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revision 1.52, Wed Jun 14 01:12:42 2006 UTC revision 1.93, Tue Feb 5 02:17:29 2008 UTC
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19    
20      require Exporter;      require Exporter;
21      @ISA = ('Exporter');      @ISA = ('Exporter');
22      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup ScriptSetup ScriptFinish Insure ChDir);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);
23      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);
24      use strict;      use strict;
25      use Carp qw(longmess croak);      use Carp qw(longmess croak);
# Line 31  Line 31 
31      use File::Basename;      use File::Basename;
32      use File::Path;      use File::Path;
33      use File::stat;      use File::stat;
34        use LWP::UserAgent;
35        use Time::HiRes 'gettimeofday';
36        use URI::Escape;
37        use Time::Local;
38    
39  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
40    
41  =head2 Introduction  =head2 Tracing
42    
43  This package provides simple tracing for debugging and reporting purposes. To use it simply call the  This package provides simple tracing for debugging and reporting purposes. To use it simply call the
44  L</TSetup> method to set the options and call L</Trace> to write out trace messages. Each trace  L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
45  message has a I<trace level> and I<category> associated with it. In addition, the tracing package itself  L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
46  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace  each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
47  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 the setup trace level and whose category is activated will
48  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
49  is less likely to be seen. A higher trace level passed to B<TSetup> means more trace messages will  is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
50  appear. To generate a trace message, use the following syntax.  appear.
51    
52  C<< Trace($message) if T(errors => 4); >>  =head3 Putting Trace Messages in Your Code
53    
54    To generate a trace message, use the following syntax.
55    
56        Trace($message) if T(errors => 4);
57    
58  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>
59  category is active. Note that the special category C<main> is always active, so  category is active. There is a special category C<main> that is always active, so
60    
61  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
62    
63  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
64    
# Line 58  Line 66 
66  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
67  active and the trace level is 2 or more.  active and the trace level is 2 or more.
68    
69  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
70    
71    In scripts, where no package name is available, the category defaults to C<main>.
72    
73    =head3 Custom Tracing
74    
75  To set up tracing, you call the L</TSetup> method. The method takes as input a trace level, a list  Many programs have customized tracing configured using the L</TSetup> method. This is no longer
76  of category names, and a set of options. The trace level and list of category names are  the preferred method, but a knowledge of how custom tracing works can make the more modern
77    L</Emergency Tracing> easier to understand.
78    
79    To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
80    a list of category names, and a destination. The trace level and list of category names are
81  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
82    
83  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
84    
85  sets the trace level to 3, activates 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
86  specifies that messages should be output as HTML paragraphs.  specifies that messages should be sent to the standard output.
87    
88  To turn on tracing for ALL categories, use an asterisk. The call below sets every category to  To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
89  level 3 and writes the output to the standard error output. This sort of thing might be  level 3 and writes the output to the standard error output. This sort of thing might be
90  useful in a CGI environment.  useful in a CGI environment.
91    
92  C<< TSetup('3 *', 'WARN'); >>      TSetup('3 *', 'WARN');
93    
94  In addition to HTML and file output for trace messages, you can specify that the trace messages  In addition standard error and file output for trace messages, you can specify that the trace messages
95  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
96  is useful if you are building a web page. Instead of having the trace messages interspersed with  is useful if you are building a web page. Instead of having the trace messages interspersed with
97  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
98  it easier to debug page formatting problems.  it easier to debug page formatting problems.
99    
100  Finally, you can specify that all trace messages be emitted as warnings.  Finally, you can specify that all trace messages be emitted to a file, or the standard output and
101    a file at the same time. To trace to a file, specify the filename with an output character in front
102    of it.
103    
104        TSetup('4 SQL', ">$fileName");
105    
106    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
107    bracket.
108    
109        TSetup('3 *', "+>$fileName");
110    
111  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>.
112  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.
113  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
114  being used out in the field.  being used out in the field.
115    
116    =head3 Trace Levels
117    
118  There is no hard and fast rule on how to use trace levels. The following is therefore only  There is no hard and fast rule on how to use trace levels. The following is therefore only
119  a suggestion.  a suggestion.
120    
# Line 118  Line 145 
145    
146  =back  =back
147    
148    The format of trace messages is important because some utilities analyze trace files.
149    There are three fields-- the time stamp, the category name, and the text.
150    The time stamp is between square brackets and the category name between angle brackets.
151    After the category name there is a colon (C<:>) followed by the message text.
152    If the square brackets or angle brackets are missing, then the trace management
153    utilities assume that they are encountering a set of pre-formatted lines.
154    
155    Note, however, that this formatting is done automatically by the tracing functions. You
156    only need to know about it if you want to parse a trace file.
157    
158    =head3 Emergency Tracing
159    
160    Sometimes, you need a way for tracing to happen automatically without putting parameters
161    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
162    from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.
163    Emergency tracing requires you specify a tracing key. For command-line tools, the key is
164    taken from the C<TRACING> environment variable. For web services, the key is taken from
165    a cookie. Either way, the key tells the tracing facility who you are, so that you control
166    the tracing in your environment without stepping on other users.
167    
168    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
169    generate one for you.
170    
171    You can activate and de-activate emergency tracing from the debugging control panel, as
172    well as display the trace file itself.
173    
174    To enable emergency tracing in your code, call
175    
176        ETracing($cgi)
177    
178    from a web script and
179    
180        ETracing()
181    
182    from a command-line script.
183    
184    The web script will look for the tracing key in the cookies, and the command-line
185    script will look for it in the C<TRACING> environment variable. If you are
186    using the L</StandardScript> or L</StandardSetup> methods, emergency tracing
187    will be configured automatically.
188    
189    NOTE: to configure emergency tracing from the command line instead of the Debugging
190    Control Panel (see below), use the C<trace.pl> script.
191    
192    =head3 Debugging Control Panel
193    
194    The debugging control panel provides several tools to assist in development of
195    SEED and Sprout software. You access the debugging control panel from the URL
196    C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,
197    for example, the panel access point for the development NMPDR system is
198    C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to
199    find out what the password is. From this page, you can also specify a tracing
200    key. If you don't specify a key, one will be generated for you.
201    
202    =head4 Emergency Tracing Form
203    
204    At the bottom of the debugging control panel is a form that allows you to
205    specify a trace level and tracing categories. Special and common categories
206    are listed with check boxes. You can hold your mouse over a check box to see
207    what its category does. In general, however, a category name is the same as
208    the name of the package in which the trace message occurs.
209    
210    Additional categories can be entered in an input box, delimited by spaces or commas.
211    
212    The B<Activate> button turns on Emergency tracing at the level you specify with the
213    specified categories active. The B<Terminate> button turns tracing off. The
214    B<Show File> button displays the current contents of the trace file. The tracing
215    form at the bottom of the control panel is designed for emergency tracing, so it
216    will only affect programs that call L</ETracing>, L</StandardScript>,
217    or L</StandardSetup>.
218    
219    =head4 Script Form
220    
221    The top form of the debugging control panel allows you to enter a tiny script and
222    have the output generated in a formatted table. Certain object variables are
223    predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),
224    and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.
225    
226    The last line of the script must be a scalar, but it can be a reference to a hash,
227    a list, a list of lists, and various other combinations. If you select the appropriate
228    data type in the dropdown box, the output will be formatted accordingly. The form
229    also has controls for specifying tracing. These controls override any emergency
230    tracing in effect.
231    
232    =head4 Database Query Forms
233    
234    The forms between the script form and the emergency tracing form allow you to
235    make queries against the database. The FIG query form allows simple queries against
236    a single FIG table. The Sprout query form uses the B<GetAll> method to do a
237    multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>
238    package, and it takes five parameters.
239    
240        GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
241    
242    Each of the five parameters corresponds to a text box on the query form:
243    
244    =over 4
245    
246    =item Objects
247    
248    Comma-separated list containing the names of the entity and relationship objects to be retrieved.
249    
250    =item Filter
251    
252    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
253    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
254    B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a
255    field, I<objectName> is the name of the entity or relationship object containing the field, and
256    I<number> is the 1-based position of the object in the object list. Any parameters
257    specified in the filter clause should be specified in the B<Params> field.
258    The fields in a filter clause can come from primary entity relations,
259    relationship relations, or secondary entity relations; however, all of the
260    entities and relationships involved must be included in the list of object names.
261    
262    =item Params
263    
264    List of the parameters to be substituted in for the parameters marks in the filter clause. This
265    is a comma-separated list without any quoting or escaping.
266    
267    =item fields
268    
269    Comma-separated list of the fields to be returned in each element of the list returned. Fields
270    are specified in the same manner as in the filter clause.
271    
272    =item count
273    
274    Maximum number of records to return. If omitted or 0, all available records will be returned.
275    
276    =back
277    
278    B<GetAll> automatically joins together the entities and relationships listed in the object
279    names. This simplifies the coding of the filter clause, but it means that some queries are
280    not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation
281    that has yet to be addressed.
282    
283  =cut  =cut
284    
285  # Declare the configuration variables.  # Declare the configuration variables.
# Line 134  Line 296 
296  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
297  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
298    
299  =head2 Public Methods  =head2 Tracing Methods
300    
301    =head3 Setups
302    
303        my $count = Tracer::Setups();
304    
305    Return the number of times L</TSetup> has been called.
306    
307    This method allows for the creation of conditional tracing setups where, for example, we
308    may want to set up tracing if nobody else has done it before us.
309    
310    =cut
311    
312    sub Setups {
313        return $SetupCount;
314    }
315    
316  =head3 TSetup  =head3 TSetup
317    
318  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
319    
320  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
321  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 197  Line 374 
374          }          }
375          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
376              open TRACEFILE, $target;              open TRACEFILE, $target;
377              print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";
378              close TRACEFILE;              close TRACEFILE;
379              $Destination = ">$target";              $Destination = ">$target";
380          } else {          } else {
# Line 210  Line 387 
387      $SetupCount++;      $SetupCount++;
388  }  }
389    
390  =head3 StandardSetup  =head3 SetLevel
391    
392  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
393    
394  This method performs standard command-line parsing and tracing setup. The return  Modify the trace level. A higher trace level will cause more messages to appear.
 values are a hash of the command-line options and a list of the positional  
 parameters. Tracing is automatically set up and the command-line options are  
 validated.  
395    
396  This is a complex method that does a lot of grunt work. The parameters can  =over 4
 be more easily understood, however, once they are examined individually.  
397    
398  The I<categories> parameter is the most obtuse. It is a reference to a list of  =item newLevel
 special-purpose tracing categories. Most tracing categories are PERL package  
 names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,  
 B<ERDB>, and B<SproutLoad> packages, you would specify the categories  
399    
400      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
401    
402  This would cause trace messages in the specified three packages to appear in  =back
 the output. There are threer special tracing categories that are automatically  
 handled by this method. In other words, if you used L</TSetup> you would need  
 to include these categories manually, but if you use this method they are turned  
 on automatically.  
403    
404  =over 4  =cut
405    
406  =item FIG  sub SetLevel {
407        $TraceLevel = $_[0];
408    }
409    
410  Turns on trace messages inside the B<FIG> package.  =head3 ParseTraceDate
411    
412  =item SQL      my $time = Tracer::ParseTraceDate($dateString);
413    
414  Traces SQL commands and activity.  Convert a date from the trace file into a PERL timestamp.
415    
416  =item Tracer  =over 4
417    
418  Traces error messages and call stacks.  =item dateString
419    
420    The date string from the trace file. The format of the string is determined by the
421    L</Now> method.
422    
423    =item RETURN
424    
425    Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
426    the time string is invalid.
427    
428  =back  =back
429    
430  C<SQL> is only turned on if the C<-sql> option is specified in the command line.  =cut
 The trace level is specified using the C<-trace> command-line option. For example,  
 the following command line for C<TransactFeatures> turns on SQL tracing and runs  
 all tracing at level 3.  
431    
432      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  sub ParseTraceDate {
433        # Get the parameters.
434        my ($dateString) = @_;
435        # Declare the return variable.
436        my $retVal;
437        # Parse the date.
438        if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {
439            # Create a time object. Note we need to convert the day, month,
440            # and year to a different base. Years count from 1900, and
441            # the internal month value is relocated to January = 0.
442            $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);
443        }
444        # Return the result.
445        return $retVal;
446    }
447    
448  Standard tracing is output to the standard output and echoed to the file  =head3 LogErrors
 C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the  
 process ID. You can also specify the C<user> parameter to put a user ID  
 instead of a process ID in the trace file name. So, for example  
449    
450  The default trace level is 2. To get all messages, specify a trace level of 4.      Tracer::LogErrors($fileName);
 For a genome-by-genome update, use 3.  
451    
452      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  Route the standard error output to a log file.
453    
454  would send the trace output to C<traceBruce.log> in the temporary directory.  =over 4
455    
456  The I<options> parameter is a reference to a hash containing the command-line  =item fileName
 options, their default values, and an explanation of what they mean. Command-line  
 options may be in the form of switches or keywords. In the case of a switch, the  
 option value is 1 if it is specified and 0 if it is not specified. In the case  
 of a keyword, the value is separated from the option name by an equal sign. You  
 can see this last in the command-line example above.  
457    
458  You can specify a different default trace level by setting C<$options->{trace}>  Name of the file to receive the error output.
 prior to calling this method.  
459    
460  An example at this point would help. Consider, for example, the command-line utility  =back
 C<TransactFeatures>. It accepts a list of positional parameters plus the options  
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
461    
462      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  =cut
                         { safe => [0, "use database transactions"],  
                           noAlias => [0, "do not expect aliases in CHANGE transactions"],  
                           start => [' ', "start with this genome"],  
                           tblFiles => [0, "output TBL files containing the corrected IDs"] },  
                         "command transactionDirectory IDfile",  
                       @ARGV);  
463    
464    sub LogErrors {
465        # Get the file name.
466        my ($fileName) = @_;
467        # Open the file as the standard error output.
468        open STDERR, '>', $fileName;
469    }
470    
471  The call to C<ParseCommand> specifies the default values for the options and  =head3 Trace
 stores the actual options in a hash that is returned as C<$options>. The  
 positional parameters are returned in C<@parameters>.  
472    
473  The following is a sample command line for C<TransactFeatures>.      Trace($message);
474    
475      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  Write a trace message to the target location specified in L</TSetup>. If there has not been
476    any prior call to B<TSetup>.
477    
478  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  =over 4
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<FIG>, C<Tracer>, and <DocUtils>. C<FIG> and C<Tracer> are standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
479    
480      { trace => 2, sql => 0, safe => 0,  =item message
       noAlias => 1, start => ' ', tblFiles => 0 }  
481    
482  Use of C<StandardSetup> in this way provides a simple way of performing  Message to write.
 standard tracing setup and command-line parsing. Note that the caller is  
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
483    
484  If the C<background> option is specified on the command line, then the  =back
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
485    
486      -user=Bruce -background  =cut
487    
488  then the trace output would go to C<traceBruce.log>, the standard output to  sub Trace {
489  C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to      # Get the parameters.
490  simplify starting a command in the background.      my ($message) = @_;
491        # Get the timestamp.
492        my $timeStamp = Now();
493        # Format the message. Note we strip off any line terminators at the end.
494        my $prefix = "[$timeStamp] <$LastCategory>: ";
495        my $formatted = $prefix . Strip($message);
496        # Process according to the destination.
497        if ($Destination eq "TEXT") {
498            # Write the message to the standard output.
499            print "$formatted\n";
500        } elsif ($Destination eq "ERROR") {
501            # Write the message to the error output.
502            print STDERR "$formatted\n";
503        } elsif ($Destination eq "QUEUE") {
504            # Push the message into the queue.
505            push @Queue, "$formatted";
506        } elsif ($Destination eq "HTML") {
507            # Convert the message to HTML and write it to the standard output.
508            my $escapedMessage = CGI::escapeHTML($message);
509            print "<p>$timeStamp $LastCategory: $escapedMessage</p>\n";
510        } elsif ($Destination eq "WARN") {
511           # Emit the message as a warning.
512           warn $message;
513        } elsif ($Destination =~ m/^>>/) {
514            # Write the trace message to an output file.
515            (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
516            print TRACING "$formatted\n";
517            close TRACING;
518            # If the Tee flag is on, echo it to the standard output.
519            if ($TeeFlag) {
520                print "$formatted\n";
521            }
522        }
523    }
524    
525  Finally, if the special option C<-h> is specified, the option names will  =head3 T
 be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
526    
527      TransactFeatures -h      my $switch = T($category, $traceLevel);
528    
529  he would see the following output.      or
530    
531      TransactFeatures [options] command transactionDirectory IDfile      my $switch = T($traceLevel);
         -trace    tracing level (default 2)  
         -sql      trace SQL commands  
         -safe     use database transactions  
         -noAlias  do not expect aliases in CHANGE transactions  
         -start    start with this genome  
         -tblFiles output TBL files containing the corrected IDs  
532    
533  The caller has the option of modifying the tracing scheme by placing a value  Return TRUE if the trace level is at or above a specified value and the specified category
534  for C<trace> in the incoming options hash. The default value can be overridden,  is active, else FALSE. If no category is specified, the caller's package name is used.
 or the tracing to the standard output can be turned off by suffixing a minus  
 sign to the trace level. So, for example,  
535    
536      { trace => [0, "tracing level (default 0)"],  =over 4
        ...  
537    
538  would set the default trace level to 0 instead of 2, while  =item category
539    
540      { trace => ["2-", "tracing level (default 2)"],  Category to which the message belongs. If not specified, the caller's package name is
541         ...  used.
542    
543  would leave the default at 2, but trace only to the log file, not to the  =item traceLevel
 standard output.  
544    
545  The parameters to this method are as follows.  Relevant tracing level.
546    
547  =over 4  =item RETURN
548    
549  =item categories  TRUE if a message at the specified trace level would appear in the trace, else FALSE.
550    
551  Reference to a list of tracing category names. These should be names of  =back
 packages whose internal workings will need to be debugged to get the  
 command working.  
552    
553  =item options  =cut
554    
555  Reference to a hash containing the legal options for the current command mapped  sub T {
556        # Declare the return variable.
557        my $retVal = 0;
558        # Only proceed if tracing is turned on.
559        if ($Destination ne "NONE") {
560            # Get the parameters.
561            my ($category, $traceLevel) = @_;
562            if (!defined $traceLevel) {
563                # Here we have no category, so we need to get the calling package.
564                # The calling package is normally the first parameter. If it is
565                # omitted, the first parameter will be the tracelevel. So, the
566                # first thing we do is shift the so-called category into the
567                # $traceLevel variable where it belongs.
568                $traceLevel = $category;
569                my ($package, $fileName, $line) = caller;
570                # If there is no calling package, we default to "main".
571                if (!$package) {
572                    $category = "main";
573                } else {
574                    my @cats = split /::/, $package;
575                    $category = $cats[$#cats];
576                }
577            }
578            # Save the category name.
579            $LastCategory = $category;
580            # Convert it to lower case before we hash it.
581            $category = lc $category;
582            # Use the category and tracelevel to compute the result.
583            if (ref $traceLevel) {
584                Confess("Bad trace level.");
585            } elsif (ref $TraceLevel) {
586                Confess("Bad trace config.");
587            }
588            $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
589        }
590        # Return the computed result.
591        return $retVal;
592    }
593    
594    =head3 QTrace
595    
596        my $data = QTrace($format);
597    
598    Return the queued trace data in the specified format.
599    
600    =over 4
601    
602    =item format
603    
604    C<html> to format the data as an HTML list, C<text> to format it as straight text.
605    
606    =back
607    
608    =cut
609    
610    sub QTrace {
611        # Get the parameter.
612        my ($format) = @_;
613        # Create the return variable.
614        my $retVal = "";
615        # Only proceed if there is an actual queue.
616        if (@Queue) {
617            # Process according to the format.
618            if ($format =~ m/^HTML$/i) {
619                # Convert the queue into an HTML list.
620                $retVal = "<ul>\n";
621                for my $line (@Queue) {
622                    my $escapedLine = CGI::escapeHTML($line);
623                    $retVal .= "<li>$escapedLine</li>\n";
624                }
625                $retVal .= "</ul>\n";
626            } elsif ($format =~ m/^TEXT$/i) {
627                # Convert the queue into a list of text lines.
628                $retVal = join("\n", @Queue) . "\n";
629            }
630            # Clear the queue.
631            @Queue = ();
632        }
633        # Return the formatted list.
634        return $retVal;
635    }
636    
637    =head3 Confess
638    
639        Confess($message);
640    
641    Trace the call stack and abort the program with the specified message. When used with
642    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
643    So, for example
644    
645        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
646    
647    Will abort the program with a stack trace if the value of C<$recNum> is negative.
648    
649    =over 4
650    
651    =item message
652    
653    Message to include in the trace.
654    
655    =back
656    
657    =cut
658    
659    sub Confess {
660        # Get the parameters.
661        my ($message) = @_;
662        if (! defined($FIG_Config::no_tool_hdr)) {
663            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
664            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
665            # Only proceed if the tool header file is actually present.
666            if (-f $toolHeaderFile) {
667                my @lines = GetFile($toolHeaderFile);
668                Trace("Tool header has " . scalar(@lines) . " lines.");
669            }
670        }
671        # Trace the call stack.
672        Cluck($message);
673        # Abort the program.
674        croak(">>> $message");
675    }
676    
677    =head3 Assert
678    
679        Assert($condition1, $condition2, ... $conditionN);
680    
681    Return TRUE if all the conditions are true. This method can be used in conjunction with
682    the OR operator and the L</Confess> method as a debugging assert.
683    So, for example
684    
685        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
686    
687    Will abort the program with a stack trace if the value of C<$recNum> is negative.
688    
689    =cut
690    sub Assert {
691        my $retVal = 1;
692        LOOP: for my $condition (@_) {
693            if (! $condition) {
694                $retVal = 0;
695                last LOOP;
696            }
697        }
698        return $retVal;
699    }
700    
701    =head3 Cluck
702    
703        Cluck($message);
704    
705    Trace the call stack. Note that for best results, you should qualify the call with a
706    trace condition. For example,
707    
708        Cluck("Starting record parse.") if T(3);
709    
710    will only trace the stack if the trace level for the package is 3 or more.
711    
712    =over 4
713    
714    =item message
715    
716    Message to include in the trace.
717    
718    =back
719    
720    =cut
721    
722    sub Cluck {
723        # Get the parameters.
724        my ($message) = @_;
725        # Trace what's happening.
726        Trace("Stack trace for event: $message");
727        my $confession = longmess($message);
728        # Convert the confession to a series of trace messages. Note we skip any
729        # messages relating to calls into Tracer.
730        for my $line (split /\s*\n/, $confession) {
731            Trace($line) if ($line !~ /Tracer\.pm/);
732        }
733    }
734    
735    =head3 ScriptSetup
736    
737        my ($cgi, $varHash) = ScriptSetup($noTrace);
738    
739    Perform standard tracing and debugging setup for scripts. The value returned is
740    the CGI object followed by a pre-built variable hash. At the end of the script,
741    the client should call L</ScriptFinish> to output the web page.
742    
743    This method calls L</ETracing> to configure tracing, which allows the tracing
744    to be configured via the emergency tracing form on the debugging control panel.
745    Tracing will then be turned on automatically for all programs that use the L</ETracing>
746    method, which includes every program that uses this method or L</StandardSetup>.
747    
748    =over 4
749    
750    =item noTrace (optional)
751    
752    If specified, tracing will be suppressed. This is useful if the script wants to set up
753    tracing manually.
754    
755    =item RETURN
756    
757    Returns a two-element list consisting of a CGI query object and a variable hash for
758    the output page.
759    
760    =back
761    
762    =cut
763    
764    sub ScriptSetup {
765        # Get the parameters.
766        my ($noTrace) = @_;
767        # Get the CGI query object.
768        my $cgi = CGI->new();
769        # Set up tracing if it's not suppressed.
770        ETracing($cgi) unless $noTrace;
771        # Create the variable hash.
772        my $varHash = { results => '' };
773        # Return the query object and variable hash.
774        return ($cgi, $varHash);
775    }
776    
777    =head3 ETracing
778    
779        ETracing($parameter);
780    
781    Set up emergency tracing. Emergency tracing is tracing that is turned
782    on automatically for any program that calls this method. The emergency
783    tracing parameters are stored in a a file identified by a tracing key.
784    If this method is called with a CGI object, then the tracing key is
785    taken from a cookie. If it is called with no parameters, then the tracing
786    key is taken from an environment variable. If it is called with a string,
787    the tracing key is that string.
788    
789    =over 4
790    
791    =item parameter
792    
793    A parameter from which the tracing key is computed. If it is a scalar,
794    that scalar is used as the tracing key. If it is a CGI object, the
795    tracing key is taken from the C<IP> cookie. If it is omitted, the
796    tracing key is taken from the C<TRACING> environment variable. If it
797    is a CGI object and emergency tracing is not on, the C<Trace> and
798    C<TF> parameters will be used to determine the type of tracing.
799    
800    =back
801    
802    =cut
803    
804    sub ETracing {
805        # Get the parameter.
806        my ($parameter) = @_;
807        # Check for CGI mode.
808        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
809        # Default to no tracing except errors.
810        my ($tracing, $dest) = ("0", "WARN");
811        # Check for emergency tracing.
812        my $tkey = EmergencyKey($parameter);
813        my $emergencyFile = EmergencyFileName($tkey);
814        if (-e $emergencyFile) {
815            # We have the file. Read in the data.
816            my @tracing = GetFile($emergencyFile);
817            # Pull off the time limit.
818            my $expire = shift @tracing;
819            # Convert it to seconds.
820            $expire *= 3600;
821            # Check the file data.
822            my $stat = stat($emergencyFile);
823            my ($now) = gettimeofday;
824            if ($now - $stat->mtime > $expire) {
825                # Delete the expired file.
826                unlink $emergencyFile;
827            } else {
828                # Emergency tracing is on. Pull off the destination and
829                # the trace level;
830                $dest = shift @tracing;
831                my $level = shift @tracing;
832                # Convert the destination to a real tracing destination.
833                # temp directory.
834                $dest = EmergencyTracingDest($tkey, $dest);
835                # Insure Tracer is specified.
836                my %moduleHash = map { $_ => 1 } @tracing;
837                $moduleHash{Tracer} = 1;
838                # Set the trace parameter.
839                $tracing = join(" ", $level, sort keys %moduleHash);
840            }
841        } elsif (defined $cgi) {
842            # There's no emergency tracing, but we have a CGI object, so check
843            # for tracing from the form parameters.
844            if ($cgi->param('Trace')) {
845                # Here the user has requested tracing via a form.
846                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
847                $tracing = $cgi->param('Trace') . " Tracer";
848            }
849        }
850        # Setup the tracing we've determined from all the stuff above.
851        TSetup($tracing, $dest);
852        # If we're a web script, trace the parameter and environment data.
853        if (defined $cgi) {
854            TraceParms($cgi);
855        }
856    }
857    
858    =head3 EmergencyFileName
859    
860        my $fileName = Tracer::EmergencyFileName($tkey);
861    
862    Return the emergency tracing file name. This is the file that specifies
863    the tracing information.
864    
865    =over 4
866    
867    =item tkey
868    
869    Tracing key for the current program.
870    
871    =item RETURN
872    
873    Returns the name of the file to contain the emergency tracing information.
874    
875    =back
876    
877    =cut
878    
879    sub EmergencyFileName {
880        # Get the parameters.
881        my ($tkey) = @_;
882        # Compute the emergency tracing file name.
883        return "$FIG_Config::temp/Emergency$tkey.txt";
884    }
885    
886    =head3 EmergencyFileTarget
887    
888        my $fileName = Tracer::EmergencyFileTarget($tkey);
889    
890    Return the emergency tracing target file name. This is the file that receives
891    the tracing output for file-based tracing.
892    
893    =over 4
894    
895    =item tkey
896    
897    Tracing key for the current program.
898    
899    =item RETURN
900    
901    Returns the name of the file to contain the trace output.
902    
903    =back
904    
905    =cut
906    
907    sub EmergencyFileTarget {
908        # Get the parameters.
909        my ($tkey) = @_;
910        # Compute the emergency tracing file name.
911        return "$FIG_Config::temp/trace$tkey.log";
912    }
913    
914    =head3 EmergencyTracingDest
915    
916        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
917    
918    This method converts an emergency tracing destination to a real
919    tracing destination. The main difference is that if the
920    destination is C<FILE> or C<APPEND>, we convert it to file
921    output. If the destination is C<DUAL>, we convert it to file
922    and standard output.
923    
924    =over 4
925    
926    =item tkey
927    
928    Tracing key for this environment.
929    
930    =item myDest
931    
932    Destination from the emergency tracing file.
933    
934    =item RETURN
935    
936    Returns a destination that can be passed into L</TSetup>.
937    
938    =back
939    
940    =cut
941    
942    sub EmergencyTracingDest {
943        # Get the parameters.
944        my ($tkey, $myDest) = @_;
945        # Declare the return variable.
946        my $retVal = $myDest;
947        # Process according to the destination value.
948        if ($myDest eq 'FILE') {
949            $retVal = ">" . EmergencyFileTarget($tkey);
950        } elsif ($myDest eq 'APPEND') {
951            $retVal = ">>" . EmergencyFileTarget($tkey);
952        } elsif ($myDest eq 'DUAL') {
953            $retVal = "+>" . EmergencyFileTarget($tkey);
954        }
955        # Return the result.
956        return $retVal;
957    }
958    
959    =head3 Emergency
960    
961        Emergency($key, $hours, $dest, $level, @modules);
962    
963    Turn on emergency tracing. This method is normally invoked over the web from
964    a debugging console, but it can also be called by the C<trace.pl> script.
965    The caller specifies the duration of the emergency in hours, the desired tracing
966    destination, the trace level, and a list of the trace modules to activate.
967    For the length of the duration, when a program in an environment with the
968    specified tracing key active invokes a Sprout CGI script, tracing will be
969    turned on automatically. See L</TSetup> for more about tracing setup and
970    L</ETracing> for more about emergency tracing.
971    
972    =over 4
973    
974    =item tkey
975    
976    The tracing key. This is used to identify the control file and the trace file.
977    
978    =item hours
979    
980    Number of hours to keep emergency tracing alive.
981    
982    =item dest
983    
984    Tracing destination. If no path information is specified for a file
985    destination, it is put in the FIG temporary directory.
986    
987    =item level
988    
989    Tracing level. A higher level means more trace messages.
990    
991    =item modules
992    
993    A list of the tracing modules to activate.
994    
995    =back
996    
997    =cut
998    
999    sub Emergency {
1000        # Get the parameters.
1001        my ($tkey, $hours, $dest, $level, @modules) = @_;
1002        # Create the emergency file.
1003        my $specFile = EmergencyFileName($tkey);
1004        my $outHandle = Open(undef, ">$specFile");
1005        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1006    }
1007    
1008    =head3 EmergencyKey
1009    
1010        my $tkey = EmergencyKey($parameter);
1011    
1012    Return the Key to be used for emergency tracing. This could be an IP address,
1013     a session ID, or a user name, depending on the environment.
1014    
1015    =over 4
1016    
1017    =item parameter
1018    
1019    Parameter defining the method for finding the tracing key. If it is a scalar,
1020    then it is presumed to be the tracing key itself. If it is a CGI object, then
1021    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1022    taken from the C<TRACING> environment variable.
1023    
1024    =item RETURN
1025    
1026    Returns the key to be used for labels in emergency tracing.
1027    
1028    =back
1029    
1030    =cut
1031    
1032    sub EmergencyKey {
1033        # Get the parameters.
1034        my ($parameter) = @_;
1035        # Declare the return variable.
1036        my $retVal;
1037        # Determine the parameter type.
1038        if (! defined $parameter) {
1039            # Here we're supposed to check the environment.
1040            $retVal = $ENV{TRACING};
1041        } else {
1042            my $ptype = ref $parameter;
1043            if ($ptype eq 'CGI') {
1044                # Here we were invoked from a web page. Look for a cookie.
1045                $retVal = $parameter->cookie('IP');
1046            } elsif (! $ptype) {
1047                # Here the key was passed in.
1048                $retVal = $parameter;
1049            }
1050        }
1051        # If no luck finding a key, use the PID.
1052        if (! defined $retVal) {
1053            $retVal = $$;
1054        }
1055        # Return the result.
1056        return $retVal;
1057    }
1058    
1059    
1060    =head3 TraceParms
1061    
1062        Tracer::TraceParms($cgi);
1063    
1064    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1065    at level CGI => 4.
1066    
1067    =over 4
1068    
1069    =item cgi
1070    
1071    CGI query object containing the parameters to trace.
1072    
1073    =back
1074    
1075    =cut
1076    
1077    sub TraceParms {
1078        # Get the parameters.
1079        my ($cgi) = @_;
1080        if (T(CGI => 3)) {
1081            # Here we want to trace the parameter data.
1082            my @names = $cgi->param;
1083            for my $parmName (sort @names) {
1084                # Note we skip the Trace parameters, which are for our use only.
1085                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1086                    my @values = $cgi->param($parmName);
1087                    Trace("CGI: $parmName = " . join(", ", @values));
1088                }
1089            }
1090            # Display the request method.
1091            my $method = $cgi->request_method();
1092            Trace("Method: $method");
1093        }
1094        if (T(CGI => 4)) {
1095            # Here we want the environment data too.
1096            for my $envName (sort keys %ENV) {
1097                Trace("ENV: $envName = $ENV{$envName}");
1098            }
1099        }
1100    }
1101    
1102    =head3 ScriptFinish
1103    
1104        ScriptFinish($webData, $varHash);
1105    
1106    Output a web page at the end of a script. Either the string to be output or the
1107    name of a template file can be specified. If the second parameter is omitted,
1108    it is assumed we have a string to be output; otherwise, it is assumed we have the
1109    name of a template file. The template should have the variable C<DebugData>
1110    specified in any form that invokes a standard script. If debugging mode is turned
1111    on, a form field will be put in that allows the user to enter tracing data.
1112    Trace messages will be placed immediately before the terminal C<BODY> tag in
1113    the output, formatted as a list.
1114    
1115    A typical standard script would loook like the following.
1116    
1117        BEGIN {
1118            # Print the HTML header.
1119            print "CONTENT-TYPE: text/html\n\n";
1120        }
1121        use Tracer;
1122        use CGI;
1123        use FIG;
1124        # ... more uses ...
1125    
1126        my ($cgi, $varHash) = ScriptSetup();
1127        eval {
1128            # ... get data from $cgi, put it in $varHash ...
1129        };
1130        if ($@) {
1131            Trace("Script Error: $@") if T(0);
1132        }
1133        ScriptFinish("Html/MyTemplate.html", $varHash);
1134    
1135    The idea here is that even if the script fails, you'll see trace messages and
1136    useful output.
1137    
1138    =over 4
1139    
1140    =item webData
1141    
1142    A string containing either the full web page to be written to the output or the
1143    name of a template file from which the page is to be constructed. If the name
1144    of a template file is specified, then the second parameter must be present;
1145    otherwise, it must be absent.
1146    
1147    =item varHash (optional)
1148    
1149    If specified, then a reference to a hash mapping variable names for a template
1150    to their values. The template file will be read into memory, and variable markers
1151    will be replaced by data in this hash reference.
1152    
1153    =back
1154    
1155    =cut
1156    
1157    sub ScriptFinish {
1158        # Get the parameters.
1159        my ($webData, $varHash) = @_;
1160        # Check for a template file situation.
1161        my $outputString;
1162        if (defined $varHash) {
1163            # Here we have a template file. We need to determine the template type.
1164            my $template;
1165            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1166                $template = "$FIG_Config::template_url/$webData";
1167            } else {
1168                $template = "<<$webData";
1169            }
1170            $outputString = PageBuilder::Build($template, $varHash, "Html");
1171        } else {
1172            # Here the user gave us a raw string.
1173            $outputString = $webData;
1174        }
1175        # Check for trace messages.
1176        if ($Destination ne "NONE" && $TraceLevel > 0) {
1177            # We have trace messages, so we want to put them at the end of the body. This
1178            # is either at the end of the whole string or at the beginning of the BODY
1179            # end-tag.
1180            my $pos = length $outputString;
1181            if ($outputString =~ m#</body>#gi) {
1182                $pos = (pos $outputString) - 7;
1183            }
1184            # If the trace messages were queued, we unroll them. Otherwise, we display the
1185            # destination.
1186            my $traceHtml;
1187            if ($Destination eq "QUEUE") {
1188                $traceHtml = QTrace('Html');
1189            } elsif ($Destination =~ /^>>(.+)$/) {
1190                # Here the tracing output it to a file. We code it as a hyperlink so the user
1191                # can copy the file name into the clipboard easily.
1192                my $actualDest = $1;
1193                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1194            } else {
1195                # Here we have one of the special destinations.
1196                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1197            }
1198            substr $outputString, $pos, 0, $traceHtml;
1199        }
1200        # Write the output string.
1201        print $outputString;
1202    }
1203    
1204    =head2 Command-Line Utility Methods
1205    
1206    =head3 SendSMS
1207    
1208        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1209    
1210    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1211    user name, password, and API ID for the relevant account in the hash reference variable
1212    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1213    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1214    is C<2561022>, then the FIG_Config file must contain
1215    
1216        $phone =  { user => 'BruceTheHumanPet',
1217                    password => 'silly',
1218                    api_id => '2561022' };
1219    
1220    The original purpose of this method was to insure Bruce would be notified immediately when the
1221    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1222    when you call this method.
1223    
1224    The message ID will be returned if successful, and C<undef> if an error occurs.
1225    
1226    =over 4
1227    
1228    =item phoneNumber
1229    
1230    Phone number to receive the message, in international format. A United States phone number
1231    would be prefixed by "1". A British phone number would be prefixed by "44".
1232    
1233    =item msg
1234    
1235    Message to send to the specified phone.
1236    
1237    =item RETURN
1238    
1239    Returns the message ID if successful, and C<undef> if the message could not be sent.
1240    
1241    =back
1242    
1243    =cut
1244    
1245    sub SendSMS {
1246        # Get the parameters.
1247        my ($phoneNumber, $msg) = @_;
1248        # Declare the return variable. If we do not change it, C<undef> will be returned.
1249        my $retVal;
1250        # Only proceed if we have phone support.
1251        if (! defined $FIG_Config::phone) {
1252            Trace("Phone support not present in FIG_Config.") if T(1);
1253        } else {
1254            # Get the phone data.
1255            my $parms = $FIG_Config::phone;
1256            # Get the Clickatell URL.
1257            my $url = "http://api.clickatell.com/http/";
1258            # Create the user agent.
1259            my $ua = LWP::UserAgent->new;
1260            # Request a Clickatell session.
1261            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1262                                         password => $parms->{password},
1263                                         api_id => $parms->{api_id},
1264                                         to => $phoneNumber,
1265                                         text => $msg});
1266            # Check for an error.
1267            if (! $resp->is_success) {
1268                Trace("Alert failed.") if T(1);
1269            } else {
1270                # Get the message ID.
1271                my $rstring = $resp->content;
1272                if ($rstring =~ /^ID:\s+(.*)$/) {
1273                    $retVal = $1;
1274                } else {
1275                    Trace("Phone attempt failed with $rstring") if T(1);
1276                }
1277            }
1278        }
1279        # Return the result.
1280        return $retVal;
1281    }
1282    
1283    =head3 StandardSetup
1284    
1285        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1286    
1287    This method performs standard command-line parsing and tracing setup. The return
1288    values are a hash of the command-line options and a list of the positional
1289    parameters. Tracing is automatically set up and the command-line options are
1290    validated.
1291    
1292    This is a complex method that does a lot of grunt work. The parameters can
1293    be more easily understood, however, once they are examined individually.
1294    
1295    The I<categories> parameter is the most obtuse. It is a reference to a list of
1296    special-purpose tracing categories. Most tracing categories are PERL package
1297    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1298    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1299    
1300        ["Sprout", "SproutLoad", "ERDB"]
1301    
1302    This would cause trace messages in the specified three packages to appear in
1303    the output. There are two special tracing categories that are automatically
1304    handled by this method. In other words, if you used L</TSetup> you would need
1305    to include these categories manually, but if you use this method they are turned
1306    on automatically.
1307    
1308    =over 4
1309    
1310    =item SQL
1311    
1312    Traces SQL commands and activity.
1313    
1314    =item Tracer
1315    
1316    Traces error messages and call stacks.
1317    
1318    =back
1319    
1320    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1321    The trace level is specified using the C<-trace> command-line option. For example,
1322    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1323    all tracing at level 3.
1324    
1325        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1326    
1327    Standard tracing is output to the standard output and echoed to the file
1328    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1329    process ID. You can also specify the C<user> parameter to put a user ID
1330    instead of a process ID in the trace file name. So, for example
1331    
1332    The default trace level is 2. To get all messages, specify a trace level of 4.
1333    For a genome-by-genome update, use 3.
1334    
1335        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1336    
1337    would send the trace output to C<traceBruce.log> in the temporary directory.
1338    
1339    The I<options> parameter is a reference to a hash containing the command-line
1340    options, their default values, and an explanation of what they mean. Command-line
1341    options may be in the form of switches or keywords. In the case of a switch, the
1342    option value is 1 if it is specified and 0 if it is not specified. In the case
1343    of a keyword, the value is separated from the option name by an equal sign. You
1344    can see this last in the command-line example above.
1345    
1346    You can specify a different default trace level by setting C<$options->{trace}>
1347    prior to calling this method.
1348    
1349    An example at this point would help. Consider, for example, the command-line utility
1350    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1351    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1352    the following code.
1353    
1354        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1355                            { safe => [0, "use database transactions"],
1356                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1357                              start => [' ', "start with this genome"],
1358                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1359                            "<command> <transactionDirectory> <IDfile>",
1360                          @ARGV);
1361    
1362    
1363    The call to C<ParseCommand> specifies the default values for the options and
1364    stores the actual options in a hash that is returned as C<$options>. The
1365    positional parameters are returned in C<@parameters>.
1366    
1367    The following is a sample command line for C<TransactFeatures>.
1368    
1369        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1370    
1371    Single and double hyphens are equivalent. So, you could also code the
1372    above command as
1373    
1374        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1375    
1376    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1377    parameters, and would find themselves in I<@parameters> after executing the
1378    above code fragment. The tracing would be set to level 2, and the categories
1379    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1380    and C<DocUtils> was included because it came in within the first parameter
1381    to this method. The I<$options> hash would be
1382    
1383        { trace => 2, sql => 0, safe => 0,
1384          noAlias => 1, start => ' ', tblFiles => 0 }
1385    
1386    Use of C<StandardSetup> in this way provides a simple way of performing
1387    standard tracing setup and command-line parsing. Note that the caller is
1388    not even aware of the command-line switches C<-trace> and C<-sql>, which
1389    are used by this method to control the tracing. If additional tracing features
1390    need to be added in the future, they can be processed by this method without
1391    upsetting the command-line utilities.
1392    
1393    If the C<background> option is specified on the command line, then the
1394    standard and error outputs will be directed to files in the temporary
1395    directory, using the same suffix as the trace file. So, if the command
1396    line specified
1397    
1398        -user=Bruce -background
1399    
1400    then the trace output would go to C<traceBruce.log>, the standard output to
1401    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1402    simplify starting a command in the background.
1403    
1404    The user name is also used as the tracing key for L</Emergency Tracing>.
1405    Specifying a value of C<E> for the trace level causes emergency tracing to
1406    be used instead of custom tracing. If the user name is not specified,
1407    the tracing key is taken from the C<Tracing> environment variable. If there
1408    is no value for that variable, the tracing key will be computed from the PID.
1409    
1410    Finally, if the special option C<-help> is specified, the option
1411    names will be traced at level 0 and the program will exit without processing.
1412    This provides a limited help capability. For example, if the user enters
1413    
1414        TransactFeatures -help
1415    
1416    he would see the following output.
1417    
1418        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1419            -trace    tracing level (default E)
1420            -sql      trace SQL commands
1421            -safe     use database transactions
1422            -noAlias  do not expect aliases in CHANGE transactions
1423            -start    start with this genome
1424            -tblFiles output TBL files containing the corrected IDs
1425    
1426    The caller has the option of modifying the tracing scheme by placing a value
1427    for C<trace> in the incoming options hash. The default value can be overridden,
1428    or the tracing to the standard output can be turned off by suffixing a minus
1429    sign to the trace level. So, for example,
1430    
1431        { trace => [0, "tracing level (default 0)"],
1432           ...
1433    
1434    would set the default trace level to 0 instead of E, while
1435    
1436        { trace => ["2-", "tracing level (default 2)"],
1437           ...
1438    
1439    would set the default to 2, but trace only to the log file, not to the
1440    standard output.
1441    
1442    The parameters to this method are as follows.
1443    
1444    =over 4
1445    
1446    =item categories
1447    
1448    Reference to a list of tracing category names. These should be names of
1449    packages whose internal workings will need to be debugged to get the
1450    command working.
1451    
1452    =item options
1453    
1454    Reference to a hash containing the legal options for the current command mapped
1455  to their default values and descriptions. The user can override the defaults  to their default values and descriptions. The user can override the defaults
1456  by specifying the options as command-line switches prefixed by a hyphen.  by specifying the options as command-line switches prefixed by a hyphen.
1457  Tracing-related options may be added to this hash. If the C<-h> option is  Tracing-related options may be added to this hash. If the C<-h> option is
# Line 406  Line 1483 
1483  sub StandardSetup {  sub StandardSetup {
1484      # Get the parameters.      # Get the parameters.
1485      my ($categories, $options, $parmHelp, @argv) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
1486        # Get the default tracing key.
1487        my $tkey = EmergencyKey();
1488      # Add the tracing options.      # Add the tracing options.
1489      if (! exists $options->{trace}) {      if (! exists $options->{trace}) {
1490          $options->{trace} = [2, "tracing level"];          $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1491      }      }
1492      $options->{sql} = [0, "turn on SQL tracing"];      $options->{sql} = [0, "turn on SQL tracing"];
1493      $options->{h} = [0, "display command-line options"];      $options->{help} = [0, "display command-line options"];
1494      $options->{user} = [$$, "trace log file name suffix"];      $options->{user} = [$tkey, "tracing key"];
1495      $options->{background} = [0, "spool standard and error output"];      $options->{background} = [0, "spool standard and error output"];
1496      # Create a parsing hash from the options hash. The parsing hash      # Create a parsing hash from the options hash. The parsing hash
1497      # contains the default values rather than the default value      # contains the default values rather than the default value
# Line 436  Line 1515 
1515          my $errFileName = "$FIG_Config::temp/err$suffix.log";          my $errFileName = "$FIG_Config::temp/err$suffix.log";
1516          open STDOUT, ">$outFileName";          open STDOUT, ">$outFileName";
1517          open STDERR, ">$errFileName";          open STDERR, ">$errFileName";
1518            # Check for phone support. If we have phone support and a phone number,
1519            # we want to turn it on.
1520            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1521                $retOptions->{phone} = $ENV{PHONE};
1522            }
1523      }      }
1524      # Now we want to set up tracing. First, we need to know if SQL is to      # Now we want to set up tracing. First, we need to know if the user
1525      # be traced.      # wants emergency tracing.
1526        if ($retOptions->{trace} eq 'E') {
1527            ETracing($retOptions->{user});
1528        } else {
1529            # Here the tracing is controlled from the command line.
1530      my @cats = @{$categories};      my @cats = @{$categories};
1531      if ($retOptions->{sql}) {      if ($retOptions->{sql}) {
1532          push @cats, "SQL";          push @cats, "SQL";
1533      }      }
1534      # Add the default categories.      # Add the default categories.
1535      push @cats, "Tracer", "FIG";          push @cats, "Tracer";
1536      # Next, we create the category string by joining the categories.      # Next, we create the category string by joining the categories.
1537      my $cats = join(" ", @cats);      my $cats = join(" ", @cats);
1538      # Check to determine whether or not the caller wants to turn off tracing      # Check to determine whether or not the caller wants to turn off tracing
# Line 479  Line 1567 
1567      }      }
1568      # Now set up the tracing.      # Now set up the tracing.
1569      TSetup("$traceLevel $cats", $traceMode);      TSetup("$traceLevel $cats", $traceMode);
1570      # Check for the "h" option. If it is specified, dump the command-line      }
1571        # Check for the "help" option. If it is specified, dump the command-line
1572      # options and exit the program.      # options and exit the program.
1573      if ($retOptions->{h}) {      if ($retOptions->{help}) {
1574          $0 =~ m#[/\\](\w+)(\.pl)?$#i;          $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1575          Trace("$1 [options] $parmHelp") if T(0);          print "$1 [options] $parmHelp\n";
1576          for my $key (sort keys %{$options}) {          for my $key (sort keys %{$options}) {
1577              my $name = Pad($key, $longestName, 0, ' ');              my $name = Pad($key, $longestName, 0, ' ');
1578              my $desc = $options->{$key}->[1];              my $desc = $options->{$key}->[1];
1579              if ($options->{$key}->[0]) {              if ($options->{$key}->[0]) {
1580                  $desc .= " (default " . $options->{$key}->[0] . ")";                  $desc .= " (default " . $options->{$key}->[0] . ")";
1581              }              }
1582              Trace("  $name $desc") if T(0);              print "  $name $desc\n";
1583          }          }
1584          exit(0);          exit(0);
1585      }      }
1586        # Trace the options, if applicable.
1587        if (T(3)) {
1588            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1589            Trace("Selected options: " . join(", ", sort @parms) . ".");
1590        }
1591      # Return the parsed parameters.      # Return the parsed parameters.
1592      return ($retOptions, @retParameters);      return ($retOptions, @retParameters);
1593  }  }
1594    
1595  =head3 Setups  =head3 ReadOptions
1596    
1597  C<< my $count = Tracer::Setups(); >>      my %options = Tracer::ReadOptions($fileName);
1598    
1599  Return the number of times L</TSetup> has been called.  Read a set of options from a file. Each option is encoded in a line of text that has the
1600    format
1601    
1602  This method allows for the creation of conditional tracing setups where, for example, we  I<optionName>C<=>I<optionValue>C<; >I<comment>
 may want to set up tracing if nobody else has done it before us.  
1603    
1604  =cut  The option name must consist entirely of letters, digits, and the punctuation characters
1605    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1606    character is a semi-colon will be ignored. The return hash will map each option name to
1607    the corresponding option value.
1608    
1609  sub Setups {  =over 4
     return $SetupCount;  
 }  
1610    
1611  =head3 Open  =item fileName
1612    
1613  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  Name of the file containing the option data.
1614    
1615  Open a file.  =item RETURN
1616    
1617  The I<$fileSpec> is essentially the second argument of the PERL C<open>  Returns a hash mapping the option names specified in the file to their corresponding option
1618  function. The mode is specified using Unix-like shell information. So, for  value.
 example,  
1619    
1620      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =back
1621    
1622  would open for output appended to the specified file, and  =cut
1623    
1624      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  sub ReadOptions {
1625        # Get the parameters.
1626        my ($fileName) = @_;
1627        # Open the file.
1628        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1629        # Count the number of records read.
1630        my ($records, $comments) = 0;
1631        # Create the return hash.
1632        my %retVal = ();
1633        # Loop through the file, accumulating key-value pairs.
1634        while (my $line = <CONFIGFILE>) {
1635            # Denote we've read a line.
1636            $records++;
1637            # Determine the line type.
1638            if ($line =~ /^\s*[\n\r]/) {
1639                # A blank line is a comment.
1640                $comments++;
1641            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1642                # Here we have an option assignment.
1643                retVal{$1} = $2;
1644            } elsif ($line =~ /^\s*;/) {
1645                # Here we have a text comment.
1646                $comments++;
1647            } else {
1648                # Here we have an invalid line.
1649                Trace("Invalid option statement in record $records.") if T(0);
1650            }
1651        }
1652        # Return the hash created.
1653        return %retVal;
1654    }
1655    
1656  would open a pipe that sorts the records written and removes duplicates. Note  =head3 GetOptions
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
1657    
1658      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");      Tracer::GetOptions(\%defaults, \%options);
1659    
1660  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  Merge a specified set of options into a table of defaults. This method takes two hash references
1661  the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a  as input and uses the data from the second to update the first. If the second does not exist,
1662  failed open will throw an exception and the third parameter will be used to construct  there will be no effect. An error will be thrown if one of the entries in the second hash does not
1663  an error message. If the parameter is omitted, a standard message is constructed  exist in the first.
 using the file spec.  
1664    
1665      Could not open "/usr/spool/news/twitlog"  Consider the following example.
1666    
1667  Note that the mode characters are automatically cleaned from the file name.      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
1668    
1669      Could not open "/usr/spool/news/twitlog": file not found.  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1670    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1671    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1672    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1673    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1674    
1675  In some versions of PERL the only error message we get is a number, which      {databaseType => 'Oracle'}
 corresponds to the C++ C<errno> value.  
1676    
1677      Could not open "/usr/spool/news/twitlog": 6.  an error will occur because the B<databaseType> option does not exist.
1678    
1679  =over 4  =over 4
1680    
1681  =item fileHandle  =item defaults
   
 File handle. If this parameter is C<undef>, a file handle will be generated  
 and returned as the value of this method.  
   
 =item fileSpec  
1682    
1683  File name and mode, as per the PERL C<open> function.  Table of default option values.
1684    
1685  =item message (optional)  =item options
1686    
1687  Error message to use if the open fails. If omitted, a standard error message  Table of overrides, if any.
 will be generated. In either case, the error information from the file system  
 is appended to the message. To specify a conditional open that does not throw  
 an error if it fails, use C<0>.  
1688    
1689  =item RETURN  =item RETURN
1690    
1691  Returns the name of the file handle assigned to the file, or C<undef> if the  Returns a reference to the default table passed in as the first parameter.
 open failed.  
1692    
1693  =back  =back
1694    
1695  =cut  =cut
1696    
1697  sub Open {  sub GetOptions {
1698      # Get the parameters.      # Get the parameters.
1699      my ($fileHandle, $fileSpec, $message) = @_;      my ($defaults, $options) = @_;
1700      # Attempt to open the file.      # Check for overrides.
1701      my $rv = open $fileHandle, $fileSpec;      if ($options) {
1702      # If the open failed, generate an error message.          # Loop through the overrides.
1703      if (! $rv) {          while (my ($option, $setting) = each %{$options}) {
1704          # Save the system error message.              # Insure this override exists.
1705          my $sysMessage = $!;              if (!exists $defaults->{$option}) {
1706          # See if we need a default message.                  croak "Unrecognized option $option encountered.";
1707          if (!$message) {              } else {
1708              # Clean any obvious mode characters and leading spaces from the                  # Apply the override.
1709              # filename.                  $defaults->{$option} = $setting;
             my ($fileName) = FindNamePart($fileSpec);  
             $message = "Could not open \"$fileName\"";  
1710          }          }
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
1711      }      }
1712      # Return the file handle.      }
1713      return $fileHandle;      # Return the merged table.
1714        return $defaults;
1715  }  }
1716    
1717  =head3 FindNamePart  =head3 MergeOptions
   
 C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>  
   
 Extract the portion of a file specification that contains the file name.  
   
 A file specification is the string passed to an C<open> call. It specifies the file  
 mode and name. In a truly complex situation, it can specify a pipe sequence. This  
 method assumes that the file name is whatever follows the first angle bracket  
 sequence.  So, for example, in the following strings the file name is  
 C</usr/fig/myfile.txt>.  
1718    
1719      >>/usr/fig/myfile.txt      Tracer::MergeOptions(\%table, \%defaults);
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
1720    
1721  If the method cannot find a file name using its normal methods, it will return the  Merge default values into a hash table. This method looks at the key-value pairs in the
1722  whole incoming string.  second (default) hash, and if a matching key is not found in the first hash, the default
1723    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1724    checking and no return value.
1725    
1726  =over 4  =over 4
1727    
1728  =item fileSpec  =item table
1729    
1730  File specification string from which the file name is to be extracted.  Hash table to be updated with the default values.
1731    
1732  =item RETURN  =item defaults
1733    
1734  Returns a three-element list. The first element contains the file name portion of  Default values to be merged into the first hash table if they are not already present.
 the specified string, or the whole string if a file name cannot be found via normal  
 methods. The second element contains the start position of the file name portion and  
 the third element contains the length.  
1735    
1736  =back  =back
1737    
1738  =cut  =cut
1739  #: Return Type $;  
1740  sub FindNamePart {  sub MergeOptions {
1741      # Get the parameters.      # Get the parameters.
1742      my ($fileSpec) = @_;      my ($table, $defaults) = @_;
1743      # Default to the whole input string.      # Loop through the defaults.
1744      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);      while (my ($key, $value) = each %{$defaults}) {
1745      # Parse out the file name if we can.          if (!exists $table->{$key}) {
1746      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {              $table->{$key} = $value;
1747          $retVal = $2;          }
         $len = length $retVal;  
         $pos = (length $fileSpec) - (length $3) - $len;  
1748      }      }
     # Return the result.  
     return ($retVal, $pos, $len);  
1749  }  }
1750    
1751  =head3 OpenDir  =head3 ParseCommand
1752    
1753  C<< my @files = OpenDir($dirName, $filtered, $flag); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1754    
1755  Open a directory and return all the file names. This function essentially performs  Parse a command line consisting of a list of parameters. The initial parameters may be option
1756  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1757  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  off and merged into a table of default options. The remainder of the command line is
1758  or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be  returned as a list of positional arguments. For example, consider the following invocation.
 filtered out of the return list. If the directory does not open and I<$flag> is not  
 set, an exception is thrown. So, for example,  
1759    
1760      my @files = OpenDir("/Volumes/fig/contigs", 1);      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1761    
1762  is effectively the same as  In this case, the list @words will be treated as a command line and there are two options available,
1763    B<errors> and B<logFile>. If @words has the following format
1764    
1765      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");      -logFile=error.log apple orange rutabaga
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
1766    
1767  Similarly, the following code  then at the end of the invocation, C<$options> will be
1768    
1769      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);      { errors => 0, logFile => 'error.log' }
1770    
1771  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  and C<@arguments> will contain
1772  automatically returns an empty list if the directory fails to open.  
1773        apple orange rutabaga
1774    
1775    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1776    support for quote characters. Options can be specified with single or double hyphens.
1777    
1778  =over 4  =over 4
1779    
1780  =item dirName  =item optionTable
1781    
1782  Name of the directory to open.  Table of default options.
1783    
1784  =item filtered  =item inputList
1785    
1786  TRUE if files whose names begin with a period (C<.>) should be automatically removed  List of words on the command line.
 from the list, else FALSE.  
1787    
1788  =item flag  =item RETURN
1789    
1790  TRUE if a failure to open is okay, else FALSE  Returns a reference to the option table and a list of the positional arguments.
1791    
1792  =back  =back
1793    
1794  =cut  =cut
1795  #: Return Type @;  
1796  sub OpenDir {  sub ParseCommand {
1797      # Get the parameters.      # Get the parameters.
1798      my ($dirName, $filtered, $flag) = @_;      my ($optionTable, @inputList) = @_;
1799      # Declare the return variable.      # Process any options in the input list.
1800      my @retVal = ();      my %overrides = ();
1801      # Open the directory.      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1802      if (opendir(my $dirHandle, $dirName)) {          # Get the current option.
1803          # The directory opened successfully. Get the appropriate list according to the          my $arg = shift @inputList;
1804          # strictures of the filter parameter.          # Pull out the option name.
1805          if ($filtered) {          $arg =~ /^--?([^=]*)/g;
1806              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;          my $name = $1;
1807            # Check for an option value.
1808            if ($arg =~ /\G=(.*)$/g) {
1809                # Here we have a value for the option.
1810                $overrides{$name} = UnEscape($1);
1811          } else {          } else {
1812              @retVal = readdir $dirHandle;              # Here there is no value, so we use 1.
1813                $overrides{$name} = 1;
1814          }          }
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
1815      }      }
1816      # Return the result.      # Merge the options into the defaults.
1817      return @retVal;      GetOptions($optionTable, \%overrides);
1818        # Translate the remaining parameters.
1819        my @retVal = ();
1820        for my $inputParm (@inputList) {
1821            push @retVal, UnEscape($inputParm);
1822  }  }
1823        # Return the results.
1824  =head3 SetLevel      return ($optionTable, @retVal);
   
 C<< Tracer::SetLevel($newLevel); >>  
   
 Modify the trace level. A higher trace level will cause more messages to appear.  
   
 =over 4  
   
 =item newLevel  
   
 Proposed new trace level.  
   
 =back  
   
 =cut  
   
 sub SetLevel {  
     $TraceLevel = $_[0];  
1825  }  }
1826    
 =head3 Now  
   
 C<< my $string = Tracer::Now(); >>  
1827    
1828  Return a displayable time stamp containing the local time.  =head2 File Utility Methods
   
 =cut  
1829    
1830  sub Now {  =head3 GetFile
     my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);  
     my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .  
                  _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);  
     return $retVal;  
 }  
1831    
1832  # Pad a number to 2 digits.      my @fileContents = Tracer::GetFile($fileName);
 sub _p2 {  
     my ($value) = @_;  
     $value = "0$value" if ($value < 10);  
     return $value;  
 }  
1833    
1834  =head3 LogErrors      or
1835    
1836  C<< Tracer::LogErrors($fileName); >>      my $fileContents = Tracer::GetFile($fileName);
1837    
1838  Route the standard error output to a log file.  Return the entire contents of a file. In list context, line-ends are removed and
1839    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1840    
1841  =over 4  =over 4
1842    
1843  =item fileName  =item fileName
1844    
1845  Name of the file to receive the error output.  Name of the file to read.
1846    
1847    =item RETURN
1848    
1849    In a list context, returns the entire file as a list with the line terminators removed.
1850    In a scalar context, returns the entire file as a string. If an error occurs opening
1851    the file, an empty list will be returned.
1852    
1853  =back  =back
1854    
1855  =cut  =cut
1856    
1857  sub LogErrors {  sub GetFile {
1858      # Get the file name.      # Get the parameters.
1859      my ($fileName) = @_;      my ($fileName) = @_;
1860      # Open the file as the standard error output.      # Declare the return variable.
1861      open STDERR, '>', $fileName;      my @retVal = ();
1862        # Open the file for input.
1863        my $handle = Open(undef, "<$fileName");
1864        # Read the whole file into the return variable, stripping off any terminator
1865        # characters.
1866        my $lineCount = 0;
1867        while (my $line = <$handle>) {
1868            $lineCount++;
1869            $line = Strip($line);
1870            push @retVal, $line;
1871        }
1872        # Close it.
1873        close $handle;
1874        my $actualLines = @retVal;
1875        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
1876        # Return the file's contents in the desired format.
1877        if (wantarray) {
1878            return @retVal;
1879        } else {
1880            return join "\n", @retVal;
1881        }
1882  }  }
1883    
1884  =head3 ReadOptions  =head3 PutFile
   
 C<< my %options = Tracer::ReadOptions($fileName); >>  
   
 Read a set of options from a file. Each option is encoded in a line of text that has the  
 format  
1885    
1886  I<optionName>C<=>I<optionValue>C<; >I<comment>      Tracer::PutFile($fileName, \@lines);
1887    
1888  The option name must consist entirely of letters, digits, and the punctuation characters  Write out a file from a list of lines of text.
 C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  
 character is a semi-colon will be ignored. The return hash will map each option name to  
 the corresponding option value.  
1889    
1890  =over 4  =over 4
1891    
1892  =item fileName  =item fileName
1893    
1894  Name of the file containing the option data.  Name of the output file.
1895    
1896  =item RETURN  =item lines
1897    
1898  Returns a hash mapping the option names specified in the file to their corresponding option  Reference to a list of text lines. The lines will be written to the file in order, with trailing
1899  value.  new-line characters. Alternatively, may be a string, in which case the string will be written without
1900    modification.
1901    
1902  =back  =back
1903    
1904  =cut  =cut
1905    
1906  sub ReadOptions {  sub PutFile {
1907      # Get the parameters.      # Get the parameters.
1908      my ($fileName) = @_;      my ($fileName, $lines) = @_;
1909      # Open the file.      # Open the output file.
1910      (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");      my $handle = Open(undef, ">$fileName");
1911      # Count the number of records read.      # Count the lines written.
1912      my ($records, $comments) = 0;      if (ref $lines ne 'ARRAY') {
1913      # Create the return hash.          # Here we have a scalar, so we write it raw.
1914      my %retVal = ();          print $handle $lines;
1915      # Loop through the file, accumulating key-value pairs.          Trace("Scalar put to file $fileName.") if T(File => 3);
1916      while (my $line = <CONFIGFILE>) {      } else {
1917          # Denote we've read a line.          # Write the lines one at a time.
1918          $records++;          my $count = 0;
1919          # Determine the line type.          for my $line (@{$lines}) {
1920          if ($line =~ /^\s*[\n\r]/) {              print $handle "$line\n";
1921              # A blank line is a comment.              $count++;
             $comments++;  
         } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {  
             # Here we have an option assignment.  
             retVal{$1} = $2;  
         } elsif ($line =~ /^\s*;/) {  
             # Here we have a text comment.  
             $comments++;  
         } else {  
             # Here we have an invalid line.  
             Trace("Invalid option statement in record $records.") if T(0);  
1922          }          }
1923            Trace("$count lines put to file $fileName.") if T(File => 3);
1924      }      }
1925      # Return the hash created.      # Close the output file.
1926      return %retVal;      close $handle;
1927  }  }
1928    
1929  =head3 GetOptions  =head3 ParseRecord
   
 C<< Tracer::GetOptions(\%defaults, \%options); >>  
   
 Merge a specified set of options into a table of defaults. This method takes two hash references  
 as input and uses the data from the second to update the first. If the second does not exist,  
 there will be no effect. An error will be thrown if one of the entries in the second hash does not  
 exist in the first.  
   
 Consider the following example.  
   
 C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  
   
 In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  
 B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  
 B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and  
 the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  
 will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  
1930    
1931  C<< {databaseType => 'Oracle'} >>      my @fields = Tracer::ParseRecord($line);
1932    
1933  an error will occur because the B<databaseType> option does not exist.  Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1934    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1935    These will automatically be converted.
1936    
1937  =over 4  =over 4
1938    
1939  =item defaults  =item line
   
 Table of default option values.  
   
 =item options  
1940    
1941  Table of overrides, if any.  Line of data containing the tab-delimited fields.
1942    
1943  =item RETURN  =item RETURN
1944    
1945  Returns a reference to the default table passed in as the first parameter.  Returns a list of the fields found in the data line.
1946    
1947  =back  =back
1948    
1949  =cut  =cut
1950    
1951  sub GetOptions {  sub ParseRecord {
1952      # Get the parameters.      # Get the parameter.
1953      my ($defaults, $options) = @_;      my ($line) = @_;
1954      # Check for overrides.      # Remove the trailing new-line, if any.
1955      if ($options) {      chomp $line;
1956          # Loop through the overrides.      # Split the line read into pieces using the tab character.
1957          while (my ($option, $setting) = each %{$options}) {      my @retVal = split /\t/, $line;
1958              # Insure this override exists.      # Trim and fix the escapes in each piece.
1959              if (!exists $defaults->{$option}) {      for my $value (@retVal) {
1960                  croak "Unrecognized option $option encountered.";          # Trim leading whitespace.
1961              } else {          $value =~ s/^\s+//;
1962                  # Apply the override.          # Trim trailing whitespace.
1963                  $defaults->{$option} = $setting;          $value =~ s/\s+$//;
1964              }          # Delete the carriage returns.
1965          }          $value =~ s/\r//g;
1966            # Convert the escapes into their real values.
1967            $value =~ s/\\t/"\t"/ge;
1968            $value =~ s/\\n/"\n"/ge;
1969      }      }
1970      # Return the merged table.      # Return the result.
1971      return $defaults;      return @retVal;
1972  }  }
1973    
1974  =head3 MergeOptions  =head3 Merge
1975    
1976  C<< Tracer::MergeOptions(\%table, \%defaults); >>      my @mergedList = Tracer::Merge(@inputList);
1977    
1978  Merge default values into a hash table. This method looks at the key-value pairs in the  Sort a list of strings and remove duplicates.
 second (default) hash, and if a matching key is not found in the first hash, the default  
 pair is copied in. The process is similar to L</GetOptions>, but there is no error-  
 checking and no return value.  
1979    
1980  =over 4  =over 4
1981    
1982  =item table  =item inputList
1983    
1984  Hash table to be updated with the default values.  List of scalars to sort and merge.
1985    
1986  =item defaults  =item RETURN
1987    
1988  Default values to be merged into the first hash table if they are not already present.  Returns a list containing the same elements sorted in ascending order with duplicates
1989    removed.
1990    
1991  =back  =back
1992    
1993  =cut  =cut
1994    
1995  sub MergeOptions {  sub Merge {
1996      # Get the parameters.      # Get the input list in sort order.
1997      my ($table, $defaults) = @_;      my @inputList = sort @_;
1998      # Loop through the defaults.      # Only proceed if the list has at least two elements.
1999      while (my ($key, $value) = each %{$defaults}) {      if (@inputList > 1) {
2000          if (!exists $table->{$key}) {          # Now we want to move through the list splicing out duplicates.
2001              $table->{$key} = $value;          my $i = 0;
2002            while ($i < @inputList) {
2003                # Get the current entry.
2004                my $thisEntry = $inputList[$i];
2005                # Find out how many elements duplicate the current entry.
2006                my $j = $i + 1;
2007                my $dup1 = $i + 1;
2008                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2009                # If the number is nonzero, splice out the duplicates found.
2010                if ($j > $dup1) {
2011                    splice @inputList, $dup1, $j - $dup1;
2012                }
2013                # Now the element at position $dup1 is different from the element before it
2014                # at position $i. We push $i forward one position and start again.
2015                $i++;
2016          }          }
2017      }      }
2018        # Return the merged list.
2019        return @inputList;
2020  }  }
2021    
2022  =head3 Trace  =head3 Open
2023    
2024  C<< Trace($message); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2025    
2026  Write a trace message to the target location specified in L</TSetup>. If there has not been  Open a file.
 any prior call to B<TSetup>.  
2027    
2028  =over 4  The I<$fileSpec> is essentially the second argument of the PERL C<open>
2029    function. The mode is specified using Unix-like shell information. So, for
2030    example,
2031    
2032  =item message      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2033    
2034  Message to write.  would open for output appended to the specified file, and
2035    
2036  =back      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2037    
2038  =cut  would open a pipe that sorts the records written and removes duplicates. Note
2039    the use of file handle syntax in the Open call. To use anonymous file handles,
2040    code as follows.
2041    
2042  sub Trace {      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
     # Get the parameters.  
     my ($message) = @_;  
     # Get the timestamp.  
     my $timeStamp = Now();  
     # Format the message. Note we strip off any line terminators at the end.  
     my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);  
     # Process according to the destination.  
     if ($Destination eq "TEXT") {  
         # Write the message to the standard output.  
         print "$formatted\n";  
     } elsif ($Destination eq "ERROR") {  
         # Write the message to the error output.  
         print STDERR "$formatted\n";  
     } elsif ($Destination eq "QUEUE") {  
         # Push the message into the queue.  
         push @Queue, "$formatted";  
     } elsif ($Destination eq "HTML") {  
         # Convert the message to HTML and write it to the standard output.  
         my $escapedMessage = CGI::escapeHTML($message);  
         print "<p>$formatted</p>\n";  
     } elsif ($Destination eq "WARN") {  
        # Emit the message as a warning.  
        warn $message;  
     } elsif ($Destination =~ m/^>>/) {  
         # Write the trace message to an output file.  
         (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";  
         print TRACING "$formatted\n";  
         close TRACING;  
         # If the Tee flag is on, echo it to the standard output.  
         if ($TeeFlag) {  
             print "$formatted\n";  
         }  
     }  
 }  
2043    
2044  =head3 T  The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2045    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2046    failed open will throw an exception and the third parameter will be used to construct
2047    an error message. If the parameter is omitted, a standard message is constructed
2048    using the file spec.
2049    
2050        Could not open "/usr/spool/news/twitlog"
2051    
2052  C<< my $switch = T($category, $traceLevel); >>  Note that the mode characters are automatically cleaned from the file name.
2053    The actual error message from the file system will be captured and appended to the
2054    message in any case.
2055    
2056      or      Could not open "/usr/spool/news/twitlog": file not found.
2057    
2058  C<< my $switch = T($traceLevel); >>  In some versions of PERL the only error message we get is a number, which
2059    corresponds to the C++ C<errno> value.
2060    
2061  Return TRUE if the trace level is at or above a specified value and the specified category      Could not open "/usr/spool/news/twitlog": 6.
 is active, else FALSE. If no category is specified, the caller's package name is used.  
2062    
2063  =over 4  =over 4
2064    
2065  =item category  =item fileHandle
2066    
2067  Category to which the message belongs. If not specified, the caller's package name is  File handle. If this parameter is C<undef>, a file handle will be generated
2068  used.  and returned as the value of this method.
2069    
2070  =item traceLevel  =item fileSpec
2071    
2072  Relevant tracing level.  File name and mode, as per the PERL C<open> function.
2073    
2074    =item message (optional)
2075    
2076    Error message to use if the open fails. If omitted, a standard error message
2077    will be generated. In either case, the error information from the file system
2078    is appended to the message. To specify a conditional open that does not throw
2079    an error if it fails, use C<0>.
2080    
2081  =item RETURN  =item RETURN
2082    
2083  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  Returns the name of the file handle assigned to the file, or C<undef> if the
2084    open failed.
2085    
2086  =back  =back
2087    
2088  =cut  =cut
2089    
2090  sub T {  sub Open {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
2091          # Get the parameters.          # Get the parameters.
2092          my ($category, $traceLevel) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2093          if (!defined $traceLevel) {      # Attempt to open the file.
2094              # Here we have no category, so we need to get the calling package.      my $rv = open $fileHandle, $fileSpec;
2095              # The calling package is normally the first parameter. If it is      # If the open failed, generate an error message.
2096              # omitted, the first parameter will be the tracelevel. So, the      if (! $rv) {
2097              # first thing we do is shift the so-called category into the          # Save the system error message.
2098              # $traceLevel variable where it belongs.          my $sysMessage = $!;
2099              $traceLevel = $category;          # See if we need a default message.
2100              my ($package, $fileName, $line) = caller;          if (!$message) {
2101              # If there is no calling package, we default to "main".              # Clean any obvious mode characters and leading spaces from the
2102              if (!$package) {              # filename.
2103                  $category = "main";              my ($fileName) = FindNamePart($fileSpec);
2104              } else {              $message = "Could not open \"$fileName\"";
                 $category = $package;  
             }  
         }  
         # Save the category name.  
         $LastCategory = $category;  
         # Convert it to lower case before we hash it.  
         $category = lc $category;  
         # Use the category and tracelevel to compute the result.  
         if (ref $traceLevel) {  
             Confess("Bad trace level.");  
         } elsif (ref $TraceLevel) {  
             Confess("Bad trace config.");  
2105          }          }
2106          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));          # Terminate with an error using the supplied message and the
2107            # error message from the file system.
2108            Confess("$message: $!");
2109      }      }
2110      # Return the computed result.      # Return the file handle.
2111      return $retVal;      return $fileHandle;
2112  }  }
2113    
2114  =head3 ParseCommand  =head3 FindNamePart
2115    
2116  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2117    
2118  Parse a command line consisting of a list of parameters. The initial parameters may be option  Extract the portion of a file specification that contains the file name.
2119  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  
2120  off and merged into a table of default options. The remainder of the command line is  A file specification is the string passed to an C<open> call. It specifies the file
2121  returned as a list of positional arguments. For example, consider the following invocation.  mode and name. In a truly complex situation, it can specify a pipe sequence. This
2122    method assumes that the file name is whatever follows the first angle bracket
2123    sequence.  So, for example, in the following strings the file name is
2124    C</usr/fig/myfile.txt>.
2125    
2126  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      >>/usr/fig/myfile.txt
2127        </usr/fig/myfile.txt
2128        | sort -u > /usr/fig/myfile.txt
2129    
2130  In this case, the list @words will be treated as a command line. There are two options available,  If the method cannot find a file name using its normal methods, it will return the
2131  B<errors> and B<logFile>. If @words has the following format  whole incoming string.
2132    
2133  C<< -logFile=error.log apple orange rutabaga >>  =over 4
2134    
2135  then at the end of the invocation, C<$options> will be  =item fileSpec
2136    
2137  C<< { errors => 0, logFile => 'error.log' } >>  File specification string from which the file name is to be extracted.
2138    
2139  and C<@arguments> will contain  =item RETURN
2140    
2141    Returns a three-element list. The first element contains the file name portion of
2142    the specified string, or the whole string if a file name cannot be found via normal
2143    methods. The second element contains the start position of the file name portion and
2144    the third element contains the length.
2145    
2146  C<< apple orange rutabaga >>  =back
2147    
2148  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  =cut
2149  support for quote characters.  #: Return Type $;
2150    sub FindNamePart {
2151        # Get the parameters.
2152        my ($fileSpec) = @_;
2153        # Default to the whole input string.
2154        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2155        # Parse out the file name if we can.
2156        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2157            $retVal = $2;
2158            $len = length $retVal;
2159            $pos = (length $fileSpec) - (length $3) - $len;
2160        }
2161        # Return the result.
2162        return ($retVal, $pos, $len);
2163    }
2164    
2165    =head3 OpenDir
2166    
2167        my @files = OpenDir($dirName, $filtered, $flag);
2168    
2169    Open a directory and return all the file names. This function essentially performs
2170    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2171    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2172    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2173    filtered out of the return list. If the directory does not open and I<$flag> is not
2174    set, an exception is thrown. So, for example,
2175    
2176        my @files = OpenDir("/Volumes/fig/contigs", 1);
2177    
2178    is effectively the same as
2179    
2180        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2181        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2182    
2183    Similarly, the following code
2184    
2185        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2186    
2187    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2188    automatically returns an empty list if the directory fails to open.
2189    
2190  =over 4  =over 4
2191    
2192  =item optionTable  =item dirName
2193    
2194  Table of default options.  Name of the directory to open.
2195    
2196  =item inputList  =item filtered
2197    
2198  List of words on the command line.  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2199    from the list, else FALSE.
2200    
2201  =item RETURN  =item flag
2202    
2203  Returns a reference to the option table and a list of the positional arguments.  TRUE if a failure to open is okay, else FALSE
2204    
2205  =back  =back
2206    
2207  =cut  =cut
2208    #: Return Type @;
2209  sub ParseCommand {  sub OpenDir {
2210      # Get the parameters.      # Get the parameters.
2211      my ($optionTable, @inputList) = @_;      my ($dirName, $filtered, $flag) = @_;
2212      # Process any options in the input list.      # Declare the return variable.
2213      my %overrides = ();      my @retVal = ();
2214      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      # Open the directory.
2215          # Get the current option.      if (opendir(my $dirHandle, $dirName)) {
2216          my $arg = shift @inputList;          # The directory opened successfully. Get the appropriate list according to the
2217          # Pull out the option name.          # strictures of the filter parameter.
2218          $arg =~ /^-([^=]*)/g;          if ($filtered) {
2219          my $name = $1;              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
         # Check for an option value.  
         if ($arg =~ /\G=(.*)$/g) {  
             # Here we have a value for the option.  
             $overrides{$name} = UnEscape($1);  
2220          } else {          } else {
2221              # Here there is no value, so we use 1.              @retVal = readdir $dirHandle;
             $overrides{$name} = 1;  
         }  
2222      }      }
2223      # Merge the options into the defaults.      } elsif (! $flag) {
2224      GetOptions($optionTable, \%overrides);          # Here the directory would not open and it's considered an error.
2225      # Translate the remaining parameters.          Confess("Could not open directory $dirName.");
     my @retVal = ();  
     for my $inputParm (@inputList) {  
         push @retVal, UnEscape($inputParm);  
2226      }      }
2227      # Return the results.      # Return the result.
2228      return ($optionTable, @retVal);      return @retVal;
2229  }  }
2230    
 =head3 Escape  
2231    
2232  C<< my $codedString = Tracer::Escape($realString); >>  =head3 Insure
2233    
2234  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines      Insure($dirName, $chmod);
2235  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
2236  result is to reverse the effect of L</UnEscape>.  Insure a directory is present.
2237    
2238  =over 4  =over 4
2239    
2240  =item realString  =item dirName
2241    
2242  String to escape.  Name of the directory to check. If it does not exist, it will be created.
2243    
2244  =item RETURN  =item chmod (optional)
2245    
2246  Escaped equivalent of the real string.  Security privileges to be given to the directory if it is created.
2247    
2248  =back  =back
2249    
2250  =cut  =cut
2251    
2252  sub Escape {  sub Insure {
2253      # Get the parameter.      my ($dirName, $chmod) = @_;
2254      my ($realString) = @_;      if (! -d $dirName) {
2255      # Initialize the return variable.          Trace("Creating $dirName directory.") if T(2);
2256      my $retVal = "";          eval {
2257      # Loop through the parameter string, looking for sequences to escape.              mkpath $dirName;
2258      while (length $realString > 0) {              # If we have permissions specified, set them here.
2259          # Look for the first sequence to escape.              if (defined($chmod)) {
2260          if ($realString =~ /^(.*?)([\n\t\r\\])/) {                  chmod $chmod, $dirName;
2261              # Here we found it. The text preceding the sequence is in $1. The sequence              }
2262              # itself is in $2. First, move the clear text to the return variable.          };
2263              $retVal .= $1;          if ($@) {
2264              # Strip the processed section off the real string.              Confess("Error creating $dirName: $@");
2265              $realString = substr $realString, (length $2) + (length $1);          }
             # Get the matched character.  
             my $char = $2;  
             # If we have a CR, we are done.  
             if ($char ne "\r") {  
                 # It's not a CR, so encode the escape sequence.  
                 $char =~ tr/\t\n/tn/;  
                 $retVal .= "\\" . $char;  
2266              }              }
2267    }
2268    
2269    =head3 ChDir
2270    
2271        ChDir($dirName);
2272    
2273    Change to the specified directory.
2274    
2275    =over 4
2276    
2277    =item dirName
2278    
2279    Name of the directory to which we want to change.
2280    
2281    =back
2282    
2283    =cut
2284    
2285    sub ChDir {
2286        my ($dirName) = @_;
2287        if (! -d $dirName) {
2288            Confess("Cannot change to directory $dirName: no such directory.");
2289          } else {          } else {
2290              # Here there are no more escape sequences. The rest of the string is          Trace("Changing to directory $dirName.") if T(File => 4);
2291              # transferred unmodified.          my $okFlag = chdir $dirName;
2292              $retVal .= $realString;          if (! $okFlag) {
2293              $realString = "";              Confess("Error switching to directory $dirName.");
2294          }          }
2295      }      }
     # Return the result.  
     return $retVal;  
2296  }  }
2297    
2298  =head3 UnEscape  =head3 SetPermissions
2299    
2300  C<< my $realString = Tracer::UnEscape($codedString); >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2301    
2302  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Set the permissions for a directory and all the files and folders inside it.
2303  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  In addition, the group ownership will be changed to the specified value.
2304  be deleted.  
2305    This method is more vulnerable than most to permission and compatability
2306    problems, so it does internal error recovery.
2307    
2308  =over 4  =over 4
2309    
2310  =item codedString  =item dirName
2311    
2312  String to un-escape.  Name of the directory to process.
2313    
2314  =item RETURN  =item group
2315    
2316  Returns a copy of the original string with the escape sequences converted to their actual  Name of the group to be assigned.
2317  values.  
2318    =item mask
2319    
2320    Permission mask. Bits that are C<1> in this mask will be ORed into the
2321    permission bits of any file or directory that does not already have them
2322    set to 1.
2323    
2324    =item otherMasks
2325    
2326    Map of search patterns to permission masks. If a directory name matches
2327    one of the patterns, that directory and all its members and subdirectories
2328    will be assigned the new pattern. For example, the following would
2329    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2330    
2331        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2332    
2333    The list is ordered, so the following would use 0777 for C<tmp1> and
2334    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2335    
2336        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2337                                                       '^tmp' => 0666);
2338    
2339    Note that the pattern matches are all case-insensitive, and only directory
2340    names are matched, not file names.
2341    
2342  =back  =back
2343    
2344  =cut  =cut
2345    
2346  sub UnEscape {  sub SetPermissions {
2347      # Get the parameter.      # Get the parameters.
2348      my ($codedString) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2349      # Initialize the return variable.      # Set up for error recovery.
2350      my $retVal = "";      eval {
2351      # Only proceed if the incoming string is nonempty.          # Switch to the specified directory.
2352      if (defined $codedString) {          ChDir($dirName);
2353          # Loop through the parameter string, looking for escape sequences. We can't do          # Get the group ID.
2354          # translating because it causes problems with the escaped slash. ("\\t" becomes          my $gid = getgrnam($group);
2355          # "\<tab>" no matter what we do.)          # Get the mask for tracing.
2356          while (length $codedString > 0) {          my $traceMask = sprintf("%04o", $mask) . "($mask)";
2357              # Look for the first escape sequence.          Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2358              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {          my $fixCount = 0;
2359                  # Here we found it. The text preceding the sequence is in $1. The sequence          my $lookCount = 0;
2360                  # itself is in $2. First, move the clear text to the return variable.          # @dirs will be a stack of directories to be processed.
2361                  $retVal .= $1;          my @dirs = (getcwd());
2362                  $codedString = substr $codedString, (2 + length $1);          while (scalar(@dirs) > 0) {
2363                  # Get the escape value.              # Get the current directory.
2364                  my $char = $2;              my $dir = pop @dirs;
2365                  # If we have a "\r", we are done.              # Check for a match to one of the specified directory names. To do
2366                  if ($char ne 'r') {              # that, we need to pull the individual part of the name off of the
2367                      # Here it's not an 'r', so we convert it.              # whole path.
2368                      $char =~ tr/\\tn/\\\t\n/;              my $simpleName = $dir;
2369                      $retVal .= $char;              if ($dir =~ m!/([^/]+)$!) {
2370                    $simpleName = $1;
2371                }
2372                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2373                # Search for a match.
2374                my $match = 0;
2375                my $i;
2376                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2377                    my $pattern = $otherMasks[$i];
2378                    if ($simpleName =~ /$pattern/i) {
2379                        $match = 1;
2380                    }
2381                  }                  }
2382                # Check for a match. Note we use $i-1 because the loop added 2
2383                # before terminating due to the match.
2384                if ($match && $otherMasks[$i-1] != $mask) {
2385                    # This directory matches one of the incoming patterns, and it's
2386                    # a different mask, so we process it recursively with that mask.
2387                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2388              } else {              } else {
2389                  # Here there are no more escape sequences. The rest of the string is                  # Here we can process normally. Get all of the non-hidden members.
2390                  # transferred unmodified.                  my @submems = OpenDir($dir, 1);
2391                  $retVal .= $codedString;                  for my $submem (@submems) {
2392                  $codedString = "";                      # Get the full name.
2393                        my $thisMem = "$dir/$submem";
2394                        Trace("Checking member $thisMem.") if T(4);
2395                        $lookCount++;
2396                        if ($lookCount % 1000 == 0) {
2397                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2398                        }
2399                        # Fix the group.
2400                        chown -1, $gid, $thisMem;
2401                        # Insure this member is not a symlink.
2402                        if (! -l $thisMem) {
2403                            # Get its info.
2404                            my $fileInfo = stat $thisMem;
2405                            # Only proceed if we got the info. Otherwise, it's a hard link
2406                            # and we want to skip it anyway.
2407                            if ($fileInfo) {
2408                                my $fileMode = $fileInfo->mode;
2409                                if (($fileMode & $mask) != $mask) {
2410                                    # Fix this member.
2411                                    $fileMode |= $mask;
2412                                    chmod $fileMode, $thisMem;
2413                                    $fixCount++;
2414                                }
2415                                # If it's a subdirectory, stack it.
2416                                if (-d $thisMem) {
2417                                    push @dirs, $thisMem;
2418                                }
2419              }              }
2420          }          }
2421      }      }
2422      # Return the result.              }
2423      return $retVal;          }
2424            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2425        };
2426        # Check for an error.
2427        if ($@) {
2428            Confess("SetPermissions error: $@");
2429        }
2430  }  }
2431    
2432  =head3 ParseRecord  =head3 GetLine
2433    
2434  C<< my @fields = Tracer::ParseRecord($line); >>      my @data = Tracer::GetLine($handle);
2435    
2436  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Read a line of data from a tab-delimited file.
 and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
 These will automatically be converted.  
2437    
2438  =over 4  =over 4
2439    
2440  =item line  =item handle
2441    
2442  Line of data containing the tab-delimited fields.  Open file handle from which to read.
2443    
2444  =item RETURN  =item RETURN
2445    
2446  Returns a list of the fields found in the data line.  Returns a list of the fields in the record read. The fields are presumed to be
2447    tab-delimited. If we are at the end of the file, then an empty list will be
2448    returned. If an empty line is read, a single list item consisting of a null
2449    string will be returned.
2450    
2451  =back  =back
2452    
2453  =cut  =cut
2454    
2455  sub ParseRecord {  sub GetLine {
2456      # Get the parameter.      # Get the parameters.
2457      my ($line) = @_;      my ($handle) = @_;
2458      # Remove the trailing new-line, if any.      # Declare the return variable.
2459      chomp $line;      my @retVal = ();
2460      # Split the line read into pieces using the tab character.      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2461      my @retVal = split /\t/, $line;      # Read from the file.
2462      # Trim and fix the escapes in each piece.      my $line = <$handle>;
2463      for my $value (@retVal) {      # Only proceed if we found something.
2464          # Trim leading whitespace.      if (defined $line) {
2465          $value =~ s/^\s+//;          # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2466          # Trim trailing whitespace.          # upload control and have a nonstandard EOL combination.
2467          $value =~ s/\s+$//;          $line =~ s/(\r|\n)+$//;
2468          # Delete the carriage returns.          # Here we do some fancy tracing to help in debugging complicated EOL marks.
2469          $value =~ s/\r//g;          if (T(File => 4)) {
2470          # Convert the escapes into their real values.              my $escapedLine = $line;
2471          $value =~ s/\\t/"\t"/ge;              $escapedLine =~ s/\n/\\n/g;
2472          $value =~ s/\\n/"\n"/ge;              $escapedLine =~ s/\r/\\r/g;
2473                $escapedLine =~ s/\t/\\t/g;
2474                Trace("Line read: -->$escapedLine<--");
2475            }
2476            # If the line is empty, return a single empty string; otherwise, parse
2477            # it into fields.
2478            if ($line eq "") {
2479                push @retVal, "";
2480            } else {
2481                push @retVal, split /\t/,$line;
2482            }
2483        } else {
2484            # Trace the reason the read failed.
2485            Trace("End of file: $!") if T(File => 3);
2486      }      }
2487      # Return the result.      # Return the result.
2488      return @retVal;      return @retVal;
2489  }  }
2490    
2491  =head3 Merge  =head3 PutLine
2492    
2493  C<< my @mergedList = Tracer::Merge(@inputList); >>      Tracer::PutLine($handle, \@fields, $eol);
2494    
2495  Sort a list of strings and remove duplicates.  Write a line of data to a tab-delimited file. The specified field values will be
2496    output in tab-separated form, with a trailing new-line.
2497    
2498  =over 4  =over 4
2499    
2500  =item inputList  =item handle
2501    
2502  List of scalars to sort and merge.  Output file handle.
2503    
2504  =item RETURN  =item fields
2505    
2506  Returns a list containing the same elements sorted in ascending order with duplicates  List of field values.
2507  removed.  
2508    =item eol (optional)
2509    
2510    End-of-line character (default is "\n").
2511    
2512  =back  =back
2513    
2514  =cut  =cut
2515    
2516  sub Merge {  sub PutLine {
2517      # Get the input list in sort order.      # Get the parameters.
2518      my @inputList = sort @_;      my ($handle, $fields, $eol) = @_;
2519      # Only proceed if the list has at least two elements.      # Write the data.
2520      if (@inputList > 1) {      print $handle join("\t", @{$fields}) . ($eol || "\n");
         # Now we want to move through the list splicing out duplicates.  
         my $i = 0;  
         while ($i < @inputList) {  
             # Get the current entry.  
             my $thisEntry = $inputList[$i];  
             # Find out how many elements duplicate the current entry.  
             my $j = $i + 1;  
             my $dup1 = $i + 1;  
             while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };  
             # If the number is nonzero, splice out the duplicates found.  
             if ($j > $dup1) {  
                 splice @inputList, $dup1, $j - $dup1;  
             }  
             # Now the element at position $dup1 is different from the element before it  
             # at position $i. We push $i forward one position and start again.  
             $i++;  
         }  
     }  
     # Return the merged list.  
     return @inputList;  
2521  }  }
2522    
 =head3 GetFile  
2523    
 C<< my @fileContents = Tracer::GetFile($fileName); >>  
2524    
2525      or  =head2 Other Useful Methods
2526    
2527  C<< my $fileContents = Tracer::GetFile($fileName); >>  =head3 ParseParm
2528    
2529  Return the entire contents of a file. In list context, line-ends are removed and      my $listValue = Tracer::ParseParm($string);
2530  each line is a list element. In scalar context, line-ends are replaced by C<\n>.  
2531    Convert a parameter into a list reference. If the parameter is undefined,
2532    an undefined value will be returned. Otherwise, it will be parsed as a
2533    comma-separated list of values.
2534    
2535  =over 4  =over 4
2536    
2537  =item fileName  =item string
2538    
2539  Name of the file to read.  Incoming string.
2540    
2541  =item RETURN  =item RETURN
2542    
2543  In a list context, returns the entire file as a list with the line terminators removed.  Returns a reference to a list of values, or C<undef> if the incoming value
2544  In a scalar context, returns the entire file as a string. If an error occurs opening  was undefined.
 the file, an empty list will be returned.  
2545    
2546  =back  =back
2547    
2548  =cut  =cut
2549    
2550  sub GetFile {  sub ParseParm {
2551      # Get the parameters.      # Get the parameters.
2552      my ($fileName) = @_;      my ($string) = @_;
2553      # Declare the return variable.      # Declare the return variable.
2554      my @retVal = ();      my $retVal;
2555      # Open the file for input.      # Check for data.
2556      my $ok = open INPUTFILE, "<$fileName";      if (defined $string) {
2557      if (!$ok) {          # We have some, so split it into a list.
2558          # If we had an error, trace it. We will automatically return a null value.          $retVal = [ split /\s*,\s*/, $string];
         Trace("Could not open \"$fileName\" for input: $!") if T(0);  
     } else {  
         # Read the whole file into the return variable, stripping off any terminator  
         # characters.  
         my $lineCount = 0;  
         while (my $line = <INPUTFILE>) {  
             $lineCount++;  
             $line = Strip($line);  
             push @retVal, $line;  
2559          }          }
2560          # Close it.      # Return the result.
2561          close INPUTFILE;      return $retVal;
         my $actualLines = @retVal;  
2562      }      }
2563      # Return the file's contents in the desired format.  
2564      if (wantarray) {  
2565          return @retVal;  
2566      } else {  
2567          return join "\n", @retVal;  =head3 Now
2568    
2569        my $string = Tracer::Now();
2570    
2571    Return a displayable time stamp containing the local time.
2572    
2573    =cut
2574    
2575    sub Now {
2576        my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
2577        my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2578                     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2579        return $retVal;
2580      }      }
2581    
2582    # Pad a number to 2 digits.
2583    sub _p2 {
2584        my ($value) = @_;
2585        $value = "0$value" if ($value < 10);
2586        return $value;
2587  }  }
2588    
2589  =head3 QTrace  =head3 Escape
2590    
2591  C<< my $data = QTrace($format); >>      my $codedString = Tracer::Escape($realString);
2592    
2593  Return the queued trace data in the specified format.  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2594    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2595    result is to reverse the effect of L</UnEscape>.
2596    
2597  =over 4  =over 4
2598    
2599  =item format  =item realString
2600    
2601  C<html> to format the data as an HTML list, C<text> to format it as straight text.  String to escape.
2602    
2603    =item RETURN
2604    
2605    Escaped equivalent of the real string.
2606    
2607  =back  =back
2608    
2609  =cut  =cut
2610    
2611  sub QTrace {  sub Escape {
2612      # Get the parameter.      # Get the parameter.
2613      my ($format) = @_;      my ($realString) = @_;
2614      # Create the return variable.      # Initialize the return variable.
2615      my $retVal = "";      my $retVal = "";
2616      # Only proceed if there is an actual queue.      # Loop through the parameter string, looking for sequences to escape.
2617      if (@Queue) {      while (length $realString > 0) {
2618          # Process according to the format.          # Look for the first sequence to escape.
2619          if ($format =~ m/^HTML$/i) {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2620              # Convert the queue into an HTML list.              # Here we found it. The text preceding the sequence is in $1. The sequence
2621              $retVal = "<ul>\n";              # itself is in $2. First, move the clear text to the return variable.
2622              for my $line (@Queue) {              $retVal .= $1;
2623                  my $escapedLine = CGI::escapeHTML($line);              # Strip the processed section off the real string.
2624                  $retVal .= "<li>$escapedLine</li>\n";              $realString = substr $realString, (length $2) + (length $1);
2625                # Get the matched character.
2626                my $char = $2;
2627                # If we have a CR, we are done.
2628                if ($char ne "\r") {
2629                    # It's not a CR, so encode the escape sequence.
2630                    $char =~ tr/\t\n/tn/;
2631                    $retVal .= "\\" . $char;
2632              }              }
2633              $retVal .= "</ul>\n";          } else {
2634          } elsif ($format =~ m/^TEXT$/i) {              # Here there are no more escape sequences. The rest of the string is
2635              # Convert the queue into a list of text lines.              # transferred unmodified.
2636              $retVal = join("\n", @Queue) . "\n";              $retVal .= $realString;
2637                $realString = "";
2638          }          }
         # Clear the queue.  
         @Queue = ();  
2639      }      }
2640      # Return the formatted list.      # Return the result.
2641      return $retVal;      return $retVal;
2642  }  }
2643    
2644  =head3 Confess  =head3 UnEscape
2645    
2646  C<< Confess($message); >>      my $realString = Tracer::UnEscape($codedString);
2647    
2648  Trace the call stack and abort the program with the specified message. When used with  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2649  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2650  So, for example  be deleted.
2651    
2652  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  =over 4
2653    
2654  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =item codedString
2655    
2656  =over 4  String to un-escape.
2657    
2658  =item message  =item RETURN
2659    
2660  Message to include in the trace.  Returns a copy of the original string with the escape sequences converted to their actual
2661    values.
2662    
2663  =back  =back
2664    
2665  =cut  =cut
2666    
2667  sub Confess {  sub UnEscape {
2668      # Get the parameters.      # Get the parameter.
2669      my ($message) = @_;      my ($codedString) = @_;
2670      # Trace the call stack.      # Initialize the return variable.
2671      Cluck($message);      my $retVal = "";
2672      # Abort the program.      # Only proceed if the incoming string is nonempty.
2673      croak(">>> $message");      if (defined $codedString) {
2674            # Loop through the parameter string, looking for escape sequences. We can't do
2675            # translating because it causes problems with the escaped slash. ("\\t" becomes
2676            # "\<tab>" no matter what we do.)
2677            while (length $codedString > 0) {
2678                # Look for the first escape sequence.
2679                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2680                    # Here we found it. The text preceding the sequence is in $1. The sequence
2681                    # itself is in $2. First, move the clear text to the return variable.
2682                    $retVal .= $1;
2683                    $codedString = substr $codedString, (2 + length $1);
2684                    # Get the escape value.
2685                    my $char = $2;
2686                    # If we have a "\r", we are done.
2687                    if ($char ne 'r') {
2688                        # Here it's not an 'r', so we convert it.
2689                        $char =~ tr/\\tn/\\\t\n/;
2690                        $retVal .= $char;
2691  }  }
2692                } else {
2693  =head3 Assert                  # Here there are no more escape sequences. The rest of the string is
2694                    # transferred unmodified.
2695  C<< Assert($condition1, $condition2, ... $conditionN); >>                  $retVal .= $codedString;
2696                    $codedString = "";
 Return TRUE if all the conditions are true. This method can be used in conjunction with  
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
   
 C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  
   
 Will abort the program with a stack trace if the value of C<$recNum> is negative.  
   
 =cut  
 sub Assert {  
     my $retVal = 1;  
     LOOP: for my $condition (@_) {  
         if (! $condition) {  
             $retVal = 0;  
             last LOOP;  
2697          }          }
2698      }      }
2699        }
2700        # Return the result.
2701      return $retVal;      return $retVal;
2702  }  }
2703    
2704  =head3 Cluck  =head3 Percent
2705    
2706  C<< Cluck($message); >>      my $percent = Tracer::Percent($number, $base);
2707    
2708  Trace the call stack. Note that for best results, you should qualify the call with a  Returns the percent of the base represented by the given number. If the base
2709  trace condition. For example,  is zero, returns zero.
2710    
2711  C<< Cluck("Starting record parse.") if T(3); >>  =over 4
2712    
2713  will only trace the stack if the trace level for the package is 3 or more.  =item number
2714    
2715  =over 4  Percent numerator.
2716    
2717  =item message  =item base
2718    
2719  Message to include in the trace.  Percent base.
2720    
2721    =item RETURN
2722    
2723    Returns the percentage of the base represented by the numerator.
2724    
2725  =back  =back
2726    
2727  =cut  =cut
2728    
2729  sub Cluck {  sub Percent {
2730      # Get the parameters.      # Get the parameters.
2731      my ($message) = @_;      my ($number, $base) = @_;
2732      # Trace what's happening.      # Declare the return variable.
2733      Trace("Stack trace for event: $message");      my $retVal = 0;
2734      my $confession = longmess($message);      # Compute the percent.
2735      # Convert the confession to a series of trace messages. Note we skip any      if ($base != 0) {
2736      # messages relating to calls into Tracer.          $retVal = $number * 100 / $base;
     for my $line (split /\s*\n/, $confession) {  
         Trace($line) if ($line !~ /Tracer\.pm/);  
2737      }      }
2738        # Return the result.
2739        return $retVal;
2740  }  }
2741    
2742  =head3 Min  =head3 Min
2743    
2744  C<< my $min = Min($value1, $value2, ... $valueN); >>      my $min = Min($value1, $value2, ... $valueN);
2745    
2746  Return the minimum argument. The arguments are treated as numbers.  Return the minimum argument. The arguments are treated as numbers.
2747    
# Line 1573  Line 2774 
2774    
2775  =head3 Max  =head3 Max
2776    
2777  C<< my $max = Max($value1, $value2, ... $valueN); >>      my $max = Max($value1, $value2, ... $valueN);
2778    
2779  Return the maximum argument. The arguments are treated as numbers.  Return the maximum argument. The arguments are treated as numbers.
2780    
# Line 1604  Line 2805 
2805      return $retVal;      return $retVal;
2806  }  }
2807    
 =head3 AddToListMap  
   
 C<< Tracer::AddToListMap(\%hash, $key, $value); >>  
   
 Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  
 is created for the key. Otherwise, the new value is pushed onto the list.  
   
 =over 4  
   
 =item hash  
   
 Reference to the target hash.  
   
 =item key  
   
 Key for which the value is to be added.  
   
 =item value  
   
 Value to add to the key's value list.  
   
 =back  
   
 =cut  
   
 sub AddToListMap {  
     # Get the parameters.  
     my ($hash, $key, $value) = @_;  
     # Process according to whether or not the key already has a value.  
     if (! exists $hash->{$key}) {  
         $hash->{$key} = [$value];  
     } else {  
         push @{$hash->{$key}}, $value;  
     }  
 }  
   
2808  =head3 DebugMode  =head3 DebugMode
2809    
2810  C<< if (Tracer::DebugMode) { ...code... } >>      if (Tracer::DebugMode) { ...code... }
2811    
2812  Return TRUE if debug mode has been turned on, else output an error  Return TRUE if debug mode has been turned on, else abort.
 page and return FALSE.  
2813    
2814  Certain CGI scripts are too dangerous to exist in the production  Certain CGI scripts are too dangerous to exist in the production
2815  environment. This method provides a simple way to prevent them  environment. This method provides a simple way to prevent them
2816  from working unless they are explicitly turned on by creating a password  from working unless they are explicitly turned on by creating a password
2817  cookie via the B<SetPassword> script.  If debugging mode  cookie via the B<SetPassword> script.  If debugging mode
2818  is not turned on, an error web page will be output directing the  is not turned on, an error will occur.
 user to enter in the correct password.  
2819    
2820  =cut  =cut
2821    
# Line 1665  Line 2828 
2828      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
2829          $retVal = 1;          $retVal = 1;
2830      } else {      } else {
2831          # Here debug mode is off, so we generate an error page.          # Here debug mode is off, so we generate an error.
2832          my $pageString = PageBuilder::Build("<Html/ErrorPage.html", {}, "Html");          Confess("Cannot use this facility without logging in.");
         print $pageString;  
2833      }      }
2834      # Return the determination indicator.      # Return the determination indicator.
2835      return $retVal;      return $retVal;
# Line 1675  Line 2837 
2837    
2838  =head3 Strip  =head3 Strip
2839    
2840  C<< my $string = Tracer::Strip($line); >>      my $string = Tracer::Strip($line);
2841    
2842  Strip all line terminators off a string. This is necessary when dealing with files  Strip all line terminators off a string. This is necessary when dealing with files
2843  that may have been transferred back and forth several times among different  that may have been transferred back and forth several times among different
# Line 1707  Line 2869 
2869    
2870  =head3 Pad  =head3 Pad
2871    
2872  C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
2873    
2874  Pad a string to a specified length. The pad character will be a  Pad a string to a specified length. The pad character will be a
2875  space, and the padding will be on the right side unless specified  space, and the padding will be on the right side unless specified
# Line 1778  Line 2940 
2940    
2941  =head3 TICK  =head3 TICK
2942    
2943  C<< my @results = TICK($commandString); >>      my @results = TICK($commandString);
2944    
2945  Perform a back-tick operation on a command. If this is a Windows environment, any leading  Perform a back-tick operation on a command. If this is a Windows environment, any leading
2946  dot-slash (C<./> will be removed. So, for example, if you were doing  dot-slash (C<./> will be removed. So, for example, if you were doing
# Line 1790  Line 2952 
2952    
2953      TICK("./protein.cgi")      TICK("./protein.cgi")
2954    
2955  it will work correctly in both environments.  it will work correctly in both environments.
2956    
2957    =over 4
2958    
2959    =item commandString
2960    
2961    The command string to pass to the system.
2962    
2963    =item RETURN
2964    
2965    Returns the standard output from the specified command, as a list.
2966    
2967    =back
2968    
2969    =cut
2970    #: Return Type @;
2971    sub TICK {
2972        # Get the parameters.
2973        my ($commandString) = @_;
2974        # Chop off the dot-slash if this is Windows.
2975        if ($FIG_Config::win_mode) {
2976            $commandString =~ s!^\./!!;
2977        }
2978        # Activate the command and return the result.
2979        return `$commandString`;
2980    }
2981    
2982    
2983    =head3 CommaFormat
2984    
2985        my $formatted = Tracer::CommaFormat($number);
2986    
2987    Insert commas into a number.
2988    
2989    =over 4
2990    
2991    =item number
2992    
2993    A sequence of digits.
2994    
2995    =item RETURN
2996    
2997    Returns the same digits with commas strategically inserted.
2998    
2999    =back
3000    
3001    =cut
3002    
3003    sub CommaFormat {
3004        # Get the parameters.
3005        my ($number) = @_;
3006        # Pad the length up to a multiple of three.
3007        my $padded = "$number";
3008        $padded = " " . $padded while length($padded) % 3 != 0;
3009        # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3010        # cause the delimiters to be included in the output stream. The
3011        # GREP removes the empty strings in between the delimiters.
3012        my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3013        # Clean out the spaces.
3014        $retVal =~ s/ //g;
3015        # Return the result.
3016        return $retVal;
3017    }
3018    
3019    
3020    =head3 CompareLists
3021    
3022        my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3023    
3024    Compare two lists of tuples, and return a hash analyzing the differences. The lists
3025    are presumed to be sorted alphabetically by the value in the $keyIndex column.
3026    The return value contains a list of items that are only in the new list
3027    (inserted) and only in the old list (deleted).
3028    
3029  =over 4  =over 4
3030    
3031  =item commandString  =item newList
   
 The command string to pass to the system.  
3032    
3033  =item RETURN  Reference to a list of new tuples.
3034    
3035  Returns the standard output from the specified command, as a list.  =item oldList
3036    
3037  =back  Reference to a list of old tuples.
3038    
3039  =cut  =item keyIndex (optional)
 #: Return Type @;  
 sub TICK {  
     # Get the parameters.  
     my ($commandString) = @_;  
     # Chop off the dot-slash if this is Windows.  
     if ($FIG_Config::win_mode) {  
         $commandString =~ s!^\./!!;  
     }  
     # Activate the command and return the result.  
     return `$commandString`;  
 }  
3040    
3041  =head3 ScriptSetup  Index into each tuple of its key field. The default is 0.
3042    
3043  C<< my ($query, $varHash) = ScriptSetup(); >>  =item RETURN
3044    
3045  Perform standard tracing and debugging setup for scripts. The value returned is  Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3046  the CGI object followed by a pre-built variable hash.  list (inserted) followed by a reference to the list of items that are only in the old
3047    list (deleted).
3048    
3049  The C<Trace> query parameter is used to determine whether or not tracing is active and  =back
 which trace modules (other than C<Tracer> and C<FIG>) should be turned on. Specifying  
 the C<CGI> trace module will trace parameter and environment information. Parameters are  
 traced at level 3 and environment variables at level 4. At the end of the script, the  
 client should call L</ScriptFinish> to output the web page.  
3050    
3051  =cut  =cut
3052    
3053  sub ScriptSetup {  sub CompareLists {
3054      # Get the CGI query object.      # Get the parameters.
3055      my $query = CGI->new();      my ($newList, $oldList, $keyIndex) = @_;
3056      # Check for tracing. Set it up if the user asked for it.      if (! defined $keyIndex) {
3057      if ($query->param('Trace')) {          $keyIndex = 0;
3058          # Set up tracing to be queued for display at the bottom of the web page.      }
3059          TSetup($query->param('Trace') . " FIG Tracer", "QUEUE");      # Declare the return variables.
3060          # Trace the parameter and environment data.      my ($inserted, $deleted) = ([], []);
3061          if (T(CGI => 3)) {      # Loop through the two lists simultaneously.
3062              # Here we want to trace the parameter data.      my ($newI, $oldI) = (0, 0);
3063              my @names = $query->param;      my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3064              for my $parmName (sort @names) {      while ($newI < $newN || $oldI < $oldN) {
3065                  # Note we skip "Trace", which is for our use only.          # Get the current object in each list. Note that if one
3066                  if ($parmName ne 'Trace') {          # of the lists is past the end, we'll get undef.
3067                      my @values = $query->param($parmName);          my $newItem = $newList->[$newI];
3068                      Trace("CGI: $parmName = " . join(", ", @values));          my $oldItem = $oldList->[$oldI];
3069                  }          if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3070              }              # The old item is not in the new list, so mark it deleted.
3071          }              push @{$deleted}, $oldItem;
3072          if (T(CGI => 4)) {              $oldI++;
3073              # Here we want the environment data too.          } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3074              for my $envName (sort keys %ENV) {              # The new item is not in the old list, so mark it inserted.
3075                  Trace("ENV: $envName = $ENV{$envName}");              push @{$inserted}, $newItem;
3076              }              $newI++;
3077          }          } else {
3078      } else {              # The item is in both lists, so push forward.
3079          # Here tracing is to be turned off. All we allow is errors traced into the              $oldI++;
3080          # error log.              $newI++;
         TSetup("0", "WARN");  
3081      }      }
     # Create the variable hash.  
     my $varHash = { DebugData => '' };  
     # If we're in DEBUG mode, set up the debug mode data for forms.  
     if (Tracer::DebugMode) {  
         $varHash->{DebugData} = GetFile("Html/DebugFragment.html");  
3082      }      }
3083      # Return the query object and variable hash.      # Return the result.
3084      return ($query, $varHash);      return ($inserted, $deleted);
3085  }  }
3086    
3087  =head3 ScriptFinish  =head3 GenerateURL
   
 C<< ScriptFinish($webData, $varHash); >>  
3088    
3089  Output a web page at the end of a script. Either the string to be output or the      my $queryUrl = Tracer::GenerateURL($page, %parameters);
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
3090    
3091  A typical standard script would loook like the following.  Generate a GET-style URL for the specified page with the specified parameter
3092    names and values. The values will be URL-escaped automatically. So, for
3093    example
3094    
3095      BEGIN {      Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
3096    
3097      my ($query, $varHash) = ScriptSetup();  would return
     eval {  
         # ... get data from $query, put it in $varHash ...  
     };  
     if ($@) {  
         Trace("Script Error: $@") if T(0);  
     }  
     ScriptFinish("Html/MyTemplate.html", $varHash);  
3098    
3099  The idea here is that even if the script fails, you'll see trace messages and      form.cgi?type=1;string=%22high%20pass%22%20or%20highway
 useful output.  
3100    
3101  =over 4  =over 4
3102    
3103  =item webData  =item page
3104    
3105  A string containing either the full web page to be written to the output or the  Page URL.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
3106    
3107  =item varHash (optional)  =item parameters
3108    
3109  If specified, then a reference to a hash mapping variable names for a template  Hash mapping parameter names to parameter values.
3110  to their values. The template file will be read into memory, and variable markers  
3111  will be replaced by data in this hash reference.  =item RETURN
3112    
3113    Returns a GET-style URL that goes to the specified page and passes in the
3114    specified parameters and values.
3115    
3116  =back  =back
3117    
3118  =cut  =cut
3119    
3120  sub ScriptFinish {  sub GenerateURL {
3121      # Get the parameters.      # Get the parameters.
3122      my ($webData, $varHash) = @_;      my ($page, %parameters) = @_;
3123      # Check for a template file situation.      # Prime the return variable with the page URL.
3124      my $outputString;      my $retVal = $page;
3125      if (defined $varHash) {      # Loop through the parameters, creating parameter elements in a list.
3126          # Here we have a template file. We need to apply the variables to the template.      my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3127          $outputString = PageBuilder::Build("<$webData", $varHash, "Html");      # If the list is nonempty, tack it on.
3128      } else {      if (@parmList) {
3129          # Here the user gave us a raw string.          $retVal .= "?" . join(";", @parmList);
         $outputString = $webData;  
     }  
     # Check for trace messages.  
     if ($Destination eq "QUEUE") {  
         # We have trace messages, so we want to put them at the end of the body. This  
         # is either at the end of the whole string or at the beginning of the BODY  
         # end-tag.  
         my $pos = length $outputString;  
         if ($outputString =~ m#</body>#gi) {  
             $pos = (pos $outputString) - 7;  
         }  
         substr $outputString, $pos, 0, QTrace('Html');  
3130      }      }
3131      # Write the output string.      # Return the result.
3132      print $outputString;      return $retVal;
3133  }  }
3134    
3135  =head3 Insure  =head3 ApplyURL
3136    
3137  C<< Insure($dirName); >>      Tracer::ApplyURL($table, $target, $url);
3138    
3139  Insure a directory is present.  Run through a two-dimensional table (or more accurately, a list of lists), converting the
3140    I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3141    URL column will be deleted by this process and the target column will be HTML-escaped.
3142    
3143    This provides a simple way to process the results of a database query into something
3144    displayable by combining a URL with text.
3145    
3146  =over 4  =over 4
3147    
3148  =item dirName  =item table
3149    
3150  Name of the directory to check. If it does not exist, it will be created.  Reference to a list of lists. The elements in the containing list will be updated by
3151    this method.
3152    
3153    =item target
3154    
3155    The index of the column to be converted into HTML.
3156    
3157    =item url
3158    
3159    The index of the column containing the URL. Note that the URL must have a recognizable
3160    C<http:> at the beginning.
3161    
3162  =back  =back
3163    
3164  =cut  =cut
3165    
3166  sub Insure {  sub ApplyURL {
3167      my ($dirName) = @_;      # Get the parameters.
3168      if (! -d $dirName) {      my ($table, $target, $url) = @_;
3169          Trace("Creating $dirName directory.") if T(2);      # Loop through the table.
3170          eval { mkpath $dirName; };      for my $row (@{$table}) {
3171          if ($@) {          # Apply the URL to the target cell.
3172              Confess("Error creating $dirName: $@");          $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3173          }          # Delete the URL from the row.
3174            delete $row->[$url];
3175      }      }
3176  }  }
3177    
3178  =head3 ChDir  =head3 CombineURL
3179    
3180  C<< ChDir($dirName); >>      my $combinedHtml = Tracer::CombineURL($text, $url);
3181    
3182  Change to the specified directory.  This method will convert the specified text into HTML hyperlinked to the specified
3183    URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3184    is defined and begins with an C<http:> header.
3185    
3186  =over 4  =over 4
3187    
3188  =item dirName  =item text
3189    
3190  Name of the directory to which we want to change.  Text to return. This will be HTML-escaped automatically.
3191    
3192    =item url
3193    
3194    A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3195    will be returned without any hyperlinking.
3196    
3197    =item RETURN
3198    
3199    Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3200    doesn't look right, the HTML-escaped text will be returned without any further
3201    modification.
3202    
3203  =back  =back
3204    
3205  =cut  =cut
3206    
3207  sub ChDir {  sub CombineURL {
3208      my ($dirName) = @_;      # Get the parameters.
3209      if (! -d $dirName) {      my ($text, $url) = @_;
3210          Confess("Cannot change to directory $dirName: no such directory.");      # Declare the return variable.
3211      } else {      my $retVal = CGI::escapeHTML($text);
3212          Trace("Changing to directory $dirName.") if T(4);      # Verify the URL.
3213          my $okFlag = chdir $dirName;      if (defined($url) && $url =~ m!http://!i) {
3214          if (! $okFlag) {          # It's good, so we apply it to the text.
3215              Confess("Error switching to directory $dirName.");          $retVal = "<a href=\"$url\">$retVal</a>";
         }  
3216      }      }
3217        # Return the result.
3218        return $retVal;
3219  }  }
3220    
3221  =head3 SetPermissions  =head3 Cmp
   
 C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  
3222    
3223  Set the permissions for a directory and all the files and folders inside it.      my $cmp = Tracer::Cmp($a, $b);
 In addition, the group ownership will be changed to the specified value.  
3224    
3225  This method is more vulnerable than most to permission and compatability  This method performs a universal sort comparison. Each value coming in is
3226  problems, so it does internal error recovery.  separated into a leading text part and a trailing number part. The text
3227    part is string compared, and if both parts are equal, then the number
3228    parts are compared numerically. A stream of just numbers or a stream of
3229    just strings will sort correctly, and a mixed stream will sort with the
3230    numbers first. Strings with a label and a number will sort in the
3231    expected manner instead of lexically.
3232    
3233  =over 4  =over 4
3234    
3235  =item dirName  =item a
   
 Name of the directory to process.  
   
 =item group  
   
 Name of the group to be assigned.  
   
 =item mask  
   
 Permission mask. Bits that are C<1> in this mask will be ORed into the  
 permission bits of any file or directory that does not already have them  
 set to 1.  
   
 =item otherMasks  
3236    
3237  Map of search patterns to permission masks. If a directory name matches  First item to compare.
 one of the patterns, that directory and all its members and subdirectories  
 will be assigned the new pattern. For example, the following would  
 assign 01664 to most files, but would use 01777 for directories named C<tmp>.  
3238    
3239      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  =item b
3240    
3241  The list is ordered, so the following would use 0777 for C<tmp1> and  Second item to compare.
 0666 for C<tmp>, C<tmp2>, or C<tmp3>.  
3242    
3243      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  =item RETURN
                                                    '^tmp' => 0666);  
3244    
3245  Note that the pattern matches are all case-insensitive, and only directory  Returns a negative number if the first item should sort first (is less), a positive
3246  names are matched, not file names.  number if the first item should sort second (is greater), and a zero if the items are
3247    equal.
3248    
3249  =back  =back
3250    
3251  =cut  =cut
3252    
3253  sub SetPermissions {  sub Cmp {
3254      # Get the parameters.      # Get the parameters.
3255      my ($dirName, $group, $mask, @otherMasks) = @_;      my ($a, $b) = @_;
3256      # Set up for error recovery.      # Declare the return value.
3257      eval {      my $retVal;
3258          # Switch to the specified directory.      # Check for nulls.
3259          ChDir($dirName);      if (! defined($a)) {
3260          # Get the group ID.          $retVal = (! defined($b) ? 0 : -1);
3261          my $gid = getgrnam($group);      } elsif (! defined($b)) {
3262          # Get the mask for tracing.          $retVal = 1;
         my $traceMask = sprintf("%04o", $mask) . "($mask)";  
         Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(2);  
         my $fixCount = 0;  
         my $lookCount = 0;  
         # @dirs will be a stack of directories to be processed.  
         my @dirs = (getcwd());  
         while (scalar(@dirs) > 0) {  
             # Get the current directory.  
             my $dir = pop @dirs;  
             # Check for a match to one of the specified directory names. To do  
             # that, we need to pull the individual part of the name off of the  
             # whole path.  
             my $simpleName = $dir;  
             if ($dir =~ m!/(.+)$!) {  
                 $simpleName = $1;  
             }  
             # Search for a match.  
             my $match = 0;  
             my $i;  
             for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {  
                 my $pattern = $otherMasks[$i];  
                 if ($simpleName =~ /$pattern/i) {  
                     $match = 1;  
                 }  
             }  
             # Check for a match. Note we use $i-1 because the loop added 2  
             # before terminating due to the match.  
             if ($match && $otherMasks[$i-1] != $mask) {  
                 # This directory matches one of the incoming patterns, and it's  
                 # a different mask, so we process it recursively with that mask.  
                 SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);  
3263              } else {              } else {
3264                  # Here we can process normally. Get all of the non-hidden members.          # Here we have two real values. Parse the two strings.
3265                  my @submems = OpenDir($dir, 1);          $a =~ /^(\D*)(\d*)$/;
3266                  for my $submem (@submems) {          my $aParsed = [$1, $2];
3267                      # Get the full name.          $b =~ /^(\D*)(\d*)$/;
3268                      my $thisMem = "$dir/$submem";          my $bParsed = [$1, $2];
3269                      Trace("Checking member $thisMem.") if T(4);          # Compare the string parts.
3270                      $lookCount++;          $retVal = $aParsed->[0] cmp $bParsed->[0];
3271                      if ($lookCount % 1000 == 0) {          if (! $retVal) {
3272                          Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(3);              $retVal = $aParsed->[1] <=> $bParsed->[1];
                     }  
                     # Fix the group.  
                     chown -1, $gid, $thisMem;  
                     # Insure this member is not a symlink.  
                     if (! -l $thisMem) {  
                         # Get its info.  
                         my $fileInfo = stat $thisMem;  
                         # Only proceed if we got the info. Otherwise, it's a hard link  
                         # and we want to skip it anyway.  
                         if ($fileInfo) {  
                             my $fileMode = $fileInfo->mode;  
                             if (($fileMode & $mask) == 0) {  
                                 # Fix this member.  
                                 $fileMode |= $mask;  
                                 chmod $fileMode, $thisMem;  
                                 $fixCount++;  
                             }  
                             # If it's a subdirectory, stack it.  
                             if (-d $thisMem) {  
                                 push @dirs, $thisMem;  
                             }  
                         }  
                     }  
                 }  
3273              }              }
3274          }          }
3275          Trace("$lookCount files and directories processed, $fixCount fixed.") if T(2);      # Return the result.
3276      };      return $retVal;
     # Check for an error.  
     if ($@) {  
         Confess("SetPermissions error: $@");  
     }  
3277  }  }
3278    
3279    
3280  1;  1;

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