
2462        # Get the parameters.
2463        my ($handle) = @_;
2464        # Declare the return variable.
2465        my @retVal = ();
2466        # Read from the file.
2467        my $line = <$handle>;
2468        # Only proceed if we found something.
2469        if (defined $line) {
2470            # Remove the new-line.
2471            chomp $line;
2472            # If the line is empty, return a single empty string; otherwise, parse
2473            # it into fields.
2474            if ($line eq "") {
2475                push @retVal, "";
2476            } else {
2477                push @retVal, split /\t/,$line;
2478            }
2479        }
2480        # Return the result.
2481        return @retVal;
2482    }
2483    
2484    =head3 PutLine
2485    
2486    C<< Tracer::PutLine($handle, \@fields); >>
2487    
2488    Write a line of data to a tab-delimited file. The specified field values will be
2489    output in tab-separated form, with a trailing new-line.
2490    
2491    =over 4
2492    
2493    =item handle
2494    
2495    Output file handle.
2496    
2497    =item fields
2498    
2499    List of field values.
2500    
2501    =back
2502    
2503    =cut
2504    
2505    sub PutLine {
2506        # Get the parameters.
2507        my ($handle, $fields) = @_;
2508        # Write the data.
2509        print $handle join("\t", @{$fields}) . "\n";
2510  }  }
2511    
2512    =head3 GenerateURL
2513    
2514    C<< my $queryUrl = Tracer::GenerateURL($page, %parameters); >>
2515    
2516    Generate a GET-style URL for the specified page with the specified parameter
2517    names and values. The values will be URL-escaped automatically. So, for
2518    example
2519    
2520        Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
2521    
2522    would return
2523    
2524        form.cgi?type=1&string=%22high%20pass%22%20or%20highway
2525    
2526    =over 4
2527    
2528    =item page
2529    
2530    Page URL.
2531    
2532    =item parameters
2533    
2534    Hash mapping parameter names to parameter values.
2535    
2536    =item RETURN
2537    
2538    Returns a GET-style URL that goes to the specified page and passes in the
2539    specified parameters and values.
2540    
2541    =back
2542    
2543    =cut
2544    
2545    sub GenerateURL {
2546        # Get the parameters.
2547        my ($page, %parameters) = @_;
2548        # Prime the return variable with the page URL.
2549        my $retVal = $page;
2550        # Loop through the parameters, creating parameter elements in a list.
2551        my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
2552        # If the list is nonempty, tack it on.
2553        if (@parmList) {
2554            $retVal .= "?" . join("&", @parmList);
2555        }
2556        # Return the result.
2557        return $retVal;
2558    }
2559    
2560  1;  1;

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