[Bio] / FigKernelPackages / Tracer.pm Repository:
ViewVC logotype

Diff of /FigKernelPackages/Tracer.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.63, Thu Aug 24 21:18:56 2006 UTC revision 1.95, Fri Apr 18 18:06:12 2008 UTC
# Line 1  Line 1 
1  #  # -*- perl -*-
2    ########################################################################
3  # Copyright (c) 2003-2006 University of Chicago and Fellowship  # Copyright (c) 2003-2006 University of Chicago and Fellowship
4  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
5  #  #
# Line 13  Line 14 
14  # at info@ci.uchicago.edu or the Fellowship for Interpretation of  # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15  # Genomes at veronika@thefig.info or download a copy from  # Genomes at veronika@thefig.info or download a copy from
16  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
17  #  ########################################################################
18    
19  package Tracer;  package Tracer;
20    
21      require Exporter;      require Exporter;
22      @ISA = ('Exporter');      @ISA = ('Exporter');
23      @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);
24      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);
25      use strict;      use strict;
26      use Carp qw(longmess croak);      use Carp qw(longmess croak);
# Line 32  Line 33 
33      use File::Path;      use File::Path;
34      use File::stat;      use File::stat;
35      use LWP::UserAgent;      use LWP::UserAgent;
36        use Time::HiRes 'gettimeofday';
37        use URI::Escape;
38        use Time::Local;
39    
40  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
41    
42  =head2 Introduction  =head2 Tracing
43    
44  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
45  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.
46  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,
47  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
48  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
49  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
50  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
51  appear. To generate a trace message, use the following syntax.  appear.
52    
53    =head3 Putting Trace Messages in Your Code
54    
55    To generate a trace message, use the following syntax.
56    
57  C<< Trace($message) if T(errors => 4); >>      Trace($message) if T(errors => 4);
58    
59  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>
60  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
61    
62  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
63    
64  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
65    
# Line 59  Line 67 
67  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
68  active and the trace level is 2 or more.  active and the trace level is 2 or more.
69    
70  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
71    
72  To set up tracing, you call the L</TSetup> method. The method takes as input a trace level, a list  In scripts, where no package name is available, the category defaults to C<main>.
73  of category names, and a set of options. The trace level and list of category names are  
74    =head3 Custom Tracing
75    
76    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
77    the preferred method, but a knowledge of how custom tracing works can make the more modern
78    L</Emergency Tracing> easier to understand.
79    
80    To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
81    a list of category names, and a destination. The trace level and list of category names are
82  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
83    
84  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
85    
86  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
87  specifies that messages should be output as HTML paragraphs.  specifies that messages should be sent to the standard output.
88    
89  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
90  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
91  useful in a CGI environment.  useful in a CGI environment.
92    
93  C<< TSetup('3 *', 'WARN'); >>      TSetup('3 *', 'WARN');
94    
95  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
96  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
97  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
98  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
99  it easier to debug page formatting problems.  it easier to debug page formatting problems.
100    
101  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
102    a file at the same time. To trace to a file, specify the filename with an output character in front
103    of it.
104    
105        TSetup('4 SQL', ">$fileName");
106    
107    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
108    bracket.
109    
110        TSetup('3 *', "+>$fileName");
111    
112  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>.
113  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.
114  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
115  being used out in the field.  being used out in the field.
116    
117    =head3 Trace Levels
118    
119  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
120  a suggestion.  a suggestion.
121    
# Line 119  Line 146 
146    
147  =back  =back
148    
149    The format of trace messages is important because some utilities analyze trace files.
150    There are three fields-- the time stamp, the category name, and the text.
151    The time stamp is between square brackets and the category name between angle brackets.
152    After the category name there is a colon (C<:>) followed by the message text.
153    If the square brackets or angle brackets are missing, then the trace management
154    utilities assume that they are encountering a set of pre-formatted lines.
155    
156    Note, however, that this formatting is done automatically by the tracing functions. You
157    only need to know about it if you want to parse a trace file.
158    
159    =head3 Emergency Tracing
160    
161    Sometimes, you need a way for tracing to happen automatically without putting parameters
162    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
163    from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.
164    Emergency tracing requires you specify a tracing key. For command-line tools, the key is
165    taken from the C<TRACING> environment variable. For web services, the key is taken from
166    a cookie. Either way, the key tells the tracing facility who you are, so that you control
167    the tracing in your environment without stepping on other users.
168    
169    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
170    generate one for you.
171    
172    You can activate and de-activate emergency tracing from the debugging control panel, as
173    well as display the trace file itself.
174    
175    To enable emergency tracing in your code, call
176    
177        ETracing($cgi)
178    
179    from a web script and
180    
181        ETracing()
182    
183    from a command-line script.
184    
185    The web script will look for the tracing key in the cookies, and the command-line
186    script will look for it in the C<TRACING> environment variable. If you are
187    using the L</StandardScript> or L</StandardSetup> methods, emergency tracing
188    will be configured automatically.
189    
190    NOTE: to configure emergency tracing from the command line instead of the Debugging
191    Control Panel (see below), use the C<trace.pl> script.
192    
193    =head3 Debugging Control Panel
194    
195    The debugging control panel provides several tools to assist in development of
196    SEED and Sprout software. You access the debugging control panel from the URL
197    C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,
198    for example, the panel access point for the development NMPDR system is
199    C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to
200    find out what the password is. From this page, you can also specify a tracing
201    key. If you don't specify a key, one will be generated for you.
202    
203    =head4 Emergency Tracing Form
204    
205    At the bottom of the debugging control panel is a form that allows you to
206    specify a trace level and tracing categories. Special and common categories
207    are listed with check boxes. You can hold your mouse over a check box to see
208    what its category does. In general, however, a category name is the same as
209    the name of the package in which the trace message occurs.
210    
211    Additional categories can be entered in an input box, delimited by spaces or commas.
212    
213    The B<Activate> button turns on Emergency tracing at the level you specify with the
214    specified categories active. The B<Terminate> button turns tracing off. The
215    B<Show File> button displays the current contents of the trace file. The tracing
216    form at the bottom of the control panel is designed for emergency tracing, so it
217    will only affect programs that call L</ETracing>, L</StandardScript>,
218    or L</StandardSetup>.
219    
220    =head4 Script Form
221    
222    The top form of the debugging control panel allows you to enter a tiny script and
223    have the output generated in a formatted table. Certain object variables are
224    predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),
225    and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.
226    
227    The last line of the script must be a scalar, but it can be a reference to a hash,
228    a list, a list of lists, and various other combinations. If you select the appropriate
229    data type in the dropdown box, the output will be formatted accordingly. The form
230    also has controls for specifying tracing. These controls override any emergency
231    tracing in effect.
232    
233    =head4 Database Query Forms
234    
235    The forms between the script form and the emergency tracing form allow you to
236    make queries against the database. The FIG query form allows simple queries against
237    a single FIG table. The Sprout query form uses the B<GetAll> method to do a
238    multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>
239    package, and it takes five parameters.
240    
241        GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
242    
243    Each of the five parameters corresponds to a text box on the query form:
244    
245    =over 4
246    
247    =item Objects
248    
249    Comma-separated list containing the names of the entity and relationship objects to be retrieved.
250    
251    =item Filter
252    
253    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
254    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
255    B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a
256    field, I<objectName> is the name of the entity or relationship object containing the field, and
257    I<number> is the 1-based position of the object in the object list. Any parameters
258    specified in the filter clause should be specified in the B<Params> field.
259    The fields in a filter clause can come from primary entity relations,
260    relationship relations, or secondary entity relations; however, all of the
261    entities and relationships involved must be included in the list of object names.
262    
263    =item Params
264    
265    List of the parameters to be substituted in for the parameters marks in the filter clause. This
266    is a comma-separated list without any quoting or escaping.
267    
268    =item fields
269    
270    Comma-separated list of the fields to be returned in each element of the list returned. Fields
271    are specified in the same manner as in the filter clause.
272    
273    =item count
274    
275    Maximum number of records to return. If omitted or 0, all available records will be returned.
276    
277    =back
278    
279    B<GetAll> automatically joins together the entities and relationships listed in the object
280    names. This simplifies the coding of the filter clause, but it means that some queries are
281    not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation
282    that has yet to be addressed.
283    
284  =cut  =cut
285    
286  # Declare the configuration variables.  # Declare the configuration variables.
287    
288  my $Destination = "NONE";   # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
289  my $TeeFlag = 0;            # TRUE if output is going to a file and to the  my $TeeFlag = 0;            # TRUE if output is going to a file and to the
290                              # standard output                              # standard output
291  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
# Line 135  Line 297 
297  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
298  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
299    
300  =head2 Public Methods  =head2 Tracing Methods
301    
302    =head3 Setups
303    
304        my $count = Tracer::Setups();
305    
306    Return the number of times L</TSetup> has been called.
307    
308    This method allows for the creation of conditional tracing setups where, for example, we
309    may want to set up tracing if nobody else has done it before us.
310    
311    =cut
312    
313    sub Setups {
314        return $SetupCount;
315    }
316    
317  =head3 TSetup  =head3 TSetup
318    
319  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
320    
321  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
322  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 198  Line 375 
375          }          }
376          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
377              open TRACEFILE, $target;              open TRACEFILE, $target;
378              print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";
379              close TRACEFILE;              close TRACEFILE;
380              $Destination = ">$target";              $Destination = ">$target";
381          } else {          } else {
# Line 211  Line 388 
388      $SetupCount++;      $SetupCount++;
389  }  }
390    
391  =head3 StandardSetup  =head3 SetLevel
392    
393  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
394    
395  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.  
396    
397  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.  
398    
399  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  
400    
401      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
402    
403  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.  
404    
405  =over 4  =cut
406    
407  =item FIG  sub SetLevel {
408        $TraceLevel = $_[0];
409    }
410    
411  Turns on trace messages inside the B<FIG> package.  =head3 ParseTraceDate
412    
413  =item SQL      my $time = Tracer::ParseTraceDate($dateString);
414    
415  Traces SQL commands and activity.  Convert a date from the trace file into a PERL timestamp.
416    
417  =item Tracer  =over 4
418    
419  Traces error messages and call stacks.  =item dateString
420    
421  =back  The date string from the trace file. The format of the string is determined by the
422    L</Now> method.
423    
424  C<SQL> is only turned on if the C<-sql> option is specified in the command line.  =item RETURN
 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.  
425    
426      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
427    the time string is invalid.
428    
429  Standard tracing is output to the standard output and echoed to the file  =back
 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  
430    
431  The default trace level is 2. To get all messages, specify a trace level of 4.  =cut
 For a genome-by-genome update, use 3.  
432    
433      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  sub ParseTraceDate {
434        # Get the parameters.
435        my ($dateString) = @_;
436        # Declare the return variable.
437        my $retVal;
438        # Parse the date.
439        if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {
440            # Create a time object. Note we need to convert the day, month,
441            # and year to a different base. Years count from 1900, and
442            # the internal month value is relocated to January = 0.
443            $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);
444        }
445        # Return the result.
446        return $retVal;
447    }
448    
449  would send the trace output to C<traceBruce.log> in the temporary directory.  =head3 LogErrors
450    
451  The I<options> parameter is a reference to a hash containing the command-line      Tracer::LogErrors($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.  
452    
453  You can specify a different default trace level by setting C<$options->{trace}>  Route the standard error output to a log file.
 prior to calling this method.  
454    
455  An example at this point would help. Consider, for example, the command-line utility  =over 4
 C<TransactFeatures>. It accepts a list of positional parameters plus the options  
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
456    
457      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],  =item fileName
                         { 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);  
458    
459    Name of the file to receive the error output.
460    
461  The call to C<ParseCommand> specifies the default values for the options and  =back
 stores the actual options in a hash that is returned as C<$options>. The  
 positional parameters are returned in C<@parameters>.  
462    
463  The following is a sample command line for C<TransactFeatures>.  =cut
464    
465      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  sub LogErrors {
466        # Get the file name.
467        my ($fileName) = @_;
468        # Open the file as the standard error output.
469        open STDERR, '>', $fileName;
470    }
471    
472  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  =head3 Trace
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<FIG>, C<Tracer>, and <DocUtils>. C<FIG> and C<Tracer> are standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
473    
474      { trace => 2, sql => 0, safe => 0,      Trace($message);
       noAlias => 1, start => ' ', tblFiles => 0 }  
475    
476  Use of C<StandardSetup> in this way provides a simple way of performing  Write a trace message to the target location specified in L</TSetup>. If there has not been
477  standard tracing setup and command-line parsing. Note that the caller is  any prior call to B<TSetup>.
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
478    
479  If the C<background> option is specified on the command line, then the  =over 4
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
480    
481      -user=Bruce -background  =item message
482    
483  then the trace output would go to C<traceBruce.log>, the standard output to  Message to write.
 C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to  
 simplify starting a command in the background.  
484    
485  Finally, if the special option C<-h> is specified, the option names will  =back
 be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
486    
487      TransactFeatures -h  =cut
488    
489  he would see the following output.  sub Trace {
490        # Get the parameters.
491        my ($message) = @_;
492        # Get the timestamp.
493        my $timeStamp = Now();
494        # Format the message. Note we strip off any line terminators at the end.
495        my $prefix = "[$timeStamp] <$LastCategory>: ";
496        my $formatted = $prefix . Strip($message);
497        # Process according to the destination.
498        if ($Destination eq "TEXT") {
499            # Write the message to the standard output.
500            print "$formatted\n";
501        } elsif ($Destination eq "ERROR") {
502            # Write the message to the error output.
503            print STDERR "$formatted\n";
504        } elsif ($Destination eq "QUEUE") {
505            # Push the message into the queue.
506            push @Queue, "$formatted";
507        } elsif ($Destination eq "HTML") {
508            # Convert the message to HTML and write it to the standard output.
509            my $escapedMessage = CGI::escapeHTML($message);
510            print "<p>$timeStamp $LastCategory: $escapedMessage</p>\n";
511        } elsif ($Destination eq "WARN") {
512           # Emit the message as a warning.
513           carp $message;
514        } elsif ($Destination =~ m/^>>/) {
515            # Write the trace message to an output file.
516            (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
517            print TRACING "$formatted\n";
518            close TRACING;
519            # If the Tee flag is on, echo it to the standard output.
520            if ($TeeFlag) {
521                print "$formatted\n";
522            }
523        }
524    }
525    
526      TransactFeatures [options] command transactionDirectory IDfile  =head3 T
         -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  
527    
528  The caller has the option of modifying the tracing scheme by placing a value      my $switch = T($category, $traceLevel);
 for C<trace> in the incoming options hash. The default value can be overridden,  
 or the tracing to the standard output can be turned off by suffixing a minus  
 sign to the trace level. So, for example,  
529    
530      { trace => [0, "tracing level (default 0)"],      or
        ...  
531    
532  would set the default trace level to 0 instead of 2, while      my $switch = T($traceLevel);
533    
534      { trace => ["2-", "tracing level (default 2)"],  Return TRUE if the trace level is at or above a specified value and the specified category
535         ...  is active, else FALSE. If no category is specified, the caller's package name is used.
536    
537  would leave the default at 2, but trace only to the log file, not to the  =over 4
 standard output.  
538    
539  The parameters to this method are as follows.  =item category
540    
541  =over 4  Category to which the message belongs. If not specified, the caller's package name is
542    used.
543    
544  =item categories  =item traceLevel
545    
546  Reference to a list of tracing category names. These should be names of  Relevant tracing level.
 packages whose internal workings will need to be debugged to get the  
 command working.  
547    
548  =item options  =item RETURN
549    
550  Reference to a hash containing the legal options for the current command mapped  TRUE if a message at the specified trace level would appear in the trace, else FALSE.
551  to their default values and descriptions. The user can override the defaults  
552  by specifying the options as command-line switches prefixed by a hyphen.  =back
553    
554    =cut
555    
556    sub T {
557        # Declare the return variable.
558        my $retVal = 0;
559        # Only proceed if tracing is turned on.
560        if ($Destination ne "NONE") {
561            # Get the parameters.
562            my ($category, $traceLevel) = @_;
563            if (!defined $traceLevel) {
564                # Here we have no category, so we need to get the calling package.
565                # The calling package is normally the first parameter. If it is
566                # omitted, the first parameter will be the tracelevel. So, the
567                # first thing we do is shift the so-called category into the
568                # $traceLevel variable where it belongs.
569                $traceLevel = $category;
570                my ($package, $fileName, $line) = caller;
571                # If there is no calling package, we default to "main".
572                if (!$package) {
573                    $category = "main";
574                } else {
575                    my @cats = split /::/, $package;
576                    $category = $cats[$#cats];
577                }
578            }
579            # Save the category name.
580            $LastCategory = $category;
581            # Convert it to lower case before we hash it.
582            $category = lc $category;
583            # Use the category and tracelevel to compute the result.
584            if (ref $traceLevel) {
585                Confess("Bad trace level.");
586            } elsif (ref $TraceLevel) {
587                Confess("Bad trace config.");
588            }
589            $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
590        }
591        # Return the computed result.
592        return $retVal;
593    }
594    
595    =head3 QTrace
596    
597        my $data = QTrace($format);
598    
599    Return the queued trace data in the specified format.
600    
601    =over 4
602    
603    =item format
604    
605    C<html> to format the data as an HTML list, C<text> to format it as straight text.
606    
607    =back
608    
609    =cut
610    
611    sub QTrace {
612        # Get the parameter.
613        my ($format) = @_;
614        # Create the return variable.
615        my $retVal = "";
616        # Only proceed if there is an actual queue.
617        if (@Queue) {
618            # Process according to the format.
619            if ($format =~ m/^HTML$/i) {
620                # Convert the queue into an HTML list.
621                $retVal = "<ul>\n";
622                for my $line (@Queue) {
623                    my $escapedLine = CGI::escapeHTML($line);
624                    $retVal .= "<li>$escapedLine</li>\n";
625                }
626                $retVal .= "</ul>\n";
627            } elsif ($format =~ m/^TEXT$/i) {
628                # Convert the queue into a list of text lines.
629                $retVal = join("\n", @Queue) . "\n";
630            }
631            # Clear the queue.
632            @Queue = ();
633        }
634        # Return the formatted list.
635        return $retVal;
636    }
637    
638    =head3 Confess
639    
640        Confess($message);
641    
642    Trace the call stack and abort the program with the specified message. When used with
643    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
644    So, for example
645    
646        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
647    
648    Will abort the program with a stack trace if the value of C<$recNum> is negative.
649    
650    =over 4
651    
652    =item message
653    
654    Message to include in the trace.
655    
656    =back
657    
658    =cut
659    
660    sub Confess {
661        # Get the parameters.
662        my ($message) = @_;
663        if (! defined($FIG_Config::no_tool_hdr)) {
664            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
665            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
666            # Only proceed if the tool header file is actually present.
667            if (-f $toolHeaderFile) {
668                my @lines = GetFile($toolHeaderFile);
669                Trace("Tool header has " . scalar(@lines) . " lines.");
670            }
671        }
672        # Trace the call stack.
673        Cluck($message);
674        # Abort the program.
675        croak(">>> $message");
676    }
677    
678    =head3 Assert
679    
680        Assert($condition1, $condition2, ... $conditionN);
681    
682    Return TRUE if all the conditions are true. This method can be used in conjunction with
683    the OR operator and the L</Confess> method as a debugging assert.
684    So, for example
685    
686        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
687    
688    Will abort the program with a stack trace if the value of C<$recNum> is negative.
689    
690    =cut
691    sub Assert {
692        my $retVal = 1;
693        LOOP: for my $condition (@_) {
694            if (! $condition) {
695                $retVal = 0;
696                last LOOP;
697            }
698        }
699        return $retVal;
700    }
701    
702    =head3 Cluck
703    
704        Cluck($message);
705    
706    Trace the call stack. Note that for best results, you should qualify the call with a
707    trace condition. For example,
708    
709        Cluck("Starting record parse.") if T(3);
710    
711    will only trace the stack if the trace level for the package is 3 or more.
712    
713    =over 4
714    
715    =item message
716    
717    Message to include in the trace.
718    
719    =back
720    
721    =cut
722    
723    sub Cluck {
724        # Get the parameters.
725        my ($message) = @_;
726        # Trace what's happening.
727        Trace("Stack trace for event: $message");
728        my $confession = longmess($message);
729        # Convert the confession to a series of trace messages. Note we skip any
730        # messages relating to calls into Tracer.
731        for my $line (split /\s*\n/, $confession) {
732            Trace($line) if ($line !~ /Tracer\.pm/);
733        }
734    }
735    
736    =head3 ScriptSetup
737    
738        my ($cgi, $varHash) = ScriptSetup($noTrace);
739    
740    Perform standard tracing and debugging setup for scripts. The value returned is
741    the CGI object followed by a pre-built variable hash. At the end of the script,
742    the client should call L</ScriptFinish> to output the web page.
743    
744    This method calls L</ETracing> to configure tracing, which allows the tracing
745    to be configured via the emergency tracing form on the debugging control panel.
746    Tracing will then be turned on automatically for all programs that use the L</ETracing>
747    method, which includes every program that uses this method or L</StandardSetup>.
748    
749    =over 4
750    
751    =item noTrace (optional)
752    
753    If specified, tracing will be suppressed. This is useful if the script wants to set up
754    tracing manually.
755    
756    =item RETURN
757    
758    Returns a two-element list consisting of a CGI query object and a variable hash for
759    the output page.
760    
761    =back
762    
763    =cut
764    
765    sub ScriptSetup {
766        # Get the parameters.
767        my ($noTrace) = @_;
768        # Get the CGI query object.
769        my $cgi = CGI->new();
770        # Set up tracing if it's not suppressed.
771        ETracing($cgi) unless $noTrace;
772        # Create the variable hash.
773        my $varHash = { results => '' };
774        # Return the query object and variable hash.
775        return ($cgi, $varHash);
776    }
777    
778    =head3 ETracing
779    
780        ETracing($parameter);
781    
782    Set up emergency tracing. Emergency tracing is tracing that is turned
783    on automatically for any program that calls this method. The emergency
784    tracing parameters are stored in a a file identified by a tracing key.
785    If this method is called with a CGI object, then the tracing key is
786    taken from a cookie. If it is called with no parameters, then the tracing
787    key is taken from an environment variable. If it is called with a string,
788    the tracing key is that string.
789    
790    =over 4
791    
792    =item parameter
793    
794    A parameter from which the tracing key is computed. If it is a scalar,
795    that scalar is used as the tracing key. If it is a CGI object, the
796    tracing key is taken from the C<IP> cookie. If it is omitted, the
797    tracing key is taken from the C<TRACING> environment variable. If it
798    is a CGI object and emergency tracing is not on, the C<Trace> and
799    C<TF> parameters will be used to determine the type of tracing.
800    
801    =back
802    
803    =cut
804    
805    sub ETracing {
806        # Get the parameter.
807        my ($parameter) = @_;
808        # Check for CGI mode.
809        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
810        # Default to no tracing except errors.
811        my ($tracing, $dest) = ("0", "WARN");
812        # Check for emergency tracing.
813        my $tkey = EmergencyKey($parameter);
814        my $emergencyFile = EmergencyFileName($tkey);
815        if (-e $emergencyFile) {
816            # We have the file. Read in the data.
817            my @tracing = GetFile($emergencyFile);
818            # Pull off the time limit.
819            my $expire = shift @tracing;
820            # Convert it to seconds.
821            $expire *= 3600;
822            # Check the file data.
823            my $stat = stat($emergencyFile);
824            my ($now) = gettimeofday;
825            if ($now - $stat->mtime > $expire) {
826                # Delete the expired file.
827                unlink $emergencyFile;
828            } else {
829                # Emergency tracing is on. Pull off the destination and
830                # the trace level;
831                $dest = shift @tracing;
832                my $level = shift @tracing;
833                # Convert the destination to a real tracing destination.
834                # temp directory.
835                $dest = EmergencyTracingDest($tkey, $dest);
836                # Insure Tracer is specified.
837                my %moduleHash = map { $_ => 1 } @tracing;
838                $moduleHash{Tracer} = 1;
839                # Set the trace parameter.
840                $tracing = join(" ", $level, sort keys %moduleHash);
841            }
842        } elsif (defined $cgi) {
843            # There's no emergency tracing, but we have a CGI object, so check
844            # for tracing from the form parameters.
845            if ($cgi->param('Trace')) {
846                # Here the user has requested tracing via a form.
847                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
848                $tracing = $cgi->param('Trace') . " Tracer";
849            }
850        }
851        # Setup the tracing we've determined from all the stuff above.
852        TSetup($tracing, $dest);
853        # Check to see if we're a web script.
854        if (defined $cgi) {
855            # Yes we are. Trace the form and environment data.
856            TraceParms($cgi);
857            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
858            # emitted by the script in its raw form.
859            if (T(Raw => 3)) {
860                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
861            }
862        }
863    }
864    
865    =head3 EmergencyFileName
866    
867        my $fileName = Tracer::EmergencyFileName($tkey);
868    
869    Return the emergency tracing file name. This is the file that specifies
870    the tracing information.
871    
872    =over 4
873    
874    =item tkey
875    
876    Tracing key for the current program.
877    
878    =item RETURN
879    
880    Returns the name of the file to contain the emergency tracing information.
881    
882    =back
883    
884    =cut
885    
886    sub EmergencyFileName {
887        # Get the parameters.
888        my ($tkey) = @_;
889        # Compute the emergency tracing file name.
890        return "$FIG_Config::temp/Emergency$tkey.txt";
891    }
892    
893    =head3 EmergencyFileTarget
894    
895        my $fileName = Tracer::EmergencyFileTarget($tkey);
896    
897    Return the emergency tracing target file name. This is the file that receives
898    the tracing output for file-based tracing.
899    
900    =over 4
901    
902    =item tkey
903    
904    Tracing key for the current program.
905    
906    =item RETURN
907    
908    Returns the name of the file to contain the trace output.
909    
910    =back
911    
912    =cut
913    
914    sub EmergencyFileTarget {
915        # Get the parameters.
916        my ($tkey) = @_;
917        # Compute the emergency tracing file name.
918        return "$FIG_Config::temp/trace$tkey.log";
919    }
920    
921    =head3 EmergencyTracingDest
922    
923        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
924    
925    This method converts an emergency tracing destination to a real
926    tracing destination. The main difference is that if the
927    destination is C<FILE> or C<APPEND>, we convert it to file
928    output. If the destination is C<DUAL>, we convert it to file
929    and standard output.
930    
931    =over 4
932    
933    =item tkey
934    
935    Tracing key for this environment.
936    
937    =item myDest
938    
939    Destination from the emergency tracing file.
940    
941    =item RETURN
942    
943    Returns a destination that can be passed into L</TSetup>.
944    
945    =back
946    
947    =cut
948    
949    sub EmergencyTracingDest {
950        # Get the parameters.
951        my ($tkey, $myDest) = @_;
952        # Declare the return variable.
953        my $retVal = $myDest;
954        # Process according to the destination value.
955        if ($myDest eq 'FILE') {
956            $retVal = ">" . EmergencyFileTarget($tkey);
957        } elsif ($myDest eq 'APPEND') {
958            $retVal = ">>" . EmergencyFileTarget($tkey);
959        } elsif ($myDest eq 'DUAL') {
960            $retVal = "+>" . EmergencyFileTarget($tkey);
961        }
962        # Return the result.
963        return $retVal;
964    }
965    
966    =head3 Emergency
967    
968        Emergency($key, $hours, $dest, $level, @modules);
969    
970    Turn on emergency tracing. This method is normally invoked over the web from
971    a debugging console, but it can also be called by the C<trace.pl> script.
972    The caller specifies the duration of the emergency in hours, the desired tracing
973    destination, the trace level, and a list of the trace modules to activate.
974    For the length of the duration, when a program in an environment with the
975    specified tracing key active invokes a Sprout CGI script, tracing will be
976    turned on automatically. See L</TSetup> for more about tracing setup and
977    L</ETracing> for more about emergency tracing.
978    
979    =over 4
980    
981    =item tkey
982    
983    The tracing key. This is used to identify the control file and the trace file.
984    
985    =item hours
986    
987    Number of hours to keep emergency tracing alive.
988    
989    =item dest
990    
991    Tracing destination. If no path information is specified for a file
992    destination, it is put in the FIG temporary directory.
993    
994    =item level
995    
996    Tracing level. A higher level means more trace messages.
997    
998    =item modules
999    
1000    A list of the tracing modules to activate.
1001    
1002    =back
1003    
1004    =cut
1005    
1006    sub Emergency {
1007        # Get the parameters.
1008        my ($tkey, $hours, $dest, $level, @modules) = @_;
1009        # Create the emergency file.
1010        my $specFile = EmergencyFileName($tkey);
1011        my $outHandle = Open(undef, ">$specFile");
1012        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1013    }
1014    
1015    =head3 EmergencyKey
1016    
1017        my $tkey = EmergencyKey($parameter);
1018    
1019    Return the Key to be used for emergency tracing. This could be an IP address,
1020     a session ID, or a user name, depending on the environment.
1021    
1022    =over 4
1023    
1024    =item parameter
1025    
1026    Parameter defining the method for finding the tracing key. If it is a scalar,
1027    then it is presumed to be the tracing key itself. If it is a CGI object, then
1028    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1029    taken from the C<TRACING> environment variable.
1030    
1031    =item RETURN
1032    
1033    Returns the key to be used for labels in emergency tracing.
1034    
1035    =back
1036    
1037    =cut
1038    
1039    sub EmergencyKey {
1040        # Get the parameters.
1041        my ($parameter) = @_;
1042        # Declare the return variable.
1043        my $retVal;
1044        # Determine the parameter type.
1045        if (! defined $parameter) {
1046            # Here we're supposed to check the environment.
1047            $retVal = $ENV{TRACING};
1048        } else {
1049            my $ptype = ref $parameter;
1050            if ($ptype eq 'CGI') {
1051                # Here we were invoked from a web page. Look for a cookie.
1052                $retVal = $parameter->cookie('IP');
1053            } elsif (! $ptype) {
1054                # Here the key was passed in.
1055                $retVal = $parameter;
1056            }
1057        }
1058        # If no luck finding a key, use the PID.
1059        if (! defined $retVal) {
1060            $retVal = $$;
1061        }
1062        # Return the result.
1063        return $retVal;
1064    }
1065    
1066    
1067    =head3 TraceParms
1068    
1069        Tracer::TraceParms($cgi);
1070    
1071    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1072    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1073    
1074    =over 4
1075    
1076    =item cgi
1077    
1078    CGI query object containing the parameters to trace.
1079    
1080    =back
1081    
1082    =cut
1083    
1084    sub TraceParms {
1085        # Get the parameters.
1086        my ($cgi) = @_;
1087        if (T(CGI => 2)) {
1088            # Here we trace the GET-style URL for the script.
1089            Trace("URL: " . $cgi->url(-relative => 1, -query => 1));
1090        }
1091        if (T(CGI => 3)) {
1092            # Here we want to trace the parameter data.
1093            my @names = $cgi->param;
1094            for my $parmName (sort @names) {
1095                # Note we skip the Trace parameters, which are for our use only.
1096                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1097                    my @values = $cgi->param($parmName);
1098                    Trace("CGI: $parmName = " . join(", ", @values));
1099                }
1100            }
1101            # Display the request method.
1102            my $method = $cgi->request_method();
1103            Trace("Method: $method");
1104        }
1105        if (T(CGI => 4)) {
1106            # Here we want the environment data too.
1107            for my $envName (sort keys %ENV) {
1108                Trace("ENV: $envName = $ENV{$envName}");
1109            }
1110        }
1111    }
1112    
1113    =head3 TraceImages
1114    
1115        Tracer::TraceImages($htmlString);
1116    
1117    Trace information about all of an html document's images. The tracing
1118    will be for type "IMG" at level 3. The image's source string
1119    will be displayed. This is generally either the URL of the image or
1120    raw data for the image itself. If the source is too long, only the first 300
1121    characters will be shown at trace level 3. The entire source will be shown,
1122    however, at trace level 4. This method is not very smart, and might catch
1123    Javascript code, but it is still useful when debugging the arcane
1124    behavior of images in multiple browser environments.
1125    
1126    =over 4
1127    
1128    =item htmlString
1129    
1130    HTML text for an outgoing web page.
1131    
1132    =back
1133    
1134    =cut
1135    
1136    sub TraceImages {
1137        # Only proceed if we're at the proper trace level.
1138        if (T(IMG => 3)) {
1139            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1140            # into a variable called "$htmlString". This is because we expect html strings to be
1141            # long, and don't want to copy them any more than we have to.
1142            Trace(length($_[0]) . " characters in web page.");
1143            # Loop through the HTML, culling image tags.
1144            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1145                # Extract the source string and determine whether or not it's too long.
1146                my $srcString = $1;
1147                my $pos = pos($_[0]) - length($srcString);
1148                my $excess = length($srcString) - 300;
1149                # We'll put the display string in here.
1150                my $srcDisplay = $srcString;
1151                # If it's a data string, split it at the comma.
1152                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1153                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1154                # a long string, however, we only show the first 300 characters.
1155                if ($excess > 0 && ! T(IMG => 4)) {
1156                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1157                }
1158                # Output the trace message.
1159                Trace("Image tag at position $pos:\n$srcDisplay");
1160            }
1161        }
1162    }
1163    
1164    
1165    =head3 ScriptFinish
1166    
1167        ScriptFinish($webData, $varHash);
1168    
1169    Output a web page at the end of a script. Either the string to be output or the
1170    name of a template file can be specified. If the second parameter is omitted,
1171    it is assumed we have a string to be output; otherwise, it is assumed we have the
1172    name of a template file. The template should have the variable C<DebugData>
1173    specified in any form that invokes a standard script. If debugging mode is turned
1174    on, a form field will be put in that allows the user to enter tracing data.
1175    Trace messages will be placed immediately before the terminal C<BODY> tag in
1176    the output, formatted as a list.
1177    
1178    A typical standard script would loook like the following.
1179    
1180        BEGIN {
1181            # Print the HTML header.
1182            print "CONTENT-TYPE: text/html\n\n";
1183        }
1184        use Tracer;
1185        use CGI;
1186        use FIG;
1187        # ... more uses ...
1188    
1189        my ($cgi, $varHash) = ScriptSetup();
1190        eval {
1191            # ... get data from $cgi, put it in $varHash ...
1192        };
1193        if ($@) {
1194            Trace("Script Error: $@") if T(0);
1195        }
1196        ScriptFinish("Html/MyTemplate.html", $varHash);
1197    
1198    The idea here is that even if the script fails, you'll see trace messages and
1199    useful output.
1200    
1201    =over 4
1202    
1203    =item webData
1204    
1205    A string containing either the full web page to be written to the output or the
1206    name of a template file from which the page is to be constructed. If the name
1207    of a template file is specified, then the second parameter must be present;
1208    otherwise, it must be absent.
1209    
1210    =item varHash (optional)
1211    
1212    If specified, then a reference to a hash mapping variable names for a template
1213    to their values. The template file will be read into memory, and variable markers
1214    will be replaced by data in this hash reference.
1215    
1216    =back
1217    
1218    =cut
1219    
1220    sub ScriptFinish {
1221        # Get the parameters.
1222        my ($webData, $varHash) = @_;
1223        # Check for a template file situation.
1224        my $outputString;
1225        if (defined $varHash) {
1226            # Here we have a template file. We need to determine the template type.
1227            my $template;
1228            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1229                $template = "$FIG_Config::template_url/$webData";
1230            } else {
1231                $template = "<<$webData";
1232            }
1233            $outputString = PageBuilder::Build($template, $varHash, "Html");
1234        } else {
1235            # Here the user gave us a raw string.
1236            $outputString = $webData;
1237        }
1238        # Check for trace messages.
1239        if ($Destination ne "NONE" && $TraceLevel > 0) {
1240            # We have trace messages, so we want to put them at the end of the body. This
1241            # is either at the end of the whole string or at the beginning of the BODY
1242            # end-tag.
1243            my $pos = length $outputString;
1244            if ($outputString =~ m#</body>#gi) {
1245                $pos = (pos $outputString) - 7;
1246            }
1247            # If the trace messages were queued, we unroll them. Otherwise, we display the
1248            # destination.
1249            my $traceHtml;
1250            if ($Destination eq "QUEUE") {
1251                $traceHtml = QTrace('Html');
1252            } elsif ($Destination =~ /^>>(.+)$/) {
1253                # Here the tracing output it to a file. We code it as a hyperlink so the user
1254                # can copy the file name into the clipboard easily.
1255                my $actualDest = $1;
1256                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1257            } else {
1258                # Here we have one of the special destinations.
1259                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1260            }
1261            substr $outputString, $pos, 0, $traceHtml;
1262        }
1263        # Write the output string.
1264        print $outputString;
1265    }
1266    
1267    =head2 Command-Line Utility Methods
1268    
1269    =head3 SendSMS
1270    
1271        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1272    
1273    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1274    user name, password, and API ID for the relevant account in the hash reference variable
1275    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1276    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1277    is C<2561022>, then the FIG_Config file must contain
1278    
1279        $phone =  { user => 'BruceTheHumanPet',
1280                    password => 'silly',
1281                    api_id => '2561022' };
1282    
1283    The original purpose of this method was to insure Bruce would be notified immediately when the
1284    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1285    when you call this method.
1286    
1287    The message ID will be returned if successful, and C<undef> if an error occurs.
1288    
1289    =over 4
1290    
1291    =item phoneNumber
1292    
1293    Phone number to receive the message, in international format. A United States phone number
1294    would be prefixed by "1". A British phone number would be prefixed by "44".
1295    
1296    =item msg
1297    
1298    Message to send to the specified phone.
1299    
1300    =item RETURN
1301    
1302    Returns the message ID if successful, and C<undef> if the message could not be sent.
1303    
1304    =back
1305    
1306    =cut
1307    
1308    sub SendSMS {
1309        # Get the parameters.
1310        my ($phoneNumber, $msg) = @_;
1311        # Declare the return variable. If we do not change it, C<undef> will be returned.
1312        my $retVal;
1313        # Only proceed if we have phone support.
1314        if (! defined $FIG_Config::phone) {
1315            Trace("Phone support not present in FIG_Config.") if T(1);
1316        } else {
1317            # Get the phone data.
1318            my $parms = $FIG_Config::phone;
1319            # Get the Clickatell URL.
1320            my $url = "http://api.clickatell.com/http/";
1321            # Create the user agent.
1322            my $ua = LWP::UserAgent->new;
1323            # Request a Clickatell session.
1324            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1325                                         password => $parms->{password},
1326                                         api_id => $parms->{api_id},
1327                                         to => $phoneNumber,
1328                                         text => $msg});
1329            # Check for an error.
1330            if (! $resp->is_success) {
1331                Trace("Alert failed.") if T(1);
1332            } else {
1333                # Get the message ID.
1334                my $rstring = $resp->content;
1335                if ($rstring =~ /^ID:\s+(.*)$/) {
1336                    $retVal = $1;
1337                } else {
1338                    Trace("Phone attempt failed with $rstring") if T(1);
1339                }
1340            }
1341        }
1342        # Return the result.
1343        return $retVal;
1344    }
1345    
1346    =head3 StandardSetup
1347    
1348        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1349    
1350    This method performs standard command-line parsing and tracing setup. The return
1351    values are a hash of the command-line options and a list of the positional
1352    parameters. Tracing is automatically set up and the command-line options are
1353    validated.
1354    
1355    This is a complex method that does a lot of grunt work. The parameters can
1356    be more easily understood, however, once they are examined individually.
1357    
1358    The I<categories> parameter is the most obtuse. It is a reference to a list of
1359    special-purpose tracing categories. Most tracing categories are PERL package
1360    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1361    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1362    
1363        ["Sprout", "SproutLoad", "ERDB"]
1364    
1365    This would cause trace messages in the specified three packages to appear in
1366    the output. There are two special tracing categories that are automatically
1367    handled by this method. In other words, if you used L</TSetup> you would need
1368    to include these categories manually, but if you use this method they are turned
1369    on automatically.
1370    
1371    =over 4
1372    
1373    =item SQL
1374    
1375    Traces SQL commands and activity.
1376    
1377    =item Tracer
1378    
1379    Traces error messages and call stacks.
1380    
1381    =back
1382    
1383    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1384    The trace level is specified using the C<-trace> command-line option. For example,
1385    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1386    all tracing at level 3.
1387    
1388        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1389    
1390    Standard tracing is output to the standard output and echoed to the file
1391    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1392    process ID. You can also specify the C<user> parameter to put a user ID
1393    instead of a process ID in the trace file name. So, for example
1394    
1395    The default trace level is 2. To get all messages, specify a trace level of 4.
1396    For a genome-by-genome update, use 3.
1397    
1398        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1399    
1400    would send the trace output to C<traceBruce.log> in the temporary directory.
1401    
1402    The I<options> parameter is a reference to a hash containing the command-line
1403    options, their default values, and an explanation of what they mean. Command-line
1404    options may be in the form of switches or keywords. In the case of a switch, the
1405    option value is 1 if it is specified and 0 if it is not specified. In the case
1406    of a keyword, the value is separated from the option name by an equal sign. You
1407    can see this last in the command-line example above.
1408    
1409    You can specify a different default trace level by setting C<$options->{trace}>
1410    prior to calling this method.
1411    
1412    An example at this point would help. Consider, for example, the command-line utility
1413    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1414    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1415    the following code.
1416    
1417        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1418                            { safe => [0, "use database transactions"],
1419                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1420                              start => [' ', "start with this genome"],
1421                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1422                            "<command> <transactionDirectory> <IDfile>",
1423                          @ARGV);
1424    
1425    
1426    The call to C<ParseCommand> specifies the default values for the options and
1427    stores the actual options in a hash that is returned as C<$options>. The
1428    positional parameters are returned in C<@parameters>.
1429    
1430    The following is a sample command line for C<TransactFeatures>.
1431    
1432        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1433    
1434    Single and double hyphens are equivalent. So, you could also code the
1435    above command as
1436    
1437        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1438    
1439    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1440    parameters, and would find themselves in I<@parameters> after executing the
1441    above code fragment. The tracing would be set to level 2, and the categories
1442    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1443    and C<DocUtils> was included because it came in within the first parameter
1444    to this method. The I<$options> hash would be
1445    
1446        { trace => 2, sql => 0, safe => 0,
1447          noAlias => 1, start => ' ', tblFiles => 0 }
1448    
1449    Use of C<StandardSetup> in this way provides a simple way of performing
1450    standard tracing setup and command-line parsing. Note that the caller is
1451    not even aware of the command-line switches C<-trace> and C<-sql>, which
1452    are used by this method to control the tracing. If additional tracing features
1453    need to be added in the future, they can be processed by this method without
1454    upsetting the command-line utilities.
1455    
1456    If the C<background> option is specified on the command line, then the
1457    standard and error outputs will be directed to files in the temporary
1458    directory, using the same suffix as the trace file. So, if the command
1459    line specified
1460    
1461        -user=Bruce -background
1462    
1463    then the trace output would go to C<traceBruce.log>, the standard output to
1464    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1465    simplify starting a command in the background.
1466    
1467    The user name is also used as the tracing key for L</Emergency Tracing>.
1468    Specifying a value of C<E> for the trace level causes emergency tracing to
1469    be used instead of custom tracing. If the user name is not specified,
1470    the tracing key is taken from the C<Tracing> environment variable. If there
1471    is no value for that variable, the tracing key will be computed from the PID.
1472    
1473    Finally, if the special option C<-help> is specified, the option
1474    names will be traced at level 0 and the program will exit without processing.
1475    This provides a limited help capability. For example, if the user enters
1476    
1477        TransactFeatures -help
1478    
1479    he would see the following output.
1480    
1481        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1482            -trace    tracing level (default E)
1483            -sql      trace SQL commands
1484            -safe     use database transactions
1485            -noAlias  do not expect aliases in CHANGE transactions
1486            -start    start with this genome
1487            -tblFiles output TBL files containing the corrected IDs
1488    
1489    The caller has the option of modifying the tracing scheme by placing a value
1490    for C<trace> in the incoming options hash. The default value can be overridden,
1491    or the tracing to the standard output can be turned off by suffixing a minus
1492    sign to the trace level. So, for example,
1493    
1494        { trace => [0, "tracing level (default 0)"],
1495           ...
1496    
1497    would set the default trace level to 0 instead of E, while
1498    
1499        { trace => ["2-", "tracing level (default 2)"],
1500           ...
1501    
1502    would set the default to 2, but trace only to the log file, not to the
1503    standard output.
1504    
1505    The parameters to this method are as follows.
1506    
1507    =over 4
1508    
1509    =item categories
1510    
1511    Reference to a list of tracing category names. These should be names of
1512    packages whose internal workings will need to be debugged to get the
1513    command working.
1514    
1515    =item options
1516    
1517    Reference to a hash containing the legal options for the current command mapped
1518    to their default values and descriptions. The user can override the defaults
1519    by specifying the options as command-line switches prefixed by a hyphen.
1520  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
1521  specified on the command line, the option descriptions will be used to  specified on the command line, the option descriptions will be used to
1522  explain the options. To turn off tracing to the standard output, add a  explain the options. To turn off tracing to the standard output, add a
# Line 407  Line 1546 
1546  sub StandardSetup {  sub StandardSetup {
1547      # Get the parameters.      # Get the parameters.
1548      my ($categories, $options, $parmHelp, @argv) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
1549        # Get the default tracing key.
1550        my $tkey = EmergencyKey();
1551      # Add the tracing options.      # Add the tracing options.
1552      if (! exists $options->{trace}) {      if (! exists $options->{trace}) {
1553          $options->{trace} = [2, "tracing level"];          $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1554      }      }
1555      $options->{sql} = [0, "turn on SQL tracing"];      $options->{sql} = [0, "turn on SQL tracing"];
1556      $options->{h} = [0, "display command-line options"];      $options->{help} = [0, "display command-line options"];
1557      $options->{user} = [$$, "trace log file name suffix"];      $options->{user} = [$tkey, "tracing key"];
1558      $options->{background} = [0, "spool standard and error output"];      $options->{background} = [0, "spool standard and error output"];
1559      # Create a parsing hash from the options hash. The parsing hash      # Create a parsing hash from the options hash. The parsing hash
1560      # contains the default values rather than the default value      # contains the default values rather than the default value
# Line 437  Line 1578 
1578          my $errFileName = "$FIG_Config::temp/err$suffix.log";          my $errFileName = "$FIG_Config::temp/err$suffix.log";
1579          open STDOUT, ">$outFileName";          open STDOUT, ">$outFileName";
1580          open STDERR, ">$errFileName";          open STDERR, ">$errFileName";
1581            # Check for phone support. If we have phone support and a phone number,
1582            # we want to turn it on.
1583            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1584                $retOptions->{phone} = $ENV{PHONE};
1585      }      }
1586      # Now we want to set up tracing. First, we need to know if SQL is to      }
1587      # be traced.      # Now we want to set up tracing. First, we need to know if the user
1588        # wants emergency tracing.
1589        if ($retOptions->{trace} eq 'E') {
1590            ETracing($retOptions->{user});
1591        } else {
1592            # Here the tracing is controlled from the command line.
1593      my @cats = @{$categories};      my @cats = @{$categories};
1594      if ($retOptions->{sql}) {      if ($retOptions->{sql}) {
1595          push @cats, "SQL";          push @cats, "SQL";
1596      }      }
1597      # Add the default categories.      # Add the default categories.
1598      push @cats, "Tracer", "FIG";          push @cats, "Tracer";
1599      # Next, we create the category string by joining the categories.      # Next, we create the category string by joining the categories.
1600      my $cats = join(" ", @cats);      my $cats = join(" ", @cats);
1601      # Check to determine whether or not the caller wants to turn off tracing      # Check to determine whether or not the caller wants to turn off tracing
# Line 480  Line 1630 
1630      }      }
1631      # Now set up the tracing.      # Now set up the tracing.
1632      TSetup("$traceLevel $cats", $traceMode);      TSetup("$traceLevel $cats", $traceMode);
1633      # Check for the "h" option. If it is specified, dump the command-line      }
1634        # Check for the "help" option. If it is specified, dump the command-line
1635      # options and exit the program.      # options and exit the program.
1636      if ($retOptions->{h}) {      if ($retOptions->{help}) {
1637          $0 =~ m#[/\\](\w+)(\.pl)?$#i;          $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1638          Trace("$1 [options] $parmHelp") if T(0);          print "$1 [options] $parmHelp\n";
1639          for my $key (sort keys %{$options}) {          for my $key (sort keys %{$options}) {
1640              my $name = Pad($key, $longestName, 0, ' ');              my $name = Pad($key, $longestName, 0, ' ');
1641              my $desc = $options->{$key}->[1];              my $desc = $options->{$key}->[1];
1642              if ($options->{$key}->[0]) {              if ($options->{$key}->[0]) {
1643                  $desc .= " (default " . $options->{$key}->[0] . ")";                  $desc .= " (default " . $options->{$key}->[0] . ")";
             }  
             Trace("  $name $desc") if T(0);  
         }  
         exit(0);  
     }  
     # Return the parsed parameters.  
     return ($retOptions, @retParameters);  
 }  
   
 =head3 Setups  
   
 C<< my $count = Tracer::Setups(); >>  
   
 Return the number of times L</TSetup> has been called.  
   
 This method allows for the creation of conditional tracing setups where, for example, we  
 may want to set up tracing if nobody else has done it before us.  
   
 =cut  
   
 sub Setups {  
     return $SetupCount;  
 }  
   
 =head3 Open  
   
 C<< my $handle = Open($fileHandle, $fileSpec, $message); >>  
   
 Open a file.  
   
 The I<$fileSpec> is essentially the second argument of the PERL C<open>  
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
   
     Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  
   
 would open for output appended to the specified file, and  
   
     Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  
   
 would open a pipe that sorts the records written and removes duplicates. Note  
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
   
     my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  
   
 The I<$message> parameter is used if the open fails. If it is set to C<0>, then  
 the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a  
 failed open will throw an exception and the third parameter will be used to construct  
 an error message. If the parameter is omitted, a standard message is constructed  
 using the file spec.  
   
     Could not open "/usr/spool/news/twitlog"  
   
 Note that the mode characters are automatically cleaned from the file name.  
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
   
     Could not open "/usr/spool/news/twitlog": file not found.  
   
 In some versions of PERL the only error message we get is a number, which  
 corresponds to the C++ C<errno> value.  
   
     Could not open "/usr/spool/news/twitlog": 6.  
   
 =over 4  
   
 =item fileHandle  
   
 File handle. If this parameter is C<undef>, a file handle will be generated  
 and returned as the value of this method.  
   
 =item fileSpec  
   
 File name and mode, as per the PERL C<open> function.  
   
 =item message (optional)  
   
 Error message to use if the open fails. If omitted, a standard error message  
 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>.  
   
 =item RETURN  
   
 Returns the name of the file handle assigned to the file, or C<undef> if the  
 open failed.  
   
 =back  
   
 =cut  
   
 sub Open {  
     # Get the parameters.  
     my ($fileHandle, $fileSpec, $message) = @_;  
     # Attempt to open the file.  
     my $rv = open $fileHandle, $fileSpec;  
     # If the open failed, generate an error message.  
     if (! $rv) {  
         # Save the system error message.  
         my $sysMessage = $!;  
         # See if we need a default message.  
         if (!$message) {  
             # Clean any obvious mode characters and leading spaces from the  
             # filename.  
             my ($fileName) = FindNamePart($fileSpec);  
             $message = "Could not open \"$fileName\"";  
         }  
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
     }  
     # Return the file handle.  
     return $fileHandle;  
 }  
   
 =head3 FindNamePart  
   
 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>.  
   
     >>/usr/fig/myfile.txt  
     </usr/fig/myfile.txt  
     | sort -u > /usr/fig/myfile.txt  
   
 If the method cannot find a file name using its normal methods, it will return the  
 whole incoming string.  
   
 =over 4  
   
 =item fileSpec  
   
 File specification string from which the file name is to be extracted.  
   
 =item RETURN  
   
 Returns a three-element list. The first element contains the file name portion of  
 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.  
   
 =back  
   
 =cut  
 #: Return Type $;  
 sub FindNamePart {  
     # Get the parameters.  
     my ($fileSpec) = @_;  
     # Default to the whole input string.  
     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);  
     # Parse out the file name if we can.  
     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {  
         $retVal = $2;  
         $len = length $retVal;  
         $pos = (length $fileSpec) - (length $3) - $len;  
     }  
     # Return the result.  
     return ($retVal, $pos, $len);  
 }  
   
 =head3 OpenDir  
   
 C<< my @files = OpenDir($dirName, $filtered, $flag); >>  
   
 Open a directory and return all the file names. This function essentially performs  
 the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  
 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  
 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be  
 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,  
   
     my @files = OpenDir("/Volumes/fig/contigs", 1);  
   
 is effectively the same as  
   
     opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  
     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  
   
 Similarly, the following code  
   
     my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  
   
 Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  
 automatically returns an empty list if the directory fails to open.  
   
 =over 4  
   
 =item dirName  
   
 Name of the directory to open.  
   
 =item filtered  
   
 TRUE if files whose names begin with a period (C<.>) should be automatically removed  
 from the list, else FALSE.  
   
 =item flag  
   
 TRUE if a failure to open is okay, else FALSE  
   
 =back  
   
 =cut  
 #: Return Type @;  
 sub OpenDir {  
     # Get the parameters.  
     my ($dirName, $filtered, $flag) = @_;  
     # Declare the return variable.  
     my @retVal = ();  
     # Open the directory.  
     if (opendir(my $dirHandle, $dirName)) {  
         # The directory opened successfully. Get the appropriate list according to the  
         # strictures of the filter parameter.  
         if ($filtered) {  
             @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;  
         } else {  
             @retVal = readdir $dirHandle;  
         }  
     } elsif (! $flag) {  
         # Here the directory would not open and it's considered an error.  
         Confess("Could not open directory $dirName.");  
     }  
     # Return the result.  
     return @retVal;  
1644  }  }
1645                print "  $name $desc\n";
 =head3 SetLevel  
   
 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];  
1646  }  }
1647            exit(0);
 =head3 Now  
   
 C<< my $string = Tracer::Now(); >>  
   
 Return a displayable time stamp containing the local time.  
   
 =cut  
   
 sub Now {  
     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;  
1648  }  }
1649        # Trace the options, if applicable.
1650  # Pad a number to 2 digits.      if (T(3)) {
1651  sub _p2 {          my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1652      my ($value) = @_;          Trace("Selected options: " . join(", ", sort @parms) . ".");
     $value = "0$value" if ($value < 10);  
     return $value;  
1653  }  }
1654        # Return the parsed parameters.
1655  =head3 LogErrors      return ($retOptions, @retParameters);
   
 C<< Tracer::LogErrors($fileName); >>  
   
 Route the standard error output to a log file.  
   
 =over 4  
   
 =item fileName  
   
 Name of the file to receive the error output.  
   
 =back  
   
 =cut  
   
 sub LogErrors {  
     # Get the file name.  
     my ($fileName) = @_;  
     # Open the file as the standard error output.  
     open STDERR, '>', $fileName;  
1656  }  }
1657    
1658  =head3 ReadOptions  =head3 ReadOptions
1659    
1660  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1661    
1662  Read a set of options from a file. Each option is encoded in a line of text that has the  Read a set of options from a file. Each option is encoded in a line of text that has the
1663  format  format
# Line 851  Line 1718 
1718    
1719  =head3 GetOptions  =head3 GetOptions
1720    
1721  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
1722    
1723  Merge a specified set of options into a table of defaults. This method takes two hash references  Merge a specified set of options into a table of defaults. This method takes two hash references
1724  as input and uses the data from the second to update the first. If the second does not exist,  as input and uses the data from the second to update the first. If the second does not exist,
# Line 860  Line 1727 
1727    
1728  Consider the following example.  Consider the following example.
1729    
1730  C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1731    
1732  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1733  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
# Line 868  Line 1735 
1735  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1736  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1737    
1738  C<< {databaseType => 'Oracle'} >>      {databaseType => 'Oracle'}
1739    
1740  an error will occur because the B<databaseType> option does not exist.  an error will occur because the B<databaseType> option does not exist.
1741    
# Line 912  Line 1779 
1779    
1780  =head3 MergeOptions  =head3 MergeOptions
1781    
1782  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::MergeOptions(\%table, \%defaults);
1783    
1784  Merge default values into a hash table. This method looks at the key-value pairs in the  Merge default values into a hash table. This method looks at the key-value pairs in the
1785  second (default) hash, and if a matching key is not found in the first hash, the default  second (default) hash, and if a matching key is not found in the first hash, the default
# Line 944  Line 1811 
1811      }      }
1812  }  }
1813    
 =head3 Trace  
   
 C<< Trace($message); >>  
   
 Write a trace message to the target location specified in L</TSetup>. If there has not been  
 any prior call to B<TSetup>.  
   
 =over 4  
   
 =item message  
   
 Message to write.  
   
 =back  
   
 =cut  
   
 sub Trace {  
     # 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";  
         }  
     }  
 }  
   
 =head3 T  
   
 C<< my $switch = T($category, $traceLevel); >>  
   
     or  
   
 C<< my $switch = T($traceLevel); >>  
   
 Return TRUE if the trace level is at or above a specified value and the specified category  
 is active, else FALSE. If no category is specified, the caller's package name is used.  
   
 =over 4  
   
 =item category  
   
 Category to which the message belongs. If not specified, the caller's package name is  
 used.  
   
 =item traceLevel  
   
 Relevant tracing level.  
   
 =item RETURN  
   
 TRUE if a message at the specified trace level would appear in the trace, else FALSE.  
   
 =back  
   
 =cut  
   
 sub T {  
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
         # Get the parameters.  
         my ($category, $traceLevel) = @_;  
         if (!defined $traceLevel) {  
             # Here we have no category, so we need to get the calling package.  
             # The calling package is normally the first parameter. If it is  
             # omitted, the first parameter will be the tracelevel. So, the  
             # first thing we do is shift the so-called category into the  
             # $traceLevel variable where it belongs.  
             $traceLevel = $category;  
             my ($package, $fileName, $line) = caller;  
             # If there is no calling package, we default to "main".  
             if (!$package) {  
                 $category = "main";  
             } else {  
                 $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.");  
         }  
         $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));  
     }  
     # Return the computed result.  
     return $retVal;  
 }  
   
1814  =head3 ParseCommand  =head3 ParseCommand
1815    
1816  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1817    
1818  Parse a command line consisting of a list of parameters. The initial parameters may be option  Parse a command line consisting of a list of parameters. The initial parameters may be option
1819  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1820  off and merged into a table of default options. The remainder of the command line is  off and merged into a table of default options. The remainder of the command line is
1821  returned as a list of positional arguments. For example, consider the following invocation.  returned as a list of positional arguments. For example, consider the following invocation.
1822    
1823  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1824    
1825  In this case, the list @words will be treated as a command line. There are two options available,  In this case, the list @words will be treated as a command line and there are two options available,
1826  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
1827    
1828  C<< -logFile=error.log apple orange rutabaga >>      -logFile=error.log apple orange rutabaga
1829    
1830  then at the end of the invocation, C<$options> will be  then at the end of the invocation, C<$options> will be
1831    
1832  C<< { errors => 0, logFile => 'error.log' } >>      { errors => 0, logFile => 'error.log' }
1833    
1834  and C<@arguments> will contain  and C<@arguments> will contain
1835    
1836  C<< apple orange rutabaga >>      apple orange rutabaga
1837    
1838  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1839  support for quote characters.  support for quote characters. Options can be specified with single or double hyphens.
1840    
1841  =over 4  =over 4
1842    
# Line 1115  Line 1861 
1861      my ($optionTable, @inputList) = @_;      my ($optionTable, @inputList) = @_;
1862      # Process any options in the input list.      # Process any options in the input list.
1863      my %overrides = ();      my %overrides = ();
1864      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1865          # Get the current option.          # Get the current option.
1866          my $arg = shift @inputList;          my $arg = shift @inputList;
1867          # Pull out the option name.          # Pull out the option name.
1868          $arg =~ /^-([^=]*)/g;          $arg =~ /^--?([^=]*)/g;
1869          my $name = $1;          my $name = $1;
1870          # Check for an option value.          # Check for an option value.
1871          if ($arg =~ /\G=(.*)$/g) {          if ($arg =~ /\G=(.*)$/g) {
# Line 1141  Line 1887 
1887      return ($optionTable, @retVal);      return ($optionTable, @retVal);
1888  }  }
1889    
 =head3 Escape  
1890    
1891  C<< my $codedString = Tracer::Escape($realString); >>  =head2 File Utility Methods
1892    
1893  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  =head3 GetFile
1894  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
1895  result is to reverse the effect of L</UnEscape>.      my @fileContents = Tracer::GetFile($fileName);
1896    
1897        or
1898    
1899        my $fileContents = Tracer::GetFile($fileName);
1900    
1901    Return the entire contents of a file. In list context, line-ends are removed and
1902    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1903    
1904  =over 4  =over 4
1905    
1906  =item realString  =item fileName
1907    
1908  String to escape.  Name of the file to read.
1909    
1910  =item RETURN  =item RETURN
1911    
1912  Escaped equivalent of the real string.  In a list context, returns the entire file as a list with the line terminators removed.
1913    In a scalar context, returns the entire file as a string. If an error occurs opening
1914    the file, an empty list will be returned.
1915    
1916  =back  =back
1917    
1918  =cut  =cut
1919    
1920  sub Escape {  sub GetFile {
1921      # Get the parameter.      # Get the parameters.
1922      my ($realString) = @_;      my ($fileName) = @_;
1923      # Initialize the return variable.      # Declare the return variable.
1924      my $retVal = "";      my @retVal = ();
1925      # Loop through the parameter string, looking for sequences to escape.      # Open the file for input.
1926      while (length $realString > 0) {      my $handle = Open(undef, "<$fileName");
1927          # Look for the first sequence to escape.      # Read the whole file into the return variable, stripping off any terminator
1928          if ($realString =~ /^(.*?)([\n\t\r\\])/) {      # characters.
1929              # Here we found it. The text preceding the sequence is in $1. The sequence      my $lineCount = 0;
1930              # itself is in $2. First, move the clear text to the return variable.      while (my $line = <$handle>) {
1931              $retVal .= $1;          $lineCount++;
1932              # Strip the processed section off the real string.          $line = Strip($line);
1933              $realString = substr $realString, (length $2) + (length $1);          push @retVal, $line;
             # 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;  
1934              }              }
1935        # Close it.
1936        close $handle;
1937        my $actualLines = @retVal;
1938        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
1939        # Return the file's contents in the desired format.
1940        if (wantarray) {
1941            return @retVal;
1942          } else {          } else {
1943              # Here there are no more escape sequences. The rest of the string is          return join "\n", @retVal;
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
         }  
1944      }      }
     # Return the result.  
     return $retVal;  
1945  }  }
1946    
1947  =head3 UnEscape  =head3 PutFile
1948    
1949  C<< my $realString = Tracer::UnEscape($codedString); >>      Tracer::PutFile($fileName, \@lines);
1950    
1951  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Write out a file from a list of lines of text.
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
1952    
1953  =over 4  =over 4
1954    
1955  =item codedString  =item fileName
1956    
1957  String to un-escape.  Name of the output file.
1958    
1959  =item RETURN  =item lines
1960    
1961  Returns a copy of the original string with the escape sequences converted to their actual  Reference to a list of text lines. The lines will be written to the file in order, with trailing
1962  values.  new-line characters. Alternatively, may be a string, in which case the string will be written without
1963    modification.
1964    
1965  =back  =back
1966    
1967  =cut  =cut
1968    
1969  sub UnEscape {  sub PutFile {
1970      # Get the parameter.      # Get the parameters.
1971      my ($codedString) = @_;      my ($fileName, $lines) = @_;
1972      # Initialize the return variable.      # Open the output file.
1973      my $retVal = "";      my $handle = Open(undef, ">$fileName");
1974      # Only proceed if the incoming string is nonempty.      # Count the lines written.
1975      if (defined $codedString) {      if (ref $lines ne 'ARRAY') {
1976          # Loop through the parameter string, looking for escape sequences. We can't do          # Here we have a scalar, so we write it raw.
1977          # translating because it causes problems with the escaped slash. ("\\t" becomes          print $handle $lines;
1978          # "\<tab>" no matter what we do.)          Trace("Scalar put to file $fileName.") if T(File => 3);
         while (length $codedString > 0) {  
             # Look for the first escape sequence.  
             if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {  
                 # Here we found it. The text preceding the sequence is in $1. The sequence  
                 # itself is in $2. First, move the clear text to the return variable.  
                 $retVal .= $1;  
                 $codedString = substr $codedString, (2 + length $1);  
                 # Get the escape value.  
                 my $char = $2;  
                 # If we have a "\r", we are done.  
                 if ($char ne 'r') {  
                     # Here it's not an 'r', so we convert it.  
                     $char =~ tr/\\tn/\\\t\n/;  
                     $retVal .= $char;  
                 }  
1979              } else {              } else {
1980                  # Here there are no more escape sequences. The rest of the string is          # Write the lines one at a time.
1981                  # transferred unmodified.          my $count = 0;
1982                  $retVal .= $codedString;          for my $line (@{$lines}) {
1983                  $codedString = "";              print $handle "$line\n";
1984              }              $count++;
1985          }          }
1986            Trace("$count lines put to file $fileName.") if T(File => 3);
1987      }      }
1988      # Return the result.      # Close the output file.
1989      return $retVal;      close $handle;
1990  }  }
1991    
1992  =head3 ParseRecord  =head3 ParseRecord
1993    
1994  C<< my @fields = Tracer::ParseRecord($line); >>      my @fields = Tracer::ParseRecord($line);
1995    
1996  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1997  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
# Line 1303  Line 2036 
2036    
2037  =head3 Merge  =head3 Merge
2038    
2039  C<< my @mergedList = Tracer::Merge(@inputList); >>      my @mergedList = Tracer::Merge(@inputList);
2040    
2041  Sort a list of strings and remove duplicates.  Sort a list of strings and remove duplicates.
2042    
# Line 1349  Line 2082 
2082      return @inputList;      return @inputList;
2083  }  }
2084    
2085  =head3 Percent  =head3 Open
2086    
2087  C<< my $percent = Tracer::Percent($number, $base); >>      my $handle = Open($fileHandle, $fileSpec, $message);
2088    
2089  Returns the percent of the base represented by the given number. If the base  Open a file.
2090  is zero, returns zero.  
2091    The I<$fileSpec> is essentially the second argument of the PERL C<open>
2092    function. The mode is specified using Unix-like shell information. So, for
2093    example,
2094    
2095        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2096    
2097    would open for output appended to the specified file, and
2098    
2099        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2100    
2101    would open a pipe that sorts the records written and removes duplicates. Note
2102    the use of file handle syntax in the Open call. To use anonymous file handles,
2103    code as follows.
2104    
2105        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2106    
2107    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2108    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2109    failed open will throw an exception and the third parameter will be used to construct
2110    an error message. If the parameter is omitted, a standard message is constructed
2111    using the file spec.
2112    
2113        Could not open "/usr/spool/news/twitlog"
2114    
2115    Note that the mode characters are automatically cleaned from the file name.
2116    The actual error message from the file system will be captured and appended to the
2117    message in any case.
2118    
2119        Could not open "/usr/spool/news/twitlog": file not found.
2120    
2121    In some versions of PERL the only error message we get is a number, which
2122    corresponds to the C++ C<errno> value.
2123    
2124        Could not open "/usr/spool/news/twitlog": 6.
2125    
2126  =over 4  =over 4
2127    
2128  =item number  =item fileHandle
2129    
2130  Percent numerator.  File handle. If this parameter is C<undef>, a file handle will be generated
2131    and returned as the value of this method.
2132    
2133  =item base  =item fileSpec
2134    
2135  Percent base.  File name and mode, as per the PERL C<open> function.
2136    
2137    =item message (optional)
2138    
2139    Error message to use if the open fails. If omitted, a standard error message
2140    will be generated. In either case, the error information from the file system
2141    is appended to the message. To specify a conditional open that does not throw
2142    an error if it fails, use C<0>.
2143    
2144  =item RETURN  =item RETURN
2145    
2146  Returns the percentage of the base represented by the numerator.  Returns the name of the file handle assigned to the file, or C<undef> if the
2147    open failed.
2148    
2149  =back  =back
2150    
2151  =cut  =cut
2152    
2153  sub Percent {  sub Open {
2154      # Get the parameters.      # Get the parameters.
2155      my ($number, $base) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2156      # Declare the return variable.      # Attempt to open the file.
2157      my $retVal = 0;      my $rv = open $fileHandle, $fileSpec;
2158      # Compute the percent.      # If the open failed, generate an error message.
2159      if ($base != 0) {      if (! $rv) {
2160          $retVal = $number * 100 / $base;          # Save the system error message.
2161            my $sysMessage = $!;
2162            # See if we need a default message.
2163            if (!$message) {
2164                # Clean any obvious mode characters and leading spaces from the
2165                # filename.
2166                my ($fileName) = FindNamePart($fileSpec);
2167                $message = "Could not open \"$fileName\"";
2168      }      }
2169      # Return the result.          # Terminate with an error using the supplied message and the
2170      return $retVal;          # error message from the file system.
2171            Confess("$message: $!");
2172        }
2173        # Return the file handle.
2174        return $fileHandle;
2175  }  }
2176    
2177  =head3 GetFile  =head3 FindNamePart
2178    
2179  C<< my @fileContents = Tracer::GetFile($fileName); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2180    
2181      or  Extract the portion of a file specification that contains the file name.
2182    
2183    A file specification is the string passed to an C<open> call. It specifies the file
2184    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2185    method assumes that the file name is whatever follows the first angle bracket
2186    sequence.  So, for example, in the following strings the file name is
2187    C</usr/fig/myfile.txt>.
2188    
2189  C<< my $fileContents = Tracer::GetFile($fileName); >>      >>/usr/fig/myfile.txt
2190        </usr/fig/myfile.txt
2191        | sort -u > /usr/fig/myfile.txt
2192    
2193  Return the entire contents of a file. In list context, line-ends are removed and  If the method cannot find a file name using its normal methods, it will return the
2194  each line is a list element. In scalar context, line-ends are replaced by C<\n>.  whole incoming string.
2195    
2196  =over 4  =over 4
2197    
2198  =item fileName  =item fileSpec
2199    
2200  Name of the file to read.  File specification string from which the file name is to be extracted.
2201    
2202  =item RETURN  =item RETURN
2203    
2204  In a list context, returns the entire file as a list with the line terminators removed.  Returns a three-element list. The first element contains the file name portion of
2205  In a scalar context, returns the entire file as a string. If an error occurs opening  the specified string, or the whole string if a file name cannot be found via normal
2206  the file, an empty list will be returned.  methods. The second element contains the start position of the file name portion and
2207    the third element contains the length.
2208    
2209  =back  =back
2210    
2211  =cut  =cut
2212    #: Return Type $;
2213  sub GetFile {  sub FindNamePart {
2214      # Get the parameters.      # Get the parameters.
2215      my ($fileName) = @_;      my ($fileSpec) = @_;
2216      # Declare the return variable.      # Default to the whole input string.
2217      my @retVal = ();      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2218      # Open the file for input.      # Parse out the file name if we can.
2219      my $handle = Open(undef, "<$fileName");      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2220      # Read the whole file into the return variable, stripping off any terminator          $retVal = $2;
2221      # characters.          $len = length $retVal;
2222      my $lineCount = 0;          $pos = (length $fileSpec) - (length $3) - $len;
     while (my $line = <$handle>) {  
         $lineCount++;  
         $line = Strip($line);  
         push @retVal, $line;  
     }  
     # Close it.  
     close $handle;  
     my $actualLines = @retVal;  
     # Return the file's contents in the desired format.  
     if (wantarray) {  
         return @retVal;  
     } else {  
         return join "\n", @retVal;  
2223      }      }
2224        # Return the result.
2225        return ($retVal, $pos, $len);
2226  }  }
2227    
2228  =head3 PutFile  =head3 OpenDir
2229    
2230  C<< Tracer::PutFile($fileName, \@lines); >>      my @files = OpenDir($dirName, $filtered, $flag);
2231    
2232  Write out a file from a list of lines of text.  Open a directory and return all the file names. This function essentially performs
2233    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2234    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2235    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2236    filtered out of the return list. If the directory does not open and I<$flag> is not
2237    set, an exception is thrown. So, for example,
2238    
2239        my @files = OpenDir("/Volumes/fig/contigs", 1);
2240    
2241    is effectively the same as
2242    
2243        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2244        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2245    
2246    Similarly, the following code
2247    
2248        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2249    
2250    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2251    automatically returns an empty list if the directory fails to open.
2252    
2253  =over 4  =over 4
2254    
2255  =item fileName  =item dirName
2256    
2257  Name of the output file.  Name of the directory to open.
2258    
2259  =item lines  =item filtered
2260    
2261  Reference to a list of text lines. The lines will be written to the file in order, with trailing  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2262  new-line characters.  from the list, else FALSE.
2263    
2264    =item flag
2265    
2266    TRUE if a failure to open is okay, else FALSE
2267    
2268  =back  =back
2269    
2270  =cut  =cut
2271    #: Return Type @;
2272  sub PutFile {  sub OpenDir {
2273      # Get the parameters.      # Get the parameters.
2274      my ($fileName, $lines) = @_;      my ($dirName, $filtered, $flag) = @_;
2275      # Open the output file.      # Declare the return variable.
2276      my $handle = Open(undef, ">$fileName");      my @retVal = ();
2277      # Write the lines.      # Open the directory.
2278      for my $line (@{$lines}) {      if (opendir(my $dirHandle, $dirName)) {
2279          print $handle "$line\n";          # The directory opened successfully. Get the appropriate list according to the
2280            # strictures of the filter parameter.
2281            if ($filtered) {
2282                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2283            } else {
2284                @retVal = readdir $dirHandle;
2285            }
2286        } elsif (! $flag) {
2287            # Here the directory would not open and it's considered an error.
2288            Confess("Could not open directory $dirName.");
2289      }      }
2290      # Close the output file.      # Return the result.
2291      close $handle;      return @retVal;
2292  }  }
2293    
 =head3 QTrace  
2294    
2295  C<< my $data = QTrace($format); >>  =head3 Insure
2296    
2297  Return the queued trace data in the specified format.      Insure($dirName, $chmod);
2298    
2299    Insure a directory is present.
2300    
2301  =over 4  =over 4
2302    
2303  =item format  =item dirName
2304    
2305  C<html> to format the data as an HTML list, C<text> to format it as straight text.  Name of the directory to check. If it does not exist, it will be created.
2306    
2307    =item chmod (optional)
2308    
2309    Security privileges to be given to the directory if it is created.
2310    
2311  =back  =back
2312    
2313  =cut  =cut
2314    
2315  sub QTrace {  sub Insure {
2316      # Get the parameter.      my ($dirName, $chmod) = @_;
2317      my ($format) = @_;      if (! -d $dirName) {
2318      # Create the return variable.          Trace("Creating $dirName directory.") if T(2);
2319      my $retVal = "";          eval {
2320      # Only proceed if there is an actual queue.              mkpath $dirName;
2321      if (@Queue) {              # If we have permissions specified, set them here.
2322          # Process according to the format.              if (defined($chmod)) {
2323          if ($format =~ m/^HTML$/i) {                  chmod $chmod, $dirName;
             # Convert the queue into an HTML list.  
             $retVal = "<ul>\n";  
             for my $line (@Queue) {  
                 my $escapedLine = CGI::escapeHTML($line);  
                 $retVal .= "<li>$escapedLine</li>\n";  
2324              }              }
2325              $retVal .= "</ul>\n";          };
2326          } elsif ($format =~ m/^TEXT$/i) {          if ($@) {
2327              # Convert the queue into a list of text lines.              Confess("Error creating $dirName: $@");
             $retVal = join("\n", @Queue) . "\n";  
2328          }          }
         # Clear the queue.  
         @Queue = ();  
2329      }      }
     # Return the formatted list.  
     return $retVal;  
2330  }  }
2331    
2332  =head3 Confess  =head3 ChDir
   
 C<< Confess($message); >>  
   
 Trace the call stack and abort the program with the specified message. When used with  
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
2333    
2334  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      ChDir($dirName);
2335    
2336  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Change to the specified directory.
2337    
2338  =over 4  =over 4
2339    
2340  =item message  =item dirName
2341    
2342  Message to include in the trace.  Name of the directory to which we want to change.
2343    
2344  =back  =back
2345    
2346  =cut  =cut
2347    
2348  sub Confess {  sub ChDir {
2349      # Get the parameters.      my ($dirName) = @_;
2350      my ($message) = @_;      if (! -d $dirName) {
2351      # Trace the call stack.          Confess("Cannot change to directory $dirName: no such directory.");
2352      Cluck($message);      } else {
2353      # Abort the program.          Trace("Changing to directory $dirName.") if T(File => 4);
2354      croak(">>> $message");          my $okFlag = chdir $dirName;
2355  }          if (! $okFlag) {
2356                Confess("Error switching to directory $dirName.");
 =head3 Assert  
   
 C<< Assert($condition1, $condition2, ... $conditionN); >>  
   
 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;  
2357          }          }
2358      }      }
     return $retVal;  
2359  }  }
2360    
2361  =head3 Cluck  =head3 SetPermissions
   
 C<< Cluck($message); >>  
2362    
2363  Trace the call stack. Note that for best results, you should qualify the call with a      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
 trace condition. For example,  
2364    
2365  C<< Cluck("Starting record parse.") if T(3); >>  Set the permissions for a directory and all the files and folders inside it.
2366    In addition, the group ownership will be changed to the specified value.
2367    
2368  will only trace the stack if the trace level for the package is 3 or more.  This method is more vulnerable than most to permission and compatability
2369    problems, so it does internal error recovery.
2370    
2371  =over 4  =over 4
2372    
2373  =item message  =item dirName
   
 Message to include in the trace.  
2374    
2375  =back  Name of the directory to process.
2376    
2377  =cut  =item group
2378    
2379  sub Cluck {  Name of the group to be assigned.
     # Get the parameters.  
     my ($message) = @_;  
     # Trace what's happening.  
     Trace("Stack trace for event: $message");  
     my $confession = longmess($message);  
     # Convert the confession to a series of trace messages. Note we skip any  
     # messages relating to calls into Tracer.  
     for my $line (split /\s*\n/, $confession) {  
         Trace($line) if ($line !~ /Tracer\.pm/);  
     }  
 }  
2380    
2381  =head3 Min  =item mask
2382    
2383  C<< my $min = Min($value1, $value2, ... $valueN); >>  Permission mask. Bits that are C<1> in this mask will be ORed into the
2384    permission bits of any file or directory that does not already have them
2385    set to 1.
2386    
2387  Return the minimum argument. The arguments are treated as numbers.  =item otherMasks
2388    
2389  =over 4  Map of search patterns to permission masks. If a directory name matches
2390    one of the patterns, that directory and all its members and subdirectories
2391    will be assigned the new pattern. For example, the following would
2392    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2393    
2394  =item $value1, $value2, ... $valueN      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2395    
2396  List of numbers to compare.  The list is ordered, so the following would use 0777 for C<tmp1> and
2397    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2398    
2399  =item RETURN      Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2400                                                       '^tmp' => 0666);
2401    
2402  Returns the lowest number in the list.  Note that the pattern matches are all case-insensitive, and only directory
2403    names are matched, not file names.
2404    
2405  =back  =back
2406    
2407  =cut  =cut
2408    
2409  sub Min {  sub SetPermissions {
2410      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2411      my ($retVal, @values) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2412      # Loop through the remaining parameters, looking for the lowest.      # Set up for error recovery.
2413      for my $value (@values) {      eval {
2414          if ($value < $retVal) {          # Switch to the specified directory.
2415              $retVal = $value;          ChDir($dirName);
2416            # Get the group ID.
2417            my $gid = getgrnam($group);
2418            # Get the mask for tracing.
2419            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2420            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2421            my $fixCount = 0;
2422            my $lookCount = 0;
2423            # @dirs will be a stack of directories to be processed.
2424            my @dirs = (getcwd());
2425            while (scalar(@dirs) > 0) {
2426                # Get the current directory.
2427                my $dir = pop @dirs;
2428                # Check for a match to one of the specified directory names. To do
2429                # that, we need to pull the individual part of the name off of the
2430                # whole path.
2431                my $simpleName = $dir;
2432                if ($dir =~ m!/([^/]+)$!) {
2433                    $simpleName = $1;
2434                }
2435                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2436                # Search for a match.
2437                my $match = 0;
2438                my $i;
2439                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2440                    my $pattern = $otherMasks[$i];
2441                    if ($simpleName =~ /$pattern/i) {
2442                        $match = 1;
2443          }          }
2444      }      }
2445      # Return the minimum found.              # Check for a match. Note we use $i-1 because the loop added 2
2446      return $retVal;              # before terminating due to the match.
2447                if ($match && $otherMasks[$i-1] != $mask) {
2448                    # This directory matches one of the incoming patterns, and it's
2449                    # a different mask, so we process it recursively with that mask.
2450                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2451                } else {
2452                    # Here we can process normally. Get all of the non-hidden members.
2453                    my @submems = OpenDir($dir, 1);
2454                    for my $submem (@submems) {
2455                        # Get the full name.
2456                        my $thisMem = "$dir/$submem";
2457                        Trace("Checking member $thisMem.") if T(4);
2458                        $lookCount++;
2459                        if ($lookCount % 1000 == 0) {
2460                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2461                        }
2462                        # Fix the group.
2463                        chown -1, $gid, $thisMem;
2464                        # Insure this member is not a symlink.
2465                        if (! -l $thisMem) {
2466                            # Get its info.
2467                            my $fileInfo = stat $thisMem;
2468                            # Only proceed if we got the info. Otherwise, it's a hard link
2469                            # and we want to skip it anyway.
2470                            if ($fileInfo) {
2471                                my $fileMode = $fileInfo->mode;
2472                                if (($fileMode & $mask) != $mask) {
2473                                    # Fix this member.
2474                                    $fileMode |= $mask;
2475                                    chmod $fileMode, $thisMem;
2476                                    $fixCount++;
2477                                }
2478                                # If it's a subdirectory, stack it.
2479                                if (-d $thisMem) {
2480                                    push @dirs, $thisMem;
2481                                }
2482                            }
2483                        }
2484                    }
2485                }
2486            }
2487            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2488        };
2489        # Check for an error.
2490        if ($@) {
2491            Confess("SetPermissions error: $@");
2492        }
2493  }  }
2494    
2495  =head3 Max  =head3 GetLine
2496    
2497  C<< my $max = Max($value1, $value2, ... $valueN); >>      my @data = Tracer::GetLine($handle);
2498    
2499  Return the maximum argument. The arguments are treated as numbers.  Read a line of data from a tab-delimited file.
2500    
2501  =over 4  =over 4
2502    
2503  =item $value1, $value2, ... $valueN  =item handle
2504    
2505  List of numbers to compare.  Open file handle from which to read.
2506    
2507  =item RETURN  =item RETURN
2508    
2509  Returns the highest number in the list.  Returns a list of the fields in the record read. The fields are presumed to be
2510    tab-delimited. If we are at the end of the file, then an empty list will be
2511    returned. If an empty line is read, a single list item consisting of a null
2512    string will be returned.
2513    
2514  =back  =back
2515    
2516  =cut  =cut
2517    
2518  sub Max {  sub GetLine {
2519      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2520      my ($retVal, @values) = @_;      my ($handle) = @_;
2521      # Loop through the remaining parameters, looking for the highest.      # Declare the return variable.
2522      for my $value (@values) {      my @retVal = ();
2523          if ($value > $retVal) {      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2524              $retVal = $value;      # Read from the file.
2525        my $line = <$handle>;
2526        # Only proceed if we found something.
2527        if (defined $line) {
2528            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2529            # upload control and have a nonstandard EOL combination.
2530            $line =~ s/(\r|\n)+$//;
2531            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2532            if (T(File => 4)) {
2533                my $escapedLine = $line;
2534                $escapedLine =~ s/\n/\\n/g;
2535                $escapedLine =~ s/\r/\\r/g;
2536                $escapedLine =~ s/\t/\\t/g;
2537                Trace("Line read: -->$escapedLine<--");
2538            }
2539            # If the line is empty, return a single empty string; otherwise, parse
2540            # it into fields.
2541            if ($line eq "") {
2542                push @retVal, "";
2543            } else {
2544                push @retVal, split /\t/,$line;
2545          }          }
2546        } else {
2547            # Trace the reason the read failed.
2548            Trace("End of file: $!") if T(File => 3);
2549      }      }
2550      # Return the maximum found.      # Return the result.
2551      return $retVal;      return @retVal;
2552  }  }
2553    
2554  =head3 AddToListMap  =head3 PutLine
2555    
2556  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>      Tracer::PutLine($handle, \@fields, $eol);
2557    
2558  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Write a line of data to a tab-delimited file. The specified field values will be
2559  is created for the key. Otherwise, the new value is pushed onto the list.  output in tab-separated form, with a trailing new-line.
2560    
2561  =over 4  =over 4
2562    
2563  =item hash  =item handle
2564    
2565  Reference to the target hash.  Output file handle.
2566    
2567  =item key  =item fields
2568    
2569  Key for which the value is to be added.  List of field values.
2570    
2571  =item value1, value2, ... valueN  =item eol (optional)
2572    
2573  List of values to add to the key's value list.  End-of-line character (default is "\n").
2574    
2575  =back  =back
2576    
2577  =cut  =cut
2578    
2579  sub AddToListMap {  sub PutLine {
2580      # Get the parameters.      # Get the parameters.
2581      my ($hash, $key, @values) = @_;      my ($handle, $fields, $eol) = @_;
2582      # Process according to whether or not the key already has a value.      # Write the data.
2583      if (! exists $hash->{$key}) {      print $handle join("\t", @{$fields}) . ($eol || "\n");
         $hash->{$key} = [@values];  
     } else {  
         push @{$hash->{$key}}, @values;  
     }  
2584  }  }
2585    
 =head3 DebugMode  
   
 C<< if (Tracer::DebugMode) { ...code... } >>  
   
 Return TRUE if debug mode has been turned on, else output an error  
 page and return FALSE.  
   
 Certain CGI scripts are too dangerous to exist in the production  
 environment. This method provides a simple way to prevent them  
 from working unless they are explicitly turned on by creating a password  
 cookie via the B<SetPassword> script.  If debugging mode  
 is not turned on, an error web page will be output directing the  
 user to enter in the correct password.  
2586    
 =cut  
2587    
2588  sub DebugMode {  =head2 Other Useful Methods
     # Declare the return variable.  
     my $retVal = 0;  
     # Check the debug configuration.  
     my $password = CGI::cookie("DebugMode");  
     my $encrypted = Digest::MD5::md5_hex($password);  
     if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {  
         $retVal = 1;  
     } else {  
         # Here debug mode is off, so we generate an error page.  
         my $pageString = PageBuilder::Build("<<Html/ErrorPage.html", {}, "Html");  
         print $pageString;  
     }  
     # Return the determination indicator.  
     return $retVal;  
 }  
2589    
2590  =head3 Strip  =head3 ParseParm
2591    
2592  C<< my $string = Tracer::Strip($line); >>      my $listValue = Tracer::ParseParm($string);
2593    
2594  Strip all line terminators off a string. This is necessary when dealing with files  Convert a parameter into a list reference. If the parameter is undefined,
2595  that may have been transferred back and forth several times among different  an undefined value will be returned. Otherwise, it will be parsed as a
2596  operating environments.  comma-separated list of values.
2597    
2598  =over 4  =over 4
2599    
2600  =item line  =item string
2601    
2602  Line of text to be stripped.  Incoming string.
2603    
2604  =item RETURN  =item RETURN
2605    
2606  The same line of text with all the line-ending characters chopped from the end.  Returns a reference to a list of values, or C<undef> if the incoming value
2607    was undefined.
2608    
2609  =back  =back
2610    
2611  =cut  =cut
2612    
2613  sub Strip {  sub ParseParm {
2614      # Get a copy of the parameter string.      # Get the parameters.
2615      my ($string) = @_;      my ($string) = @_;
2616      my $retVal = (defined $string ? $string : "");      # Declare the return variable.
2617      # Strip the line terminator characters.      my $retVal;
2618      $retVal =~ s/(\r|\n)+$//g;      # Check for data.
2619        if (defined $string) {
2620            # We have some, so split it into a list.
2621            $retVal = [ split /\s*,\s*/, $string];
2622        }
2623      # Return the result.      # Return the result.
2624      return $retVal;      return $retVal;
2625  }  }
2626    
 =head3 Pad  
2627    
 C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>  
2628    
 Pad a string to a specified length. The pad character will be a  
 space, and the padding will be on the right side unless specified  
 in the third parameter.  
2629    
2630  =over 4  =head3 Now
2631    
2632  =item string      my $string = Tracer::Now();
2633    
2634  String to be padded.  Return a displayable time stamp containing the local time.
2635    
2636  =item len  =cut
2637    
2638  Desired length of the padded string.  sub Now {
2639        my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
2640        my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2641                     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2642        return $retVal;
2643    }
2644    
2645  =item left (optional)  # Pad a number to 2 digits.
2646    sub _p2 {
2647        my ($value) = @_;
2648        $value = "0$value" if ($value < 10);
2649        return $value;
2650    }
2651    
2652  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  =head3 Escape
2653    
2654  =item padChar (optional)      my $codedString = Tracer::Escape($realString);
2655    
2656  Character to use for padding. The default is a space.  Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2657    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2658    result is to reverse the effect of L</UnEscape>.
2659    
2660    =over 4
2661    
2662    =item realString
2663    
2664    String to escape.
2665    
2666  =item RETURN  =item RETURN
2667    
2668  Returns a copy of the original string with the pad character added to the  Escaped equivalent of the real string.
 specified end so that it achieves the desired length.  
2669    
2670  =back  =back
2671    
2672  =cut  =cut
2673    
2674  sub Pad {  sub Escape {
2675      # Get the parameters.      # Get the parameter.
2676      my ($string, $len, $left, $padChar) = @_;      my ($realString) = @_;
2677      # Compute the padding character.      # Initialize the return variable.
2678      if (! defined $padChar) {      my $retVal = "";
2679          $padChar = " ";      # Loop through the parameter string, looking for sequences to escape.
2680        while (length $realString > 0) {
2681            # Look for the first sequence to escape.
2682            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2683                # Here we found it. The text preceding the sequence is in $1. The sequence
2684                # itself is in $2. First, move the clear text to the return variable.
2685                $retVal .= $1;
2686                # Strip the processed section off the real string.
2687                $realString = substr $realString, (length $2) + (length $1);
2688                # Get the matched character.
2689                my $char = $2;
2690                # If we have a CR, we are done.
2691                if ($char ne "\r") {
2692                    # It's not a CR, so encode the escape sequence.
2693                    $char =~ tr/\t\n/tn/;
2694                    $retVal .= "\\" . $char;
2695      }      }
     # Compute the number of spaces needed.  
     my $needed = $len - length $string;  
     # Copy the string into the return variable.  
     my $retVal = $string;  
     # Only proceed if padding is needed.  
     if ($needed > 0) {  
         # Create the pad string.  
         my $pad = $padChar x $needed;  
         # Affix it to the return value.  
         if ($left) {  
             $retVal = $pad . $retVal;  
2696          } else {          } else {
2697              $retVal .= $pad;              # Here there are no more escape sequences. The rest of the string is
2698                # transferred unmodified.
2699                $retVal .= $realString;
2700                $realString = "";
2701          }          }
2702      }      }
2703      # Return the result.      # Return the result.
2704      return $retVal;      return $retVal;
2705  }  }
2706    
2707  =head3 EOF  =head3 UnEscape
   
 This is a constant that is lexically greater than any useful string.  
   
 =cut  
   
 sub EOF {  
     return "\xFF\xFF\xFF\xFF\xFF";  
 }  
   
 =head3 TICK  
   
 C<< my @results = TICK($commandString); >>  
   
 Perform a back-tick operation on a command. If this is a Windows environment, any leading  
 dot-slash (C<./> will be removed. So, for example, if you were doing  
   
     `./protein.cgi`  
   
 from inside a CGI script, it would work fine in Unix, but would issue an error message  
 in Windows complaining that C<'.'> is not a valid command. If instead you code  
2708    
2709      TICK("./protein.cgi")      my $realString = Tracer::UnEscape($codedString);
2710    
2711  it will work correctly in both environments.  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2712    a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2713    be deleted.
2714    
2715  =over 4  =over 4
2716    
2717  =item commandString  =item codedString
2718    
2719  The command string to pass to the system.  String to un-escape.
2720    
2721  =item RETURN  =item RETURN
2722    
2723  Returns the standard output from the specified command, as a list.  Returns a copy of the original string with the escape sequences converted to their actual
2724    values.
2725    
2726  =back  =back
2727    
2728  =cut  =cut
2729  #: Return Type @;  
2730  sub TICK {  sub UnEscape {
2731      # Get the parameters.      # Get the parameter.
2732      my ($commandString) = @_;      my ($codedString) = @_;
2733      # Chop off the dot-slash if this is Windows.      # Initialize the return variable.
2734      if ($FIG_Config::win_mode) {      my $retVal = "";
2735          $commandString =~ s!^\./!!;      # Only proceed if the incoming string is nonempty.
2736        if (defined $codedString) {
2737            # Loop through the parameter string, looking for escape sequences. We can't do
2738            # translating because it causes problems with the escaped slash. ("\\t" becomes
2739            # "\<tab>" no matter what we do.)
2740            while (length $codedString > 0) {
2741                # Look for the first escape sequence.
2742                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2743                    # Here we found it. The text preceding the sequence is in $1. The sequence
2744                    # itself is in $2. First, move the clear text to the return variable.
2745                    $retVal .= $1;
2746                    $codedString = substr $codedString, (2 + length $1);
2747                    # Get the escape value.
2748                    my $char = $2;
2749                    # If we have a "\r", we are done.
2750                    if ($char ne 'r') {
2751                        # Here it's not an 'r', so we convert it.
2752                        $char =~ tr/\\tn/\\\t\n/;
2753                        $retVal .= $char;
2754      }      }
2755      # Activate the command and return the result.              } else {
2756      return `$commandString`;                  # Here there are no more escape sequences. The rest of the string is
2757                    # transferred unmodified.
2758                    $retVal .= $codedString;
2759                    $codedString = "";
2760                }
2761            }
2762        }
2763        # Return the result.
2764        return $retVal;
2765  }  }
2766    
2767  =head3 ScriptSetup  =head3 Percent
   
 C<< my ($query, $varHash) = ScriptSetup(); >>  
2768    
2769  Perform standard tracing and debugging setup for scripts. The value returned is      my $percent = Tracer::Percent($number, $base);
 the CGI object followed by a pre-built variable hash.  
2770    
2771  The C<Trace> query parameter is used to determine whether or not tracing is active and  Returns the percent of the base represented by the given number. If the base
2772  which trace modules (other than C<Tracer> and C<FIG>) should be turned on. Specifying  is zero, returns zero.
 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.  
2773    
2774  =cut  =over 4
2775    
2776  sub ScriptSetup {  =item number
     # Get the CGI query object.  
     my $query = CGI->new();  
     # Check for tracing. Set it up if the user asked for it.  
     if ($query->param('Trace')) {  
         # Set up tracing to be queued for display at the bottom of the web page.  
         TSetup($query->param('Trace') . " FIG Tracer", "QUEUE");  
         # Trace the parameter and environment data.  
         if (T(CGI => 3)) {  
             # Here we want to trace the parameter data.  
             my @names = $query->param;  
             for my $parmName (sort @names) {  
                 # Note we skip "Trace", which is for our use only.  
                 if ($parmName ne 'Trace') {  
                     my @values = $query->param($parmName);  
                     Trace("CGI: $parmName = " . join(", ", @values));  
                 }  
             }  
         }  
         if (T(CGI => 4)) {  
             # Here we want the environment data too.  
             for my $envName (sort keys %ENV) {  
                 Trace("ENV: $envName = $ENV{$envName}");  
             }  
         }  
     } else {  
         # Here tracing is to be turned off. All we allow is errors traced into the  
         # error log.  
         TSetup("0", "WARN");  
     }  
     # Create the variable hash.  
     my $varHash = { DebugData => '' };  
     # If we're in DEBUG mode, set up the debug mode data for forms.  
     if (Tracer::DebugMode) {  
         $varHash->{DebugData} = GetFile("Html/DebugFragment.html");  
     }  
     # Return the query object and variable hash.  
     return ($query, $varHash);  
 }  
2777    
2778  =head3 ScriptFinish  Percent numerator.
2779    
2780  C<< ScriptFinish($webData, $varHash); >>  =item base
2781    
2782  Output a web page at the end of a script. Either the string to be output or the  Percent base.
 name of a template file can be specified. If the second parameter is omitted,  
 it is assumed we have a string to be output; otherwise, it is assumed we have the  
 name of a template file. The template should have the variable C<DebugData>  
 specified in any form that invokes a standard script. If debugging mode is turned  
 on, a form field will be put in that allows the user to enter tracing data.  
 Trace messages will be placed immediately before the terminal C<BODY> tag in  
 the output, formatted as a list.  
2783    
2784  A typical standard script would loook like the following.  =item RETURN
2785    
2786      BEGIN {  Returns the percentage of the base represented by the numerator.
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
     }  
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
2787    
2788      my ($query, $varHash) = ScriptSetup();  =back
2789      eval {  
2790          # ... get data from $query, put it in $varHash ...  =cut
2791      };  
2792      if ($@) {  sub Percent {
2793          Trace("Script Error: $@") if T(0);      # Get the parameters.
2794        my ($number, $base) = @_;
2795        # Declare the return variable.
2796        my $retVal = 0;
2797        # Compute the percent.
2798        if ($base != 0) {
2799            $retVal = $number * 100 / $base;
2800        }
2801        # Return the result.
2802        return $retVal;
2803      }      }
     ScriptFinish("Html/MyTemplate.html", $varHash);  
2804    
2805  The idea here is that even if the script fails, you'll see trace messages and  =head3 Min
2806  useful output.  
2807        my $min = Min($value1, $value2, ... $valueN);
2808    
2809    Return the minimum argument. The arguments are treated as numbers.
2810    
2811  =over 4  =over 4
2812    
2813  =item webData  =item $value1, $value2, ... $valueN
2814    
2815  A string containing either the full web page to be written to the output or the  List of numbers to compare.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
2816    
2817  =item varHash (optional)  =item RETURN
2818    
2819  If specified, then a reference to a hash mapping variable names for a template  Returns the lowest number in the list.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
2820    
2821  =back  =back
2822    
2823  =cut  =cut
2824    
2825  sub ScriptFinish {  sub Min {
2826      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
2827      my ($webData, $varHash) = @_;      my ($retVal, @values) = @_;
2828      # Check for a template file situation.      # Loop through the remaining parameters, looking for the lowest.
2829      my $outputString;      for my $value (@values) {
2830      if (defined $varHash) {          if ($value < $retVal) {
2831          # Here we have a template file. We need to apply the variables to the template.              $retVal = $value;
         $outputString = PageBuilder::Build("<<$webData", $varHash, "Html");  
     } else {  
         # Here the user gave us a raw string.  
         $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;  
2832          }          }
         substr $outputString, $pos, 0, QTrace('Html');  
2833      }      }
2834      # Write the output string.      # Return the minimum found.
2835      print $outputString;      return $retVal;
2836  }  }
2837    
2838  =head3 Insure  =head3 Max
2839    
2840  C<< Insure($dirName); >>      my $max = Max($value1, $value2, ... $valueN);
2841    
2842  Insure a directory is present.  Return the maximum argument. The arguments are treated as numbers.
2843    
2844  =over 4  =over 4
2845    
2846  =item dirName  =item $value1, $value2, ... $valueN
2847    
2848  Name of the directory to check. If it does not exist, it will be created.  List of numbers to compare.
2849    
2850    =item RETURN
2851    
2852    Returns the highest number in the list.
2853    
2854  =back  =back
2855    
2856  =cut  =cut
2857    
2858  sub Insure {  sub Max {
2859      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
2860      if (! -d $dirName) {      my ($retVal, @values) = @_;
2861          Trace("Creating $dirName directory.") if T(2);      # Loop through the remaining parameters, looking for the highest.
2862          eval { mkpath $dirName; };      for my $value (@values) {
2863          if ($@) {          if ($value > $retVal) {
2864              Confess("Error creating $dirName: $@");              $retVal = $value;
2865          }          }
2866      }      }
2867        # Return the maximum found.
2868        return $retVal;
2869  }  }
2870    
2871  =head3 ChDir  =head3 DebugMode
2872    
2873  C<< ChDir($dirName); >>      if (Tracer::DebugMode) { ...code... }
2874    
2875  Change to the specified directory.  Return TRUE if debug mode has been turned on, else abort.
2876    
2877    Certain CGI scripts are too dangerous to exist in the production
2878    environment. This method provides a simple way to prevent them
2879    from working unless they are explicitly turned on by creating a password
2880    cookie via the B<SetPassword> script.  If debugging mode
2881    is not turned on, an error will occur.
2882    
2883    =cut
2884    
2885    sub DebugMode {
2886        # Declare the return variable.
2887        my $retVal = 0;
2888        # Check the debug configuration.
2889        my $password = CGI::cookie("DebugMode");
2890        my $encrypted = Digest::MD5::md5_hex($password);
2891        if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
2892            $retVal = 1;
2893        } else {
2894            # Here debug mode is off, so we generate an error.
2895            Confess("Cannot use this facility without logging in.");
2896        }
2897        # Return the determination indicator.
2898        return $retVal;
2899    }
2900    
2901    =head3 Strip
2902    
2903        my $string = Tracer::Strip($line);
2904    
2905    Strip all line terminators off a string. This is necessary when dealing with files
2906    that may have been transferred back and forth several times among different
2907    operating environments.
2908    
2909  =over 4  =over 4
2910    
2911  =item dirName  =item line
2912    
2913  Name of the directory to which we want to change.  Line of text to be stripped.
2914    
2915    =item RETURN
2916    
2917    The same line of text with all the line-ending characters chopped from the end.
2918    
2919  =back  =back
2920    
2921  =cut  =cut
2922    
2923  sub ChDir {  sub Strip {
2924      my ($dirName) = @_;      # Get a copy of the parameter string.
2925      if (! -d $dirName) {      my ($string) = @_;
2926          Confess("Cannot change to directory $dirName: no such directory.");      my $retVal = (defined $string ? $string : "");
2927      } else {      # Strip the line terminator characters.
2928          Trace("Changing to directory $dirName.") if T(4);      $retVal =~ s/(\r|\n)+$//g;
2929          my $okFlag = chdir $dirName;      # Return the result.
2930          if (! $okFlag) {      return $retVal;
             Confess("Error switching to directory $dirName.");  
         }  
     }  
2931  }  }
2932    
2933  =head3 SendSMS  =head3 Pad
2934    
2935  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
2936    
2937  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  Pad a string to a specified length. The pad character will be a
2938  user name, password, and API ID for the relevant account in the hash reference variable  space, and the padding will be on the right side unless specified
2939  I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For  in the third parameter.
 example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID  
 is C<2561022>, then the FIG_Config file must contain  
2940    
2941      $phone =  { user => 'BruceTheHumanPet',  =over 4
                 password => 'silly',  
                 api_id => '2561022' };  
2942    
2943  The original purpose of this method was to insure Bruce would be notified immediately when the  =item string
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
2944    
2945  The message ID will be returned if successful, and C<undef> if an error occurs.  String to be padded.
2946    
2947  =over 4  =item len
2948    
2949  =item phoneNumber  Desired length of the padded string.
2950    
2951  Phone number to receive the message, in international format. A United States phone number  =item left (optional)
 would be prefixed by "1". A British phone number would be prefixed by "44".  
2952    
2953  =item msg  TRUE if the string is to be left-padded; otherwise it will be padded on the right.
2954    
2955  Message to send to the specified phone.  =item padChar (optional)
2956    
2957    Character to use for padding. The default is a space.
2958    
2959  =item RETURN  =item RETURN
2960    
2961  Returns the message ID if successful, and C<undef> if the message could not be sent.  Returns a copy of the original string with the pad character added to the
2962    specified end so that it achieves the desired length.
2963    
2964  =back  =back
2965    
2966  =cut  =cut
2967    
2968  sub SendSMS {  sub Pad {
2969      # Get the parameters.      # Get the parameters.
2970      my ($phoneNumber, $msg) = @_;      my ($string, $len, $left, $padChar) = @_;
2971      # Declare the return variable. If we do not change it, C<undef> will be returned.      # Compute the padding character.
2972      my $retVal;      if (! defined $padChar) {
2973      # Only proceed if we have phone support.          $padChar = " ";
2974      if (! defined $FIG_Config::phone) {      }
2975          Trace("Phone support not present in FIG_Config.") if T(1);      # Compute the number of spaces needed.
2976      } else {      my $needed = $len - length $string;
2977          # Get the phone data.      # Copy the string into the return variable.
2978          my $parms = $FIG_Config::phone;      my $retVal = $string;
2979          # Get the Clickatell URL.      # Only proceed if padding is needed.
2980          my $url = "http://api.clickatell.com/http/";      if ($needed > 0) {
2981          # Create the user agent.          # Create the pad string.
2982          my $ua = LWP::UserAgent->new;          my $pad = $padChar x $needed;
2983          # Request a Clickatell session.          # Affix it to the return value.
2984          my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},          if ($left) {
2985                                       password => $parms->{password},              $retVal = $pad . $retVal;
                                      api_id => $parms->{api_id},  
                                      to => $phoneNumber,  
                                      text => $msg});  
         # Check for an error.  
         if (! $resp->is_success) {  
             Trace("Alert failed.") if T(1);  
         } else {  
             # Get the message ID.  
             my $rstring = $resp->content;  
             if ($rstring =~ /^ID:\s+(.*)$/) {  
                 $retVal = $1;  
2986              } else {              } else {
2987                  Trace("Phone attempt failed with $rstring") if T(1);              $retVal .= $pad;
2988            }
2989              }              }
2990        # Return the result.
2991        return $retVal;
2992    }
2993    
2994    =head3 EOF
2995    
2996    This is a constant that is lexically greater than any useful string.
2997    
2998    =cut
2999    
3000    sub EOF {
3001        return "\xFF\xFF\xFF\xFF\xFF";
3002          }          }
3003    
3004    =head3 TICK
3005    
3006        my @results = TICK($commandString);
3007    
3008    Perform a back-tick operation on a command. If this is a Windows environment, any leading
3009    dot-slash (C<./> will be removed. So, for example, if you were doing
3010    
3011        `./protein.cgi`
3012    
3013    from inside a CGI script, it would work fine in Unix, but would issue an error message
3014    in Windows complaining that C<'.'> is not a valid command. If instead you code
3015    
3016        TICK("./protein.cgi")
3017    
3018    it will work correctly in both environments.
3019    
3020    =over 4
3021    
3022    =item commandString
3023    
3024    The command string to pass to the system.
3025    
3026    =item RETURN
3027    
3028    Returns the standard output from the specified command, as a list.
3029    
3030    =back
3031    
3032    =cut
3033    #: Return Type @;
3034    sub TICK {
3035        # Get the parameters.
3036        my ($commandString) = @_;
3037        # Chop off the dot-slash if this is Windows.
3038        if ($FIG_Config::win_mode) {
3039            $commandString =~ s!^\./!!;
3040      }      }
3041      # Return the result.      # Activate the command and return the result.
3042      return $retVal;      return `$commandString`;
3043  }  }
3044    
3045    
3046  =head3 CommaFormat  =head3 CommaFormat
3047    
3048  C<< my $formatted = Tracer::CommaFormat($number); >>      my $formatted = Tracer::CommaFormat($number);
3049    
3050  Insert commas into a number.  Insert commas into a number.
3051    
# Line 2190  Line 3078 
3078      # Return the result.      # Return the result.
3079      return $retVal;      return $retVal;
3080  }  }
 =head3 SetPermissions  
   
 C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>  
   
 Set the permissions for a directory and all the files and folders inside it.  
 In addition, the group ownership will be changed to the specified value.  
   
 This method is more vulnerable than most to permission and compatability  
 problems, so it does internal error recovery.  
   
 =over 4  
   
 =item dirName  
   
 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  
   
 Map of search patterns to permission masks. If a directory name matches  
 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>.  
3081    
     Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);  
   
 The list is ordered, so the following would use 0777 for C<tmp1> and  
 0666 for C<tmp>, C<tmp2>, or C<tmp3>.  
   
     Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,  
                                                    '^tmp' => 0666);  
   
 Note that the pattern matches are all case-insensitive, and only directory  
 names are matched, not file names.  
   
 =back  
   
 =cut  
   
 sub SetPermissions {  
     # Get the parameters.  
     my ($dirName, $group, $mask, @otherMasks) = @_;  
     # Set up for error recovery.  
     eval {  
         # Switch to the specified directory.  
         ChDir($dirName);  
         # Get the group ID.  
         my $gid = getgrnam($group);  
         # Get the mask for tracing.  
         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;  
             }  
             Trace("Simple directory name for $dir is $simpleName.") if T(4);  
             # 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);  
             } else {  
                 # Here we can process normally. Get all of the non-hidden members.  
                 my @submems = OpenDir($dir, 1);  
                 for my $submem (@submems) {  
                     # Get the full name.  
                     my $thisMem = "$dir/$submem";  
                     Trace("Checking member $thisMem.") if T(4);  
                     $lookCount++;  
                     if ($lookCount % 1000 == 0) {  
                         Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(3);  
                     }  
                     # 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) != $mask) {  
                                 # Fix this member.  
                                 $fileMode |= $mask;  
                                 chmod $fileMode, $thisMem;  
                                 $fixCount++;  
                             }  
                             # If it's a subdirectory, stack it.  
                             if (-d $thisMem) {  
                                 push @dirs, $thisMem;  
                             }  
                         }  
                     }  
                 }  
             }  
         }  
         Trace("$lookCount files and directories processed, $fixCount fixed.") if T(2);  
     };  
     # Check for an error.  
     if ($@) {  
         Confess("SetPermissions error: $@");  
     }  
 }  
3082    
3083  =head3 CompareLists  =head3 CompareLists
3084    
3085  C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3086    
3087  Compare two lists of tuples, and return a hash analyzing the differences. The lists  Compare two lists of tuples, and return a hash analyzing the differences. The lists
3088  are presumed to be sorted alphabetically by the value in the $keyIndex column.  are presumed to be sorted alphabetically by the value in the $keyIndex column.
# Line 2391  Line 3147 
3147      return ($inserted, $deleted);      return ($inserted, $deleted);
3148  }  }
3149    
3150    =head3 GenerateURL
3151    
3152        my $queryUrl = Tracer::GenerateURL($page, %parameters);
3153    
3154    Generate a GET-style URL for the specified page with the specified parameter
3155    names and values. The values will be URL-escaped automatically. So, for
3156    example
3157    
3158        Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3159    
3160    would return
3161    
3162        form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3163    
3164    =over 4
3165    
3166    =item page
3167    
3168    Page URL.
3169    
3170    =item parameters
3171    
3172    Hash mapping parameter names to parameter values.
3173    
3174    =item RETURN
3175    
3176    Returns a GET-style URL that goes to the specified page and passes in the
3177    specified parameters and values.
3178    
3179    =back
3180    
3181    =cut
3182    
3183    sub GenerateURL {
3184        # Get the parameters.
3185        my ($page, %parameters) = @_;
3186        # Prime the return variable with the page URL.
3187        my $retVal = $page;
3188        # Loop through the parameters, creating parameter elements in a list.
3189        my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3190        # If the list is nonempty, tack it on.
3191        if (@parmList) {
3192            $retVal .= "?" . join(";", @parmList);
3193        }
3194        # Return the result.
3195        return $retVal;
3196    }
3197    
3198    =head3 ApplyURL
3199    
3200        Tracer::ApplyURL($table, $target, $url);
3201    
3202    Run through a two-dimensional table (or more accurately, a list of lists), converting the
3203    I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3204    URL column will be deleted by this process and the target column will be HTML-escaped.
3205    
3206    This provides a simple way to process the results of a database query into something
3207    displayable by combining a URL with text.
3208    
3209    =over 4
3210    
3211    =item table
3212    
3213    Reference to a list of lists. The elements in the containing list will be updated by
3214    this method.
3215    
3216    =item target
3217    
3218    The index of the column to be converted into HTML.
3219    
3220    =item url
3221    
3222    The index of the column containing the URL. Note that the URL must have a recognizable
3223    C<http:> at the beginning.
3224    
3225    =back
3226    
3227    =cut
3228    
3229    sub ApplyURL {
3230        # Get the parameters.
3231        my ($table, $target, $url) = @_;
3232        # Loop through the table.
3233        for my $row (@{$table}) {
3234            # Apply the URL to the target cell.
3235            $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3236            # Delete the URL from the row.
3237            delete $row->[$url];
3238        }
3239    }
3240    
3241    =head3 CombineURL
3242    
3243        my $combinedHtml = Tracer::CombineURL($text, $url);
3244    
3245    This method will convert the specified text into HTML hyperlinked to the specified
3246    URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3247    is defined and begins with an C<http:> header.
3248    
3249    =over 4
3250    
3251    =item text
3252    
3253    Text to return. This will be HTML-escaped automatically.
3254    
3255    =item url
3256    
3257    A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3258    will be returned without any hyperlinking.
3259    
3260    =item RETURN
3261    
3262    Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3263    doesn't look right, the HTML-escaped text will be returned without any further
3264    modification.
3265    
3266    =back
3267    
3268    =cut
3269    
3270    sub CombineURL {
3271        # Get the parameters.
3272        my ($text, $url) = @_;
3273        # Declare the return variable.
3274        my $retVal = CGI::escapeHTML($text);
3275        # Verify the URL.
3276        if (defined($url) && $url =~ m!http://!i) {
3277            # It's good, so we apply it to the text.
3278            $retVal = "<a href=\"$url\">$retVal</a>";
3279        }
3280        # Return the result.
3281        return $retVal;
3282    }
3283    
3284    =head3 Cmp
3285    
3286        my $cmp = Tracer::Cmp($a, $b);
3287    
3288    This method performs a universal sort comparison. Each value coming in is
3289    separated into a leading text part and a trailing number part. The text
3290    part is string compared, and if both parts are equal, then the number
3291    parts are compared numerically. A stream of just numbers or a stream of
3292    just strings will sort correctly, and a mixed stream will sort with the
3293    numbers first. Strings with a label and a number will sort in the
3294    expected manner instead of lexically.
3295    
3296    =over 4
3297    
3298    =item a
3299    
3300    First item to compare.
3301    
3302    =item b
3303    
3304    Second item to compare.
3305    
3306    =item RETURN
3307    
3308    Returns a negative number if the first item should sort first (is less), a positive
3309    number if the first item should sort second (is greater), and a zero if the items are
3310    equal.
3311    
3312    =back
3313    
3314    =cut
3315    
3316    sub Cmp {
3317        # Get the parameters.
3318        my ($a, $b) = @_;
3319        # Declare the return value.
3320        my $retVal;
3321        # Check for nulls.
3322        if (! defined($a)) {
3323            $retVal = (! defined($b) ? 0 : -1);
3324        } elsif (! defined($b)) {
3325            $retVal = 1;
3326        } else {
3327            # Here we have two real values. Parse the two strings.
3328            $a =~ /^(\D*)(\d*)$/;
3329            my $aParsed = [$1, $2];
3330            $b =~ /^(\D*)(\d*)$/;
3331            my $bParsed = [$1, $2];
3332            # Compare the string parts.
3333            $retVal = $aParsed->[0] cmp $bParsed->[0];
3334            if (! $retVal) {
3335                $retVal = $aParsed->[1] <=> $bParsed->[1];
3336            }
3337        }
3338        # Return the result.
3339        return $retVal;
3340    }
3341    
3342    
3343  1;  1;

Legend:
Removed from v.1.63  
changed lines
  Added in v.1.95

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3