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

Diff of /FigKernelPackages/Tracer.pm

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

revision 1.67, Fri Sep 29 15:00:17 2006 UTC revision 1.93, Tue Feb 5 02:17:29 2008 UTC
# Line 19  Line 19 
19    
20      require Exporter;      require Exporter;
21      @ISA = ('Exporter');      @ISA = ('Exporter');
22      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup ScriptSetup ScriptFinish Insure ChDir);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);
23      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);      @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);
24      use strict;      use strict;
25      use Carp qw(longmess croak);      use Carp qw(longmess croak);
# Line 34  Line 34 
34      use LWP::UserAgent;      use LWP::UserAgent;
35      use Time::HiRes 'gettimeofday';      use Time::HiRes 'gettimeofday';
36      use URI::Escape;      use URI::Escape;
37        use Time::Local;
38    
39  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
40    
41  =head2 Introduction  =head2 Tracing
42    
43  This package provides simple tracing for debugging and reporting purposes. To use it simply call the  This package provides simple tracing for debugging and reporting purposes. To use it simply call the
44  L</TSetup> method to set the options and call L</Trace> to write out trace messages. Each trace  L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
45  message has a I<trace level> and I<category> associated with it. In addition, the tracing package itself  L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
46  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace  each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
47  level is less than or equal to this package's trace level and whose category is activated will  level is less than or equal to the setup trace level and whose category is activated will
48  be written. Thus, a higher trace level on a message indicates that the message  be written. Thus, a higher trace level on a message indicates that the message
49  is less likely to be seen. A higher trace level passed to B<TSetup> means more trace messages will  is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
50  appear. To generate a trace message, use the following syntax.  appear.
51    
52  C<< Trace($message) if T(errors => 4); >>  =head3 Putting Trace Messages in Your Code
53    
54    To generate a trace message, use the following syntax.
55    
56        Trace($message) if T(errors => 4);
57    
58  This statement will produce a trace message if the trace level is 4 or more and the C<errors>  This statement will produce a trace message if the trace level is 4 or more and the C<errors>
59  category is active. Note that the special category C<main> is always active, so  category is active. There is a special category C<main> that is always active, so
60    
61  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
62    
63  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
64    
# Line 61  Line 66 
66  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
67  active and the trace level is 2 or more.  active and the trace level is 2 or more.
68    
69  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
70    
71    In scripts, where no package name is available, the category defaults to C<main>.
72    
73    =head3 Custom Tracing
74    
75  To set up tracing, you call the L</TSetup> method. The method takes as input a trace level, a list  Many programs have customized tracing configured using the L</TSetup> method. This is no longer
76  of category names, and a set of options. The trace level and list of category names are  the preferred method, but a knowledge of how custom tracing works can make the more modern
77    L</Emergency Tracing> easier to understand.
78    
79    To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
80    a list of category names, and a destination. The trace level and list of category names are
81  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
82    
83  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
84    
85  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
86  specifies that messages should be output as HTML paragraphs.  specifies that messages should be sent to the standard output.
87    
88  To turn on tracing for ALL categories, use an asterisk. The call below sets every category to  To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
89  level 3 and writes the output to the standard error output. This sort of thing might be  level 3 and writes the output to the standard error output. This sort of thing might be
90  useful in a CGI environment.  useful in a CGI environment.
91    
92  C<< TSetup('3 *', 'WARN'); >>      TSetup('3 *', 'WARN');
93    
94  In addition to HTML and file output for trace messages, you can specify that the trace messages  In addition standard error and file output for trace messages, you can specify that the trace messages
95  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
96  is useful if you are building a web page. Instead of having the trace messages interspersed with  is useful if you are building a web page. Instead of having the trace messages interspersed with
97  the page output, they can be gathered together and displayed at the end of the page. This makes  the page output, they can be gathered together and displayed at the end of the page. This makes
98  it easier to debug page formatting problems.  it easier to debug page formatting problems.
99    
100  Finally, you can specify that all trace messages be emitted as warnings.  Finally, you can specify that all trace messages be emitted to a file, or the standard output and
101    a file at the same time. To trace to a file, specify the filename with an output character in front
102    of it.
103    
104        TSetup('4 SQL', ">$fileName");
105    
106    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
107    bracket.
108    
109        TSetup('3 *', "+>$fileName");
110    
111  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
112  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
113  Thus, debugging information is available and easily retrieved even when the application is  Thus, debugging information is available and easily retrieved even when the application is
114  being used out in the field.  being used out in the field.
115    
116    =head3 Trace Levels
117    
118  There is no hard and fast rule on how to use trace levels. The following is therefore only  There is no hard and fast rule on how to use trace levels. The following is therefore only
119  a suggestion.  a suggestion.
120    
# Line 121  Line 145 
145    
146  =back  =back
147    
148    The format of trace messages is important because some utilities analyze trace files.
149    There are three fields-- the time stamp, the category name, and the text.
150    The time stamp is between square brackets and the category name between angle brackets.
151    After the category name there is a colon (C<:>) followed by the message text.
152    If the square brackets or angle brackets are missing, then the trace management
153    utilities assume that they are encountering a set of pre-formatted lines.
154    
155    Note, however, that this formatting is done automatically by the tracing functions. You
156    only need to know about it if you want to parse a trace file.
157    
158    =head3 Emergency Tracing
159    
160    Sometimes, you need a way for tracing to happen automatically without putting parameters
161    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
162    from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.
163    Emergency tracing requires you specify a tracing key. For command-line tools, the key is
164    taken from the C<TRACING> environment variable. For web services, the key is taken from
165    a cookie. Either way, the key tells the tracing facility who you are, so that you control
166    the tracing in your environment without stepping on other users.
167    
168    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
169    generate one for you.
170    
171    You can activate and de-activate emergency tracing from the debugging control panel, as
172    well as display the trace file itself.
173    
174    To enable emergency tracing in your code, call
175    
176        ETracing($cgi)
177    
178    from a web script and
179    
180        ETracing()
181    
182    from a command-line script.
183    
184    The web script will look for the tracing key in the cookies, and the command-line
185    script will look for it in the C<TRACING> environment variable. If you are
186    using the L</StandardScript> or L</StandardSetup> methods, emergency tracing
187    will be configured automatically.
188    
189    NOTE: to configure emergency tracing from the command line instead of the Debugging
190    Control Panel (see below), use the C<trace.pl> script.
191    
192    =head3 Debugging Control Panel
193    
194    The debugging control panel provides several tools to assist in development of
195    SEED and Sprout software. You access the debugging control panel from the URL
196    C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,
197    for example, the panel access point for the development NMPDR system is
198    C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to
199    find out what the password is. From this page, you can also specify a tracing
200    key. If you don't specify a key, one will be generated for you.
201    
202    =head4 Emergency Tracing Form
203    
204    At the bottom of the debugging control panel is a form that allows you to
205    specify a trace level and tracing categories. Special and common categories
206    are listed with check boxes. You can hold your mouse over a check box to see
207    what its category does. In general, however, a category name is the same as
208    the name of the package in which the trace message occurs.
209    
210    Additional categories can be entered in an input box, delimited by spaces or commas.
211    
212    The B<Activate> button turns on Emergency tracing at the level you specify with the
213    specified categories active. The B<Terminate> button turns tracing off. The
214    B<Show File> button displays the current contents of the trace file. The tracing
215    form at the bottom of the control panel is designed for emergency tracing, so it
216    will only affect programs that call L</ETracing>, L</StandardScript>,
217    or L</StandardSetup>.
218    
219    =head4 Script Form
220    
221    The top form of the debugging control panel allows you to enter a tiny script and
222    have the output generated in a formatted table. Certain object variables are
223    predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),
224    and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.
225    
226    The last line of the script must be a scalar, but it can be a reference to a hash,
227    a list, a list of lists, and various other combinations. If you select the appropriate
228    data type in the dropdown box, the output will be formatted accordingly. The form
229    also has controls for specifying tracing. These controls override any emergency
230    tracing in effect.
231    
232    =head4 Database Query Forms
233    
234    The forms between the script form and the emergency tracing form allow you to
235    make queries against the database. The FIG query form allows simple queries against
236    a single FIG table. The Sprout query form uses the B<GetAll> method to do a
237    multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>
238    package, and it takes five parameters.
239    
240        GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
241    
242    Each of the five parameters corresponds to a text box on the query form:
243    
244    =over 4
245    
246    =item Objects
247    
248    Comma-separated list containing the names of the entity and relationship objects to be retrieved.
249    
250    =item Filter
251    
252    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
253    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
254    B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a
255    field, I<objectName> is the name of the entity or relationship object containing the field, and
256    I<number> is the 1-based position of the object in the object list. Any parameters
257    specified in the filter clause should be specified in the B<Params> field.
258    The fields in a filter clause can come from primary entity relations,
259    relationship relations, or secondary entity relations; however, all of the
260    entities and relationships involved must be included in the list of object names.
261    
262    =item Params
263    
264    List of the parameters to be substituted in for the parameters marks in the filter clause. This
265    is a comma-separated list without any quoting or escaping.
266    
267    =item fields
268    
269    Comma-separated list of the fields to be returned in each element of the list returned. Fields
270    are specified in the same manner as in the filter clause.
271    
272    =item count
273    
274    Maximum number of records to return. If omitted or 0, all available records will be returned.
275    
276    =back
277    
278    B<GetAll> automatically joins together the entities and relationships listed in the object
279    names. This simplifies the coding of the filter clause, but it means that some queries are
280    not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation
281    that has yet to be addressed.
282    
283  =cut  =cut
284    
285  # Declare the configuration variables.  # Declare the configuration variables.
# Line 137  Line 296 
296  my $SetupCount = 0;         # number of times TSetup called  my $SetupCount = 0;         # number of times TSetup called
297  my $AllTrace = 0;           # TRUE if we are tracing all categories.  my $AllTrace = 0;           # TRUE if we are tracing all categories.
298    
299  =head2 Public Methods  =head2 Tracing Methods
300    
301    =head3 Setups
302    
303        my $count = Tracer::Setups();
304    
305    Return the number of times L</TSetup> has been called.
306    
307    This method allows for the creation of conditional tracing setups where, for example, we
308    may want to set up tracing if nobody else has done it before us.
309    
310    =cut
311    
312    sub Setups {
313        return $SetupCount;
314    }
315    
316  =head3 TSetup  =head3 TSetup
317    
318  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
319    
320  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
321  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 200  Line 374 
374          }          }
375          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
376              open TRACEFILE, $target;              open TRACEFILE, $target;
377              print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";
378              close TRACEFILE;              close TRACEFILE;
379              $Destination = ">$target";              $Destination = ">$target";
380          } else {          } else {
# Line 213  Line 387 
387      $SetupCount++;      $SetupCount++;
388  }  }
389    
390  =head3 StandardSetup  =head3 SetLevel
391    
392  C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>      Tracer::SetLevel($newLevel);
393    
394  This method performs standard command-line parsing and tracing setup. The return  Modify the trace level. A higher trace level will cause more messages to appear.
 values are a hash of the command-line options and a list of the positional  
 parameters. Tracing is automatically set up and the command-line options are  
 validated.  
395    
396  This is a complex method that does a lot of grunt work. The parameters can  =over 4
 be more easily understood, however, once they are examined individually.  
397    
398  The I<categories> parameter is the most obtuse. It is a reference to a list of  =item newLevel
 special-purpose tracing categories. Most tracing categories are PERL package  
 names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,  
 B<ERDB>, and B<SproutLoad> packages, you would specify the categories  
399    
400      ["Sprout", "SproutLoad", "ERDB"]  Proposed new trace level.
401    
402  This would cause trace messages in the specified three packages to appear in  =back
 the output. There are threer special tracing categories that are automatically  
 handled by this method. In other words, if you used L</TSetup> you would need  
 to include these categories manually, but if you use this method they are turned  
 on automatically.  
403    
404  =over 4  =cut
405    
406  =item FIG  sub SetLevel {
407        $TraceLevel = $_[0];
408    }
409    
410  Turns on trace messages inside the B<FIG> package.  =head3 ParseTraceDate
411    
412  =item SQL      my $time = Tracer::ParseTraceDate($dateString);
413    
414  Traces SQL commands and activity.  Convert a date from the trace file into a PERL timestamp.
415    
416  =item Tracer  =over 4
417    
418  Traces error messages and call stacks.  =item dateString
419    
420  =back  The date string from the trace file. The format of the string is determined by the
421    L</Now> method.
422    
423  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.  
424    
425      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
426    the time string is invalid.
427    
428  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  
429    
430  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.  
431    
432      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl  sub ParseTraceDate {
433        # Get the parameters.
434        my ($dateString) = @_;
435        # Declare the return variable.
436        my $retVal;
437        # Parse the date.
438        if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {
439            # Create a time object. Note we need to convert the day, month,
440            # and year to a different base. Years count from 1900, and
441            # the internal month value is relocated to January = 0.
442            $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);
443        }
444        # Return the result.
445        return $retVal;
446    }
447    
448  would send the trace output to C<traceBruce.log> in the temporary directory.  =head3 LogErrors
449    
450  The I<options> parameter is a reference to a hash containing the command-line      Tracer::LogErrors($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.  
451    
452  You can specify a different default trace level by setting C<$options->{trace}>  Route the standard error output to a log file.
 prior to calling this method.  
453    
454  An example at this point would help. Consider, for example, the command-line utility  =over 4
 C<TransactFeatures>. It accepts a list of positional parameters plus the options  
 C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute  
 the following code.  
455    
456      my ($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);  
457    
458    Name of the file to receive the error output.
459    
460  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<$options>. The  
 positional parameters are returned in C<@parameters>.  
461    
462  The following is a sample command line for C<TransactFeatures>.  =cut
463    
464      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl  sub LogErrors {
465        # Get the file name.
466        my ($fileName) = @_;
467        # Open the file as the standard error output.
468        open STDERR, '>', $fileName;
469    }
470    
471  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional  =head3 Trace
 parameters, and would find themselves in I<@parameters> after executing the  
 above code fragment. The tracing would be set to level 2, and the categories  
 would be C<FIG>, C<Tracer>, and <DocUtils>. C<FIG> and C<Tracer> are standard,  
 and C<DocUtils> was included because it came in within the first parameter  
 to this method. The I<$options> hash would be  
472    
473      { trace => 2, sql => 0, safe => 0,      Trace($message);
       noAlias => 1, start => ' ', tblFiles => 0 }  
474    
475  Use of C<StandardSetup> in this way provides a simple way of performing  Write a trace message to the target location specified in L</TSetup>. If there has not been
476  standard tracing setup and command-line parsing. Note that the caller is  any prior call to B<TSetup>.
 not even aware of the command-line switches C<-trace> and C<-sql>, which  
 are used by this method to control the tracing. If additional tracing features  
 need to be added in the future, they can be processed by this method without  
 upsetting the command-line utilities.  
477    
478  If the C<background> option is specified on the command line, then the  =over 4
 standard and error outputs will be directed to files in the temporary  
 directory, using the same suffix as the trace file. So, if the command  
 line specified  
479    
480      -user=Bruce -background  =item message
481    
482  then the trace output would go to C<traceBruce.log>, the standard output to  Message to write.
 C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to  
 simplify starting a command in the background.  
483    
484  Finally, if the special option C<-h> is specified, the option names will  =back
 be traced at level 0 and the program will exit without processing.  
 This provides a limited help capability. For example, if the user enters  
485    
486      TransactFeatures -h  =cut
487    
488  he would see the following output.  sub Trace {
489        # Get the parameters.
490        my ($message) = @_;
491        # Get the timestamp.
492        my $timeStamp = Now();
493        # Format the message. Note we strip off any line terminators at the end.
494        my $prefix = "[$timeStamp] <$LastCategory>: ";
495        my $formatted = $prefix . Strip($message);
496        # Process according to the destination.
497        if ($Destination eq "TEXT") {
498            # Write the message to the standard output.
499            print "$formatted\n";
500        } elsif ($Destination eq "ERROR") {
501            # Write the message to the error output.
502            print STDERR "$formatted\n";
503        } elsif ($Destination eq "QUEUE") {
504            # Push the message into the queue.
505            push @Queue, "$formatted";
506        } elsif ($Destination eq "HTML") {
507            # Convert the message to HTML and write it to the standard output.
508            my $escapedMessage = CGI::escapeHTML($message);
509            print "<p>$timeStamp $LastCategory: $escapedMessage</p>\n";
510        } elsif ($Destination eq "WARN") {
511           # Emit the message as a warning.
512           warn $message;
513        } elsif ($Destination =~ m/^>>/) {
514            # Write the trace message to an output file.
515            (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
516            print TRACING "$formatted\n";
517            close TRACING;
518            # If the Tee flag is on, echo it to the standard output.
519            if ($TeeFlag) {
520                print "$formatted\n";
521            }
522        }
523    }
524    
525      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  
526    
527  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,  
528    
529      { trace => [0, "tracing level (default 0)"],      or
        ...  
530    
531  would set the default trace level to 0 instead of 2, while      my $switch = T($traceLevel);
532    
533      { trace => ["2-", "tracing level (default 2)"],  Return TRUE if the trace level is at or above a specified value and the specified category
534         ...  is active, else FALSE. If no category is specified, the caller's package name is used.
535    
536  would leave the default at 2, but trace only to the log file, not to the  =over 4
 standard output.  
537    
538  The parameters to this method are as follows.  =item category
539    
540  =over 4  Category to which the message belongs. If not specified, the caller's package name is
541    used.
542    
543  =item categories  =item traceLevel
544    
545  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.  
546    
547  =item options  =item RETURN
548    
549  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.
 to their default values and descriptions. The user can override the defaults  
 by specifying the options as command-line switches prefixed by a hyphen.  
 Tracing-related options may be added to this hash. If the C<-h> option is  
 specified on the command line, the option descriptions will be used to  
 explain the options. To turn off tracing to the standard output, add a  
 minus sign to the value for C<trace> (see above).  
   
 =item parmHelp  
   
 A string that vaguely describes the positional parameters. This is used  
 if the user specifies the C<-h> option.  
   
 =item argv  
   
 List of command line parameters, including the option switches, which must  
 precede the positional parameters and be prefixed by a hyphen.  
   
 =item RETURN  
   
 Returns a list. The first element of the list is the reference to a hash that  
 maps the command-line option switches to their values. These will either be the  
 default values or overrides specified on the command line. The remaining  
 elements of the list are the position parameters, in order.  
550    
551  =back  =back
552    
553  =cut  =cut
554    
555  sub StandardSetup {  sub T {
556        # Declare the return variable.
557        my $retVal = 0;
558        # Only proceed if tracing is turned on.
559        if ($Destination ne "NONE") {
560      # Get the parameters.      # Get the parameters.
561      my ($categories, $options, $parmHelp, @argv) = @_;          my ($category, $traceLevel) = @_;
562      # Add the tracing options.          if (!defined $traceLevel) {
563      if (! exists $options->{trace}) {              # Here we have no category, so we need to get the calling package.
564          $options->{trace} = [2, "tracing level"];              # The calling package is normally the first parameter. If it is
565      }              # omitted, the first parameter will be the tracelevel. So, the
566      $options->{sql} = [0, "turn on SQL tracing"];              # first thing we do is shift the so-called category into the
567      $options->{h} = [0, "display command-line options"];              # $traceLevel variable where it belongs.
568      $options->{user} = [$$, "trace log file name suffix"];              $traceLevel = $category;
569      $options->{background} = [0, "spool standard and error output"];              my ($package, $fileName, $line) = caller;
570      # Create a parsing hash from the options hash. The parsing hash              # If there is no calling package, we default to "main".
571      # contains the default values rather than the default value              if (!$package) {
572      # and the description. While we're at it, we'll memorize the                  $category = "main";
     # length of the longest option name.  
     my $longestName = 0;  
     my %parseOptions = ();  
     for my $key (keys %{$options}) {  
         if (length $key > $longestName) {  
             $longestName = length $key;  
         }  
         $parseOptions{$key} = $options->{$key}->[0];  
     }  
     # Parse the command line.  
     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);  
     # Get the logfile suffix.  
     my $suffix = $retOptions->{user};  
     # Check for background mode.  
     if ($retOptions->{background}) {  
         my $outFileName = "$FIG_Config::temp/out$suffix.log";  
         my $errFileName = "$FIG_Config::temp/err$suffix.log";  
         open STDOUT, ">$outFileName";  
         open STDERR, ">$errFileName";  
     }  
     # Now we want to set up tracing. First, we need to know if SQL is to  
     # be traced.  
     my @cats = @{$categories};  
     if ($retOptions->{sql}) {  
         push @cats, "SQL";  
     }  
     # Add the default categories.  
     push @cats, "Tracer", "FIG";  
     # Next, we create the category string by joining the categories.  
     my $cats = join(" ", @cats);  
     # Check to determine whether or not the caller wants to turn off tracing  
     # to the standard output.  
     my $traceLevel = $retOptions->{trace};  
     my $textOKFlag = 1;  
     if ($traceLevel =~ /^(.)-/) {  
         $traceLevel = $1;  
         $textOKFlag = 0;  
     }  
     # Now we set up the trace mode.  
     my $traceMode;  
     # Verify that we can open a file in the FIG temporary directory.  
     my $traceFileName = "$FIG_Config::temp/trace$suffix.log";  
     if (open TESTTRACE, ">$traceFileName") {  
         # Here we can trace to a file.  
         $traceMode = ">$traceFileName";  
         if ($textOKFlag) {  
             # Echo to standard output if the text-OK flag is set.  
             $traceMode = "+$traceMode";  
         }  
         # Close the test file.  
         close TESTTRACE;  
     } else {  
         # Here we can't trace to a file. We trace to the standard output if it's  
         # okay, and the error log otherwise.  
         if ($textOKFlag) {  
             $traceMode = "TEXT";  
573          } else {          } else {
574              $traceMode = "WARN";                  my @cats = split /::/, $package;
575          }                  $category = $cats[$#cats];
576      }      }
     # Now set up the tracing.  
     TSetup("$traceLevel $cats", $traceMode);  
     # Check for the "h" option. If it is specified, dump the command-line  
     # options and exit the program.  
     if ($retOptions->{h}) {  
         $0 =~ m#[/\\](\w+)(\.pl)?$#i;  
         Trace("$1 [options] $parmHelp") if T(0);  
         for my $key (sort keys %{$options}) {  
             my $name = Pad($key, $longestName, 0, ' ');  
             my $desc = $options->{$key}->[1];  
             if ($options->{$key}->[0]) {  
                 $desc .= " (default " . $options->{$key}->[0] . ")";  
577              }              }
578              Trace("  $name $desc") if T(0);          # Save the category name.
579            $LastCategory = $category;
580            # Convert it to lower case before we hash it.
581            $category = lc $category;
582            # Use the category and tracelevel to compute the result.
583            if (ref $traceLevel) {
584                Confess("Bad trace level.");
585            } elsif (ref $TraceLevel) {
586                Confess("Bad trace config.");
587          }          }
588          exit(0);          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
589      }      }
590      # Return the parsed parameters.      # Return the computed result.
591      return ($retOptions, @retParameters);      return $retVal;
592  }  }
593    
594  =head3 Setups  =head3 QTrace
595    
596  C<< my $count = Tracer::Setups(); >>      my $data = QTrace($format);
597    
598  Return the number of times L</TSetup> has been called.  Return the queued trace data in the specified format.
599    
600  This method allows for the creation of conditional tracing setups where, for example, we  =over 4
601  may want to set up tracing if nobody else has done it before us.  
602    =item format
603    
604    C<html> to format the data as an HTML list, C<text> to format it as straight text.
605    
606    =back
607    
608  =cut  =cut
609    
610  sub Setups {  sub QTrace {
611      return $SetupCount;      # Get the parameter.
612        my ($format) = @_;
613        # Create the return variable.
614        my $retVal = "";
615        # Only proceed if there is an actual queue.
616        if (@Queue) {
617            # Process according to the format.
618            if ($format =~ m/^HTML$/i) {
619                # Convert the queue into an HTML list.
620                $retVal = "<ul>\n";
621                for my $line (@Queue) {
622                    my $escapedLine = CGI::escapeHTML($line);
623                    $retVal .= "<li>$escapedLine</li>\n";
624                }
625                $retVal .= "</ul>\n";
626            } elsif ($format =~ m/^TEXT$/i) {
627                # Convert the queue into a list of text lines.
628                $retVal = join("\n", @Queue) . "\n";
629            }
630            # Clear the queue.
631            @Queue = ();
632        }
633        # Return the formatted list.
634        return $retVal;
635  }  }
636    
637  =head3 Open  =head3 Confess
638    
639  C<< my $handle = Open($fileHandle, $fileSpec, $message); >>      Confess($message);
640    
641  Open a file.  Trace the call stack and abort the program with the specified message. When used with
642    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
643    So, for example
644    
645  The I<$fileSpec> is essentially the second argument of the PERL C<open>      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
 function. The mode is specified using Unix-like shell information. So, for  
 example,  
646    
647      Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");  Will abort the program with a stack trace if the value of C<$recNum> is negative.
648    
649  would open for output appended to the specified file, and  =over 4
650    
651      Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");  =item message
652    
653  would open a pipe that sorts the records written and removes duplicates. Note  Message to include in the trace.
 the use of file handle syntax in the Open call. To use anonymous file handles,  
 code as follows.  
654    
655      my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");  =back
656    
657  The I<$message> parameter is used if the open fails. If it is set to C<0>, then  =cut
 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.  
658    
659      Could not open "/usr/spool/news/twitlog"  sub Confess {
660        # Get the parameters.
661        my ($message) = @_;
662        if (! defined($FIG_Config::no_tool_hdr)) {
663            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
664            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
665            # Only proceed if the tool header file is actually present.
666            if (-f $toolHeaderFile) {
667                my @lines = GetFile($toolHeaderFile);
668                Trace("Tool header has " . scalar(@lines) . " lines.");
669            }
670        }
671        # Trace the call stack.
672        Cluck($message);
673        # Abort the program.
674        croak(">>> $message");
675    }
676    
677  Note that the mode characters are automatically cleaned from the file name.  =head3 Assert
 The actual error message from the file system will be captured and appended to the  
 message in any case.  
678    
679      Could not open "/usr/spool/news/twitlog": file not found.      Assert($condition1, $condition2, ... $conditionN);
680    
681  In some versions of PERL the only error message we get is a number, which  Return TRUE if all the conditions are true. This method can be used in conjunction with
682  corresponds to the C++ C<errno> value.  the OR operator and the L</Confess> method as a debugging assert.
683    So, for example
684    
685      Could not open "/usr/spool/news/twitlog": 6.      Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
686    
687  =over 4  Will abort the program with a stack trace if the value of C<$recNum> is negative.
688    
689  =item fileHandle  =cut
690    sub Assert {
691        my $retVal = 1;
692        LOOP: for my $condition (@_) {
693            if (! $condition) {
694                $retVal = 0;
695                last LOOP;
696            }
697        }
698        return $retVal;
699    }
700    
701  File handle. If this parameter is C<undef>, a file handle will be generated  =head3 Cluck
 and returned as the value of this method.  
702    
703  =item fileSpec      Cluck($message);
704    
705  File name and mode, as per the PERL C<open> function.  Trace the call stack. Note that for best results, you should qualify the call with a
706    trace condition. For example,
707    
708  =item message (optional)      Cluck("Starting record parse.") if T(3);
709    
710  Error message to use if the open fails. If omitted, a standard error message  will only trace the stack if the trace level for the package is 3 or more.
 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>.  
711    
712  =item RETURN  =over 4
713    
714  Returns the name of the file handle assigned to the file, or C<undef> if the  =item message
715  open failed.  
716    Message to include in the trace.
717    
718  =back  =back
719    
720  =cut  =cut
721    
722  sub Open {  sub Cluck {
723      # Get the parameters.      # Get the parameters.
724      my ($fileHandle, $fileSpec, $message) = @_;      my ($message) = @_;
725      # Attempt to open the file.      # Trace what's happening.
726      my $rv = open $fileHandle, $fileSpec;      Trace("Stack trace for event: $message");
727      # If the open failed, generate an error message.      my $confession = longmess($message);
728      if (! $rv) {      # Convert the confession to a series of trace messages. Note we skip any
729          # Save the system error message.      # messages relating to calls into Tracer.
730          my $sysMessage = $!;      for my $line (split /\s*\n/, $confession) {
731          # See if we need a default message.          Trace($line) if ($line !~ /Tracer\.pm/);
732          if (!$message) {      }
733              # Clean any obvious mode characters and leading spaces from the  }
734              # filename.  
735              my ($fileName) = FindNamePart($fileSpec);  =head3 ScriptSetup
736              $message = "Could not open \"$fileName\"";  
737        my ($cgi, $varHash) = ScriptSetup($noTrace);
738    
739    Perform standard tracing and debugging setup for scripts. The value returned is
740    the CGI object followed by a pre-built variable hash. At the end of the script,
741    the client should call L</ScriptFinish> to output the web page.
742    
743    This method calls L</ETracing> to configure tracing, which allows the tracing
744    to be configured via the emergency tracing form on the debugging control panel.
745    Tracing will then be turned on automatically for all programs that use the L</ETracing>
746    method, which includes every program that uses this method or L</StandardSetup>.
747    
748    =over 4
749    
750    =item noTrace (optional)
751    
752    If specified, tracing will be suppressed. This is useful if the script wants to set up
753    tracing manually.
754    
755    =item RETURN
756    
757    Returns a two-element list consisting of a CGI query object and a variable hash for
758    the output page.
759    
760    =back
761    
762    =cut
763    
764    sub ScriptSetup {
765        # Get the parameters.
766        my ($noTrace) = @_;
767        # Get the CGI query object.
768        my $cgi = CGI->new();
769        # Set up tracing if it's not suppressed.
770        ETracing($cgi) unless $noTrace;
771        # Create the variable hash.
772        my $varHash = { results => '' };
773        # Return the query object and variable hash.
774        return ($cgi, $varHash);
775    }
776    
777    =head3 ETracing
778    
779        ETracing($parameter);
780    
781    Set up emergency tracing. Emergency tracing is tracing that is turned
782    on automatically for any program that calls this method. The emergency
783    tracing parameters are stored in a a file identified by a tracing key.
784    If this method is called with a CGI object, then the tracing key is
785    taken from a cookie. If it is called with no parameters, then the tracing
786    key is taken from an environment variable. If it is called with a string,
787    the tracing key is that string.
788    
789    =over 4
790    
791    =item parameter
792    
793    A parameter from which the tracing key is computed. If it is a scalar,
794    that scalar is used as the tracing key. If it is a CGI object, the
795    tracing key is taken from the C<IP> cookie. If it is omitted, the
796    tracing key is taken from the C<TRACING> environment variable. If it
797    is a CGI object and emergency tracing is not on, the C<Trace> and
798    C<TF> parameters will be used to determine the type of tracing.
799    
800    =back
801    
802    =cut
803    
804    sub ETracing {
805        # Get the parameter.
806        my ($parameter) = @_;
807        # Check for CGI mode.
808        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
809        # Default to no tracing except errors.
810        my ($tracing, $dest) = ("0", "WARN");
811        # Check for emergency tracing.
812        my $tkey = EmergencyKey($parameter);
813        my $emergencyFile = EmergencyFileName($tkey);
814        if (-e $emergencyFile) {
815            # We have the file. Read in the data.
816            my @tracing = GetFile($emergencyFile);
817            # Pull off the time limit.
818            my $expire = shift @tracing;
819            # Convert it to seconds.
820            $expire *= 3600;
821            # Check the file data.
822            my $stat = stat($emergencyFile);
823            my ($now) = gettimeofday;
824            if ($now - $stat->mtime > $expire) {
825                # Delete the expired file.
826                unlink $emergencyFile;
827            } else {
828                # Emergency tracing is on. Pull off the destination and
829                # the trace level;
830                $dest = shift @tracing;
831                my $level = shift @tracing;
832                # Convert the destination to a real tracing destination.
833                # temp directory.
834                $dest = EmergencyTracingDest($tkey, $dest);
835                # Insure Tracer is specified.
836                my %moduleHash = map { $_ => 1 } @tracing;
837                $moduleHash{Tracer} = 1;
838                # Set the trace parameter.
839                $tracing = join(" ", $level, sort keys %moduleHash);
840            }
841        } elsif (defined $cgi) {
842            # There's no emergency tracing, but we have a CGI object, so check
843            # for tracing from the form parameters.
844            if ($cgi->param('Trace')) {
845                # Here the user has requested tracing via a form.
846                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
847                $tracing = $cgi->param('Trace') . " Tracer";
848            }
849        }
850        # Setup the tracing we've determined from all the stuff above.
851        TSetup($tracing, $dest);
852        # If we're a web script, trace the parameter and environment data.
853        if (defined $cgi) {
854            TraceParms($cgi);
855        }
856    }
857    
858    =head3 EmergencyFileName
859    
860        my $fileName = Tracer::EmergencyFileName($tkey);
861    
862    Return the emergency tracing file name. This is the file that specifies
863    the tracing information.
864    
865    =over 4
866    
867    =item tkey
868    
869    Tracing key for the current program.
870    
871    =item RETURN
872    
873    Returns the name of the file to contain the emergency tracing information.
874    
875    =back
876    
877    =cut
878    
879    sub EmergencyFileName {
880        # Get the parameters.
881        my ($tkey) = @_;
882        # Compute the emergency tracing file name.
883        return "$FIG_Config::temp/Emergency$tkey.txt";
884    }
885    
886    =head3 EmergencyFileTarget
887    
888        my $fileName = Tracer::EmergencyFileTarget($tkey);
889    
890    Return the emergency tracing target file name. This is the file that receives
891    the tracing output for file-based tracing.
892    
893    =over 4
894    
895    =item tkey
896    
897    Tracing key for the current program.
898    
899    =item RETURN
900    
901    Returns the name of the file to contain the trace output.
902    
903    =back
904    
905    =cut
906    
907    sub EmergencyFileTarget {
908        # Get the parameters.
909        my ($tkey) = @_;
910        # Compute the emergency tracing file name.
911        return "$FIG_Config::temp/trace$tkey.log";
912    }
913    
914    =head3 EmergencyTracingDest
915    
916        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
917    
918    This method converts an emergency tracing destination to a real
919    tracing destination. The main difference is that if the
920    destination is C<FILE> or C<APPEND>, we convert it to file
921    output. If the destination is C<DUAL>, we convert it to file
922    and standard output.
923    
924    =over 4
925    
926    =item tkey
927    
928    Tracing key for this environment.
929    
930    =item myDest
931    
932    Destination from the emergency tracing file.
933    
934    =item RETURN
935    
936    Returns a destination that can be passed into L</TSetup>.
937    
938    =back
939    
940    =cut
941    
942    sub EmergencyTracingDest {
943        # Get the parameters.
944        my ($tkey, $myDest) = @_;
945        # Declare the return variable.
946        my $retVal = $myDest;
947        # Process according to the destination value.
948        if ($myDest eq 'FILE') {
949            $retVal = ">" . EmergencyFileTarget($tkey);
950        } elsif ($myDest eq 'APPEND') {
951            $retVal = ">>" . EmergencyFileTarget($tkey);
952        } elsif ($myDest eq 'DUAL') {
953            $retVal = "+>" . EmergencyFileTarget($tkey);
954        }
955        # Return the result.
956        return $retVal;
957    }
958    
959    =head3 Emergency
960    
961        Emergency($key, $hours, $dest, $level, @modules);
962    
963    Turn on emergency tracing. This method is normally invoked over the web from
964    a debugging console, but it can also be called by the C<trace.pl> script.
965    The caller specifies the duration of the emergency in hours, the desired tracing
966    destination, the trace level, and a list of the trace modules to activate.
967    For the length of the duration, when a program in an environment with the
968    specified tracing key active invokes a Sprout CGI script, tracing will be
969    turned on automatically. See L</TSetup> for more about tracing setup and
970    L</ETracing> for more about emergency tracing.
971    
972    =over 4
973    
974    =item tkey
975    
976    The tracing key. This is used to identify the control file and the trace file.
977    
978    =item hours
979    
980    Number of hours to keep emergency tracing alive.
981    
982    =item dest
983    
984    Tracing destination. If no path information is specified for a file
985    destination, it is put in the FIG temporary directory.
986    
987    =item level
988    
989    Tracing level. A higher level means more trace messages.
990    
991    =item modules
992    
993    A list of the tracing modules to activate.
994    
995    =back
996    
997    =cut
998    
999    sub Emergency {
1000        # Get the parameters.
1001        my ($tkey, $hours, $dest, $level, @modules) = @_;
1002        # Create the emergency file.
1003        my $specFile = EmergencyFileName($tkey);
1004        my $outHandle = Open(undef, ">$specFile");
1005        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1006    }
1007    
1008    =head3 EmergencyKey
1009    
1010        my $tkey = EmergencyKey($parameter);
1011    
1012    Return the Key to be used for emergency tracing. This could be an IP address,
1013     a session ID, or a user name, depending on the environment.
1014    
1015    =over 4
1016    
1017    =item parameter
1018    
1019    Parameter defining the method for finding the tracing key. If it is a scalar,
1020    then it is presumed to be the tracing key itself. If it is a CGI object, then
1021    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1022    taken from the C<TRACING> environment variable.
1023    
1024    =item RETURN
1025    
1026    Returns the key to be used for labels in emergency tracing.
1027    
1028    =back
1029    
1030    =cut
1031    
1032    sub EmergencyKey {
1033        # Get the parameters.
1034        my ($parameter) = @_;
1035        # Declare the return variable.
1036        my $retVal;
1037        # Determine the parameter type.
1038        if (! defined $parameter) {
1039            # Here we're supposed to check the environment.
1040            $retVal = $ENV{TRACING};
1041        } else {
1042            my $ptype = ref $parameter;
1043            if ($ptype eq 'CGI') {
1044                # Here we were invoked from a web page. Look for a cookie.
1045                $retVal = $parameter->cookie('IP');
1046            } elsif (! $ptype) {
1047                # Here the key was passed in.
1048                $retVal = $parameter;
1049            }
1050        }
1051        # If no luck finding a key, use the PID.
1052        if (! defined $retVal) {
1053            $retVal = $$;
1054        }
1055        # Return the result.
1056        return $retVal;
1057    }
1058    
1059    
1060    =head3 TraceParms
1061    
1062        Tracer::TraceParms($cgi);
1063    
1064    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1065    at level CGI => 4.
1066    
1067    =over 4
1068    
1069    =item cgi
1070    
1071    CGI query object containing the parameters to trace.
1072    
1073    =back
1074    
1075    =cut
1076    
1077    sub TraceParms {
1078        # Get the parameters.
1079        my ($cgi) = @_;
1080        if (T(CGI => 3)) {
1081            # Here we want to trace the parameter data.
1082            my @names = $cgi->param;
1083            for my $parmName (sort @names) {
1084                # Note we skip the Trace parameters, which are for our use only.
1085                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1086                    my @values = $cgi->param($parmName);
1087                    Trace("CGI: $parmName = " . join(", ", @values));
1088                }
1089            }
1090            # Display the request method.
1091            my $method = $cgi->request_method();
1092            Trace("Method: $method");
1093        }
1094        if (T(CGI => 4)) {
1095            # Here we want the environment data too.
1096            for my $envName (sort keys %ENV) {
1097                Trace("ENV: $envName = $ENV{$envName}");
1098            }
1099        }
1100    }
1101    
1102    =head3 ScriptFinish
1103    
1104        ScriptFinish($webData, $varHash);
1105    
1106    Output a web page at the end of a script. Either the string to be output or the
1107    name of a template file can be specified. If the second parameter is omitted,
1108    it is assumed we have a string to be output; otherwise, it is assumed we have the
1109    name of a template file. The template should have the variable C<DebugData>
1110    specified in any form that invokes a standard script. If debugging mode is turned
1111    on, a form field will be put in that allows the user to enter tracing data.
1112    Trace messages will be placed immediately before the terminal C<BODY> tag in
1113    the output, formatted as a list.
1114    
1115    A typical standard script would loook like the following.
1116    
1117        BEGIN {
1118            # Print the HTML header.
1119            print "CONTENT-TYPE: text/html\n\n";
1120        }
1121        use Tracer;
1122        use CGI;
1123        use FIG;
1124        # ... more uses ...
1125    
1126        my ($cgi, $varHash) = ScriptSetup();
1127        eval {
1128            # ... get data from $cgi, put it in $varHash ...
1129        };
1130        if ($@) {
1131            Trace("Script Error: $@") if T(0);
1132        }
1133        ScriptFinish("Html/MyTemplate.html", $varHash);
1134    
1135    The idea here is that even if the script fails, you'll see trace messages and
1136    useful output.
1137    
1138    =over 4
1139    
1140    =item webData
1141    
1142    A string containing either the full web page to be written to the output or the
1143    name of a template file from which the page is to be constructed. If the name
1144    of a template file is specified, then the second parameter must be present;
1145    otherwise, it must be absent.
1146    
1147    =item varHash (optional)
1148    
1149    If specified, then a reference to a hash mapping variable names for a template
1150    to their values. The template file will be read into memory, and variable markers
1151    will be replaced by data in this hash reference.
1152    
1153    =back
1154    
1155    =cut
1156    
1157    sub ScriptFinish {
1158        # Get the parameters.
1159        my ($webData, $varHash) = @_;
1160        # Check for a template file situation.
1161        my $outputString;
1162        if (defined $varHash) {
1163            # Here we have a template file. We need to determine the template type.
1164            my $template;
1165            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1166                $template = "$FIG_Config::template_url/$webData";
1167            } else {
1168                $template = "<<$webData";
1169            }
1170            $outputString = PageBuilder::Build($template, $varHash, "Html");
1171        } else {
1172            # Here the user gave us a raw string.
1173            $outputString = $webData;
1174        }
1175        # Check for trace messages.
1176        if ($Destination ne "NONE" && $TraceLevel > 0) {
1177            # We have trace messages, so we want to put them at the end of the body. This
1178            # is either at the end of the whole string or at the beginning of the BODY
1179            # end-tag.
1180            my $pos = length $outputString;
1181            if ($outputString =~ m#</body>#gi) {
1182                $pos = (pos $outputString) - 7;
1183            }
1184            # If the trace messages were queued, we unroll them. Otherwise, we display the
1185            # destination.
1186            my $traceHtml;
1187            if ($Destination eq "QUEUE") {
1188                $traceHtml = QTrace('Html');
1189            } elsif ($Destination =~ /^>>(.+)$/) {
1190                # Here the tracing output it to a file. We code it as a hyperlink so the user
1191                # can copy the file name into the clipboard easily.
1192                my $actualDest = $1;
1193                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1194            } else {
1195                # Here we have one of the special destinations.
1196                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1197            }
1198            substr $outputString, $pos, 0, $traceHtml;
1199        }
1200        # Write the output string.
1201        print $outputString;
1202    }
1203    
1204    =head2 Command-Line Utility Methods
1205    
1206    =head3 SendSMS
1207    
1208        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1209    
1210    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1211    user name, password, and API ID for the relevant account in the hash reference variable
1212    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1213    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1214    is C<2561022>, then the FIG_Config file must contain
1215    
1216        $phone =  { user => 'BruceTheHumanPet',
1217                    password => 'silly',
1218                    api_id => '2561022' };
1219    
1220    The original purpose of this method was to insure Bruce would be notified immediately when the
1221    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1222    when you call this method.
1223    
1224    The message ID will be returned if successful, and C<undef> if an error occurs.
1225    
1226    =over 4
1227    
1228    =item phoneNumber
1229    
1230    Phone number to receive the message, in international format. A United States phone number
1231    would be prefixed by "1". A British phone number would be prefixed by "44".
1232    
1233    =item msg
1234    
1235    Message to send to the specified phone.
1236    
1237    =item RETURN
1238    
1239    Returns the message ID if successful, and C<undef> if the message could not be sent.
1240    
1241    =back
1242    
1243    =cut
1244    
1245    sub SendSMS {
1246        # Get the parameters.
1247        my ($phoneNumber, $msg) = @_;
1248        # Declare the return variable. If we do not change it, C<undef> will be returned.
1249        my $retVal;
1250        # Only proceed if we have phone support.
1251        if (! defined $FIG_Config::phone) {
1252            Trace("Phone support not present in FIG_Config.") if T(1);
1253        } else {
1254            # Get the phone data.
1255            my $parms = $FIG_Config::phone;
1256            # Get the Clickatell URL.
1257            my $url = "http://api.clickatell.com/http/";
1258            # Create the user agent.
1259            my $ua = LWP::UserAgent->new;
1260            # Request a Clickatell session.
1261            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1262                                         password => $parms->{password},
1263                                         api_id => $parms->{api_id},
1264                                         to => $phoneNumber,
1265                                         text => $msg});
1266            # Check for an error.
1267            if (! $resp->is_success) {
1268                Trace("Alert failed.") if T(1);
1269            } else {
1270                # Get the message ID.
1271                my $rstring = $resp->content;
1272                if ($rstring =~ /^ID:\s+(.*)$/) {
1273                    $retVal = $1;
1274                } else {
1275                    Trace("Phone attempt failed with $rstring") if T(1);
1276          }          }
         # Terminate with an error using the supplied message and the  
         # error message from the file system.  
         Confess("$message: $!");  
1277      }      }
1278      # Return the file handle.      }
1279      return $fileHandle;      # Return the result.
1280        return $retVal;
1281  }  }
1282    
1283  =head3 FindNamePart  =head3 StandardSetup
1284    
1285  C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>      my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1286    
1287  Extract the portion of a file specification that contains the file name.  This method performs standard command-line parsing and tracing setup. The return
1288    values are a hash of the command-line options and a list of the positional
1289    parameters. Tracing is automatically set up and the command-line options are
1290    validated.
1291    
1292  A file specification is the string passed to an C<open> call. It specifies the file  This is a complex method that does a lot of grunt work. The parameters can
1293  mode and name. In a truly complex situation, it can specify a pipe sequence. This  be more easily understood, however, once they are examined individually.
 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>.  
1294    
1295      >>/usr/fig/myfile.txt  The I<categories> parameter is the most obtuse. It is a reference to a list of
1296      </usr/fig/myfile.txt  special-purpose tracing categories. Most tracing categories are PERL package
1297      | sort -u > /usr/fig/myfile.txt  names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1298    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1299    
1300  If the method cannot find a file name using its normal methods, it will return the      ["Sprout", "SproutLoad", "ERDB"]
1301  whole incoming string.  
1302    This would cause trace messages in the specified three packages to appear in
1303    the output. There are two special tracing categories that are automatically
1304    handled by this method. In other words, if you used L</TSetup> you would need
1305    to include these categories manually, but if you use this method they are turned
1306    on automatically.
1307    
1308  =over 4  =over 4
1309    
1310  =item fileSpec  =item SQL
1311    
1312  File specification string from which the file name is to be extracted.  Traces SQL commands and activity.
1313    
1314  =item RETURN  =item Tracer
1315    
1316  Returns a three-element list. The first element contains the file name portion of  Traces error messages and call stacks.
 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.  
1317    
1318  =back  =back
1319    
1320  =cut  C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1321  #: Return Type $;  The trace level is specified using the C<-trace> command-line option. For example,
1322  sub FindNamePart {  the following command line for C<TransactFeatures> turns on SQL tracing and runs
1323      # Get the parameters.  all tracing at level 3.
     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);  
 }  
1324    
1325  =head3 OpenDir      TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1326    
1327  C<< my @files = OpenDir($dirName, $filtered, $flag); >>  Standard tracing is output to the standard output and echoed to the file
1328    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1329    process ID. You can also specify the C<user> parameter to put a user ID
1330    instead of a process ID in the trace file name. So, for example
1331    
1332  Open a directory and return all the file names. This function essentially performs  The default trace level is 2. To get all messages, specify a trace level of 4.
1333  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  For a genome-by-genome update, use 3.
 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),  
 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,  
1334    
1335      my @files = OpenDir("/Volumes/fig/contigs", 1);      TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1336    
1337  is effectively the same as  would send the trace output to C<traceBruce.log> in the temporary directory.
1338    
1339      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");  The I<options> parameter is a reference to a hash containing the command-line
1340      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);  options, their default values, and an explanation of what they mean. Command-line
1341    options may be in the form of switches or keywords. In the case of a switch, the
1342    option value is 1 if it is specified and 0 if it is not specified. In the case
1343    of a keyword, the value is separated from the option name by an equal sign. You
1344    can see this last in the command-line example above.
1345    
1346  Similarly, the following code  You can specify a different default trace level by setting C<$options->{trace}>
1347    prior to calling this method.
1348    
1349      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);  An example at this point would help. Consider, for example, the command-line utility
1350    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1351    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1352    the following code.
1353    
1354  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and      my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1355  automatically returns an empty list if the directory fails to open.                          { safe => [0, "use database transactions"],
1356                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1357                              start => [' ', "start with this genome"],
1358                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1359                            "<command> <transactionDirectory> <IDfile>",
1360                          @ARGV);
1361    
 =over 4  
1362    
1363  =item dirName  The call to C<ParseCommand> specifies the default values for the options and
1364    stores the actual options in a hash that is returned as C<$options>. The
1365    positional parameters are returned in C<@parameters>.
1366    
1367  Name of the directory to open.  The following is a sample command line for C<TransactFeatures>.
1368    
1369  =item filtered      TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1370    
1371  TRUE if files whose names begin with a period (C<.>) should be automatically removed  Single and double hyphens are equivalent. So, you could also code the
1372  from the list, else FALSE.  above command as
1373    
1374  =item flag      TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1375    
1376  TRUE if a failure to open is okay, else FALSE  In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1377    parameters, and would find themselves in I<@parameters> after executing the
1378    above code fragment. The tracing would be set to level 2, and the categories
1379    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1380    and C<DocUtils> was included because it came in within the first parameter
1381    to this method. The I<$options> hash would be
1382    
1383  =back      { trace => 2, sql => 0, safe => 0,
1384          noAlias => 1, start => ' ', tblFiles => 0 }
1385    
1386  =cut  Use of C<StandardSetup> in this way provides a simple way of performing
1387  #: Return Type @;  standard tracing setup and command-line parsing. Note that the caller is
1388  sub OpenDir {  not even aware of the command-line switches C<-trace> and C<-sql>, which
1389      # Get the parameters.  are used by this method to control the tracing. If additional tracing features
1390      my ($dirName, $filtered, $flag) = @_;  need to be added in the future, they can be processed by this method without
1391      # Declare the return variable.  upsetting the command-line utilities.
     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 $dirName.");  
     }  
     # Return the result.  
     return @retVal;  
 }  
1392    
1393  =head3 SetLevel  If the C<background> option is specified on the command line, then the
1394    standard and error outputs will be directed to files in the temporary
1395    directory, using the same suffix as the trace file. So, if the command
1396    line specified
1397    
1398  C<< Tracer::SetLevel($newLevel); >>      -user=Bruce -background
1399    
1400  Modify the trace level. A higher trace level will cause more messages to appear.  then the trace output would go to C<traceBruce.log>, the standard output to
1401    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1402    simplify starting a command in the background.
1403    
1404  =over 4  The user name is also used as the tracing key for L</Emergency Tracing>.
1405    Specifying a value of C<E> for the trace level causes emergency tracing to
1406    be used instead of custom tracing. If the user name is not specified,
1407    the tracing key is taken from the C<Tracing> environment variable. If there
1408    is no value for that variable, the tracing key will be computed from the PID.
1409    
1410  =item newLevel  Finally, if the special option C<-help> is specified, the option
1411    names will be traced at level 0 and the program will exit without processing.
1412    This provides a limited help capability. For example, if the user enters
1413    
1414  Proposed new trace level.      TransactFeatures -help
1415    
1416  =back  he would see the following output.
1417    
1418  =cut      TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1419            -trace    tracing level (default E)
1420            -sql      trace SQL commands
1421            -safe     use database transactions
1422            -noAlias  do not expect aliases in CHANGE transactions
1423            -start    start with this genome
1424            -tblFiles output TBL files containing the corrected IDs
1425    
1426  sub SetLevel {  The caller has the option of modifying the tracing scheme by placing a value
1427      $TraceLevel = $_[0];  for C<trace> in the incoming options hash. The default value can be overridden,
1428  }  or the tracing to the standard output can be turned off by suffixing a minus
1429    sign to the trace level. So, for example,
1430    
1431  =head3 Now      { trace => [0, "tracing level (default 0)"],
1432           ...
1433    
1434  C<< my $string = Tracer::Now(); >>  would set the default trace level to 0 instead of E, while
1435    
1436  Return a displayable time stamp containing the local time.      { trace => ["2-", "tracing level (default 2)"],
1437           ...
1438    
1439  =cut  would set the default to 2, but trace only to the log file, not to the
1440    standard output.
1441    
1442  sub Now {  The parameters to this method are as follows.
     my ($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 $retVal;  
 }  
1443    
1444  # Pad a number to 2 digits.  =over 4
1445  sub _p2 {  
1446      my ($value) = @_;  =item categories
1447      $value = "0$value" if ($value < 10);  
1448      return $value;  Reference to a list of tracing category names. These should be names of
1449  }  packages whose internal workings will need to be debugged to get the
1450    command working.
1451    
1452  =head3 LogErrors  =item options
1453    
1454  C<< Tracer::LogErrors($fileName); >>  Reference to a hash containing the legal options for the current command mapped
1455    to their default values and descriptions. The user can override the defaults
1456    by specifying the options as command-line switches prefixed by a hyphen.
1457    Tracing-related options may be added to this hash. If the C<-h> option is
1458    specified on the command line, the option descriptions will be used to
1459    explain the options. To turn off tracing to the standard output, add a
1460    minus sign to the value for C<trace> (see above).
1461    
1462  Route the standard error output to a log file.  =item parmHelp
1463    
1464  =over 4  A string that vaguely describes the positional parameters. This is used
1465    if the user specifies the C<-h> option.
1466    
1467  =item fileName  =item argv
1468    
1469  Name of the file to receive the error output.  List of command line parameters, including the option switches, which must
1470    precede the positional parameters and be prefixed by a hyphen.
1471    
1472    =item RETURN
1473    
1474    Returns a list. The first element of the list is the reference to a hash that
1475    maps the command-line option switches to their values. These will either be the
1476    default values or overrides specified on the command line. The remaining
1477    elements of the list are the position parameters, in order.
1478    
1479  =back  =back
1480    
1481  =cut  =cut
1482    
1483  sub LogErrors {  sub StandardSetup {
1484      # Get the file name.      # Get the parameters.
1485      my ($fileName) = @_;      my ($categories, $options, $parmHelp, @argv) = @_;
1486      # Open the file as the standard error output.      # Get the default tracing key.
1487      open STDERR, '>', $fileName;      my $tkey = EmergencyKey();
1488        # Add the tracing options.
1489        if (! exists $options->{trace}) {
1490            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1491        }
1492        $options->{sql} = [0, "turn on SQL tracing"];
1493        $options->{help} = [0, "display command-line options"];
1494        $options->{user} = [$tkey, "tracing key"];
1495        $options->{background} = [0, "spool standard and error output"];
1496        # Create a parsing hash from the options hash. The parsing hash
1497        # contains the default values rather than the default value
1498        # and the description. While we're at it, we'll memorize the
1499        # length of the longest option name.
1500        my $longestName = 0;
1501        my %parseOptions = ();
1502        for my $key (keys %{$options}) {
1503            if (length $key > $longestName) {
1504                $longestName = length $key;
1505            }
1506            $parseOptions{$key} = $options->{$key}->[0];
1507        }
1508        # Parse the command line.
1509        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1510        # Get the logfile suffix.
1511        my $suffix = $retOptions->{user};
1512        # Check for background mode.
1513        if ($retOptions->{background}) {
1514            my $outFileName = "$FIG_Config::temp/out$suffix.log";
1515            my $errFileName = "$FIG_Config::temp/err$suffix.log";
1516            open STDOUT, ">$outFileName";
1517            open STDERR, ">$errFileName";
1518            # Check for phone support. If we have phone support and a phone number,
1519            # we want to turn it on.
1520            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1521                $retOptions->{phone} = $ENV{PHONE};
1522            }
1523        }
1524        # Now we want to set up tracing. First, we need to know if the user
1525        # wants emergency tracing.
1526        if ($retOptions->{trace} eq 'E') {
1527            ETracing($retOptions->{user});
1528        } else {
1529            # Here the tracing is controlled from the command line.
1530            my @cats = @{$categories};
1531            if ($retOptions->{sql}) {
1532                push @cats, "SQL";
1533            }
1534            # Add the default categories.
1535            push @cats, "Tracer";
1536            # Next, we create the category string by joining the categories.
1537            my $cats = join(" ", @cats);
1538            # Check to determine whether or not the caller wants to turn off tracing
1539            # to the standard output.
1540            my $traceLevel = $retOptions->{trace};
1541            my $textOKFlag = 1;
1542            if ($traceLevel =~ /^(.)-/) {
1543                $traceLevel = $1;
1544                $textOKFlag = 0;
1545            }
1546            # Now we set up the trace mode.
1547            my $traceMode;
1548            # Verify that we can open a file in the FIG temporary directory.
1549            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1550            if (open TESTTRACE, ">$traceFileName") {
1551                # Here we can trace to a file.
1552                $traceMode = ">$traceFileName";
1553                if ($textOKFlag) {
1554                    # Echo to standard output if the text-OK flag is set.
1555                    $traceMode = "+$traceMode";
1556                }
1557                # Close the test file.
1558                close TESTTRACE;
1559            } else {
1560                # Here we can't trace to a file. We trace to the standard output if it's
1561                # okay, and the error log otherwise.
1562                if ($textOKFlag) {
1563                    $traceMode = "TEXT";
1564                } else {
1565                    $traceMode = "WARN";
1566                }
1567            }
1568            # Now set up the tracing.
1569            TSetup("$traceLevel $cats", $traceMode);
1570        }
1571        # Check for the "help" option. If it is specified, dump the command-line
1572        # options and exit the program.
1573        if ($retOptions->{help}) {
1574            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1575            print "$1 [options] $parmHelp\n";
1576            for my $key (sort keys %{$options}) {
1577                my $name = Pad($key, $longestName, 0, ' ');
1578                my $desc = $options->{$key}->[1];
1579                if ($options->{$key}->[0]) {
1580                    $desc .= " (default " . $options->{$key}->[0] . ")";
1581                }
1582                print "  $name $desc\n";
1583            }
1584            exit(0);
1585        }
1586        # Trace the options, if applicable.
1587        if (T(3)) {
1588            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1589            Trace("Selected options: " . join(", ", sort @parms) . ".");
1590        }
1591        # Return the parsed parameters.
1592        return ($retOptions, @retParameters);
1593  }  }
1594    
1595  =head3 ReadOptions  =head3 ReadOptions
1596    
1597  C<< my %options = Tracer::ReadOptions($fileName); >>      my %options = Tracer::ReadOptions($fileName);
1598    
1599  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
1600  format  format
# Line 853  Line 1655 
1655    
1656  =head3 GetOptions  =head3 GetOptions
1657    
1658  C<< Tracer::GetOptions(\%defaults, \%options); >>      Tracer::GetOptions(\%defaults, \%options);
   
 Merge a specified set of options into a table of defaults. This method takes two hash references  
 as input and uses the data from the second to update the first. If the second does not exist,  
 there will be no effect. An error will be thrown if one of the entries in the second hash does not  
 exist in the first.  
   
 Consider the following example.  
   
 C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  
   
 In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  
 B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  
 B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and  
 the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  
 will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  
   
 C<< {databaseType => 'Oracle'} >>  
   
 an error will occur because the B<databaseType> option does not exist.  
   
 =over 4  
   
 =item defaults  
   
 Table of default option values.  
   
 =item options  
   
 Table of overrides, if any.  
   
 =item RETURN  
   
 Returns a reference to the default table passed in as the first parameter.  
   
 =back  
   
 =cut  
   
 sub GetOptions {  
     # Get the parameters.  
     my ($defaults, $options) = @_;  
     # Check for overrides.  
     if ($options) {  
         # Loop through the overrides.  
         while (my ($option, $setting) = each %{$options}) {  
             # Insure this override exists.  
             if (!exists $defaults->{$option}) {  
                 croak "Unrecognized option $option encountered.";  
             } else {  
                 # Apply the override.  
                 $defaults->{$option} = $setting;  
             }  
         }  
     }  
     # Return the merged table.  
     return $defaults;  
 }  
   
 =head3 MergeOptions  
   
 C<< Tracer::MergeOptions(\%table, \%defaults); >>  
   
 Merge default values into a hash table. This method looks at the key-value pairs in the  
 second (default) hash, and if a matching key is not found in the first hash, the default  
 pair is copied in. The process is similar to L</GetOptions>, but there is no error-  
 checking and no return value.  
   
 =over 4  
   
 =item table  
   
 Hash table to be updated with the default values.  
   
 =item defaults  
   
 Default values to be merged into the first hash table if they are not already present.  
1659    
1660  =back  Merge a specified set of options into a table of defaults. This method takes two hash references
1661    as input and uses the data from the second to update the first. If the second does not exist,
1662  =cut  there will be no effect. An error will be thrown if one of the entries in the second hash does not
1663    exist in the first.
 sub MergeOptions {  
     # Get the parameters.  
     my ($table, $defaults) = @_;  
     # Loop through the defaults.  
     while (my ($key, $value) = each %{$defaults}) {  
         if (!exists $table->{$key}) {  
             $table->{$key} = $value;  
         }  
     }  
 }  
   
 =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";  
         }  
     }  
 }  
1664    
1665  =head3 T  Consider the following example.
1666    
1667  C<< my $switch = T($category, $traceLevel); >>      my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1668    
1669      or  In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1670    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1671    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1672    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1673    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1674    
1675  C<< my $switch = T($traceLevel); >>      {databaseType => 'Oracle'}
1676    
1677  Return TRUE if the trace level is at or above a specified value and the specified category  an error will occur because the B<databaseType> option does not exist.
 is active, else FALSE. If no category is specified, the caller's package name is used.  
1678    
1679  =over 4  =over 4
1680    
1681  =item category  =item defaults
1682    
1683  Category to which the message belongs. If not specified, the caller's package name is  Table of default option values.
 used.  
1684    
1685  =item traceLevel  =item options
1686    
1687  Relevant tracing level.  Table of overrides, if any.
1688    
1689  =item RETURN  =item RETURN
1690    
1691  TRUE if a message at the specified trace level would appear in the trace, else FALSE.  Returns a reference to the default table passed in as the first parameter.
1692    
1693  =back  =back
1694    
1695  =cut  =cut
1696    
1697  sub T {  sub GetOptions {
     # Declare the return variable.  
     my $retVal = 0;  
     # Only proceed if tracing is turned on.  
     if ($Destination ne "NONE") {  
1698          # Get the parameters.          # Get the parameters.
1699          my ($category, $traceLevel) = @_;      my ($defaults, $options) = @_;
1700          if (!defined $traceLevel) {      # Check for overrides.
1701              # Here we have no category, so we need to get the calling package.      if ($options) {
1702              # The calling package is normally the first parameter. If it is          # Loop through the overrides.
1703              # omitted, the first parameter will be the tracelevel. So, the          while (my ($option, $setting) = each %{$options}) {
1704              # first thing we do is shift the so-called category into the              # Insure this override exists.
1705              # $traceLevel variable where it belongs.              if (!exists $defaults->{$option}) {
1706              $traceLevel = $category;                  croak "Unrecognized option $option encountered.";
             my ($package, $fileName, $line) = caller;  
             # If there is no calling package, we default to "main".  
             if (!$package) {  
                 $category = "main";  
1707              } else {              } else {
1708                  $category = $package;                  # Apply the override.
1709                    $defaults->{$option} = $setting;
1710              }              }
1711          }          }
         # 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.");  
1712          }          }
1713          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));      # Return the merged table.
1714        return $defaults;
1715    }
1716    
1717    =head3 MergeOptions
1718    
1719        Tracer::MergeOptions(\%table, \%defaults);
1720    
1721    Merge default values into a hash table. This method looks at the key-value pairs in the
1722    second (default) hash, and if a matching key is not found in the first hash, the default
1723    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1724    checking and no return value.
1725    
1726    =over 4
1727    
1728    =item table
1729    
1730    Hash table to be updated with the default values.
1731    
1732    =item defaults
1733    
1734    Default values to be merged into the first hash table if they are not already present.
1735    
1736    =back
1737    
1738    =cut
1739    
1740    sub MergeOptions {
1741        # Get the parameters.
1742        my ($table, $defaults) = @_;
1743        # Loop through the defaults.
1744        while (my ($key, $value) = each %{$defaults}) {
1745            if (!exists $table->{$key}) {
1746                $table->{$key} = $value;
1747            }
1748      }      }
     # Return the computed result.  
     return $retVal;  
1749  }  }
1750    
1751  =head3 ParseCommand  =head3 ParseCommand
1752    
1753  C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>      my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1754    
1755  Parse a command line consisting of a list of parameters. The initial parameters may be option  Parse a command line consisting of a list of parameters. The initial parameters may be option
1756  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1757  off and merged into a table of default options. The remainder of the command line is  off and merged into a table of default options. The remainder of the command line is
1758  returned as a list of positional arguments. For example, consider the following invocation.  returned as a list of positional arguments. For example, consider the following invocation.
1759    
1760  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1761    
1762  In this case, the list @words will be treated as a command line. There are two options available,  In this case, the list @words will be treated as a command line and there are two options available,
1763  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
1764    
1765  C<< -logFile=error.log apple orange rutabaga >>      -logFile=error.log apple orange rutabaga
1766    
1767  then at the end of the invocation, C<$options> will be  then at the end of the invocation, C<$options> will be
1768    
1769  C<< { errors => 0, logFile => 'error.log' } >>      { errors => 0, logFile => 'error.log' }
1770    
1771  and C<@arguments> will contain  and C<@arguments> will contain
1772    
1773  C<< apple orange rutabaga >>      apple orange rutabaga
1774    
1775  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1776  support for quote characters.  support for quote characters. Options can be specified with single or double hyphens.
1777    
1778  =over 4  =over 4
1779    
# Line 1117  Line 1798 
1798      my ($optionTable, @inputList) = @_;      my ($optionTable, @inputList) = @_;
1799      # Process any options in the input list.      # Process any options in the input list.
1800      my %overrides = ();      my %overrides = ();
1801      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1802          # Get the current option.          # Get the current option.
1803          my $arg = shift @inputList;          my $arg = shift @inputList;
1804          # Pull out the option name.          # Pull out the option name.
1805          $arg =~ /^-([^=]*)/g;          $arg =~ /^--?([^=]*)/g;
1806          my $name = $1;          my $name = $1;
1807          # Check for an option value.          # Check for an option value.
1808          if ($arg =~ /\G=(.*)$/g) {          if ($arg =~ /\G=(.*)$/g) {
# Line 1143  Line 1824 
1824      return ($optionTable, @retVal);      return ($optionTable, @retVal);
1825  }  }
1826    
 =head3 Escape  
1827    
1828  C<< my $codedString = Tracer::Escape($realString); >>  =head2 File Utility Methods
1829    
1830  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines  =head3 GetFile
1831  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The  
1832  result is to reverse the effect of L</UnEscape>.      my @fileContents = Tracer::GetFile($fileName);
1833    
1834        or
1835    
1836        my $fileContents = Tracer::GetFile($fileName);
1837    
1838    Return the entire contents of a file. In list context, line-ends are removed and
1839    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1840    
1841  =over 4  =over 4
1842    
1843  =item realString  =item fileName
1844    
1845  String to escape.  Name of the file to read.
1846    
1847  =item RETURN  =item RETURN
1848    
1849  Escaped equivalent of the real string.  In a list context, returns the entire file as a list with the line terminators removed.
1850    In a scalar context, returns the entire file as a string. If an error occurs opening
1851    the file, an empty list will be returned.
1852    
1853  =back  =back
1854    
1855  =cut  =cut
1856    
1857  sub Escape {  sub GetFile {
1858      # Get the parameter.      # Get the parameters.
1859      my ($realString) = @_;      my ($fileName) = @_;
1860      # Initialize the return variable.      # Declare the return variable.
1861      my $retVal = "";      my @retVal = ();
1862      # Loop through the parameter string, looking for sequences to escape.      # Open the file for input.
1863      while (length $realString > 0) {      my $handle = Open(undef, "<$fileName");
1864          # Look for the first sequence to escape.      # Read the whole file into the return variable, stripping off any terminator
1865          if ($realString =~ /^(.*?)([\n\t\r\\])/) {      # characters.
1866              # Here we found it. The text preceding the sequence is in $1. The sequence      my $lineCount = 0;
1867              # itself is in $2. First, move the clear text to the return variable.      while (my $line = <$handle>) {
1868              $retVal .= $1;          $lineCount++;
1869              # Strip the processed section off the real string.          $line = Strip($line);
1870              $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;  
1871              }              }
1872        # Close it.
1873        close $handle;
1874        my $actualLines = @retVal;
1875        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
1876        # Return the file's contents in the desired format.
1877        if (wantarray) {
1878            return @retVal;
1879          } else {          } else {
1880              # Here there are no more escape sequences. The rest of the string is          return join "\n", @retVal;
             # transferred unmodified.  
             $retVal .= $realString;  
             $realString = "";  
         }  
1881      }      }
     # Return the result.  
     return $retVal;  
1882  }  }
1883    
1884  =head3 UnEscape  =head3 PutFile
1885    
1886  C<< my $realString = Tracer::UnEscape($codedString); >>      Tracer::PutFile($fileName, \@lines);
1887    
1888  Replace escape sequences with their actual equivalents. C<\t> will be replaced by  Write out a file from a list of lines of text.
 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will  
 be deleted.  
1889    
1890  =over 4  =over 4
1891    
1892  =item codedString  =item fileName
1893    
1894  String to un-escape.  Name of the output file.
1895    
1896  =item RETURN  =item lines
1897    
1898  Returns a copy of the original string with the escape sequences converted to their actual  Reference to a list of text lines. The lines will be written to the file in order, with trailing
1899  values.  new-line characters. Alternatively, may be a string, in which case the string will be written without
1900    modification.
1901    
1902  =back  =back
1903    
1904  =cut  =cut
1905    
1906  sub UnEscape {  sub PutFile {
1907      # Get the parameter.      # Get the parameters.
1908      my ($codedString) = @_;      my ($fileName, $lines) = @_;
1909      # Initialize the return variable.      # Open the output file.
1910      my $retVal = "";      my $handle = Open(undef, ">$fileName");
1911      # Only proceed if the incoming string is nonempty.      # Count the lines written.
1912      if (defined $codedString) {      if (ref $lines ne 'ARRAY') {
1913          # Loop through the parameter string, looking for escape sequences. We can't do          # Here we have a scalar, so we write it raw.
1914          # translating because it causes problems with the escaped slash. ("\\t" becomes          print $handle $lines;
1915          # "\<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;  
                 }  
1916              } else {              } else {
1917                  # Here there are no more escape sequences. The rest of the string is          # Write the lines one at a time.
1918                  # transferred unmodified.          my $count = 0;
1919                  $retVal .= $codedString;          for my $line (@{$lines}) {
1920                  $codedString = "";              print $handle "$line\n";
1921              }              $count++;
1922          }          }
1923            Trace("$count lines put to file $fileName.") if T(File => 3);
1924      }      }
1925      # Return the result.      # Close the output file.
1926      return $retVal;      close $handle;
1927  }  }
1928    
1929  =head3 ParseRecord  =head3 ParseRecord
1930    
1931  C<< my @fields = Tracer::ParseRecord($line); >>      my @fields = Tracer::ParseRecord($line);
1932    
1933  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
1934  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 1305  Line 1973 
1973    
1974  =head3 Merge  =head3 Merge
1975    
1976  C<< my @mergedList = Tracer::Merge(@inputList); >>      my @mergedList = Tracer::Merge(@inputList);
1977    
1978  Sort a list of strings and remove duplicates.  Sort a list of strings and remove duplicates.
1979    
# Line 1351  Line 2019 
2019      return @inputList;      return @inputList;
2020  }  }
2021    
2022  =head3 Percent  =head3 Open
2023    
2024        my $handle = Open($fileHandle, $fileSpec, $message);
2025    
2026    Open a file.
2027    
2028    The I<$fileSpec> is essentially the second argument of the PERL C<open>
2029    function. The mode is specified using Unix-like shell information. So, for
2030    example,
2031    
2032        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2033    
2034    would open for output appended to the specified file, and
2035    
2036        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2037    
2038    would open a pipe that sorts the records written and removes duplicates. Note
2039    the use of file handle syntax in the Open call. To use anonymous file handles,
2040    code as follows.
2041    
2042        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2043    
2044    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2045    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2046    failed open will throw an exception and the third parameter will be used to construct
2047    an error message. If the parameter is omitted, a standard message is constructed
2048    using the file spec.
2049    
2050        Could not open "/usr/spool/news/twitlog"
2051    
2052  C<< my $percent = Tracer::Percent($number, $base); >>  Note that the mode characters are automatically cleaned from the file name.
2053    The actual error message from the file system will be captured and appended to the
2054    message in any case.
2055    
2056  Returns the percent of the base represented by the given number. If the base      Could not open "/usr/spool/news/twitlog": file not found.
2057  is zero, returns zero.  
2058    In some versions of PERL the only error message we get is a number, which
2059    corresponds to the C++ C<errno> value.
2060    
2061        Could not open "/usr/spool/news/twitlog": 6.
2062    
2063  =over 4  =over 4
2064    
2065  =item number  =item fileHandle
2066    
2067  Percent numerator.  File handle. If this parameter is C<undef>, a file handle will be generated
2068    and returned as the value of this method.
2069    
2070  =item base  =item fileSpec
2071    
2072  Percent base.  File name and mode, as per the PERL C<open> function.
2073    
2074    =item message (optional)
2075    
2076    Error message to use if the open fails. If omitted, a standard error message
2077    will be generated. In either case, the error information from the file system
2078    is appended to the message. To specify a conditional open that does not throw
2079    an error if it fails, use C<0>.
2080    
2081  =item RETURN  =item RETURN
2082    
2083  Returns the percentage of the base represented by the numerator.  Returns the name of the file handle assigned to the file, or C<undef> if the
2084    open failed.
2085    
2086  =back  =back
2087    
2088  =cut  =cut
2089    
2090  sub Percent {  sub Open {
2091      # Get the parameters.      # Get the parameters.
2092      my ($number, $base) = @_;      my ($fileHandle, $fileSpec, $message) = @_;
2093      # Declare the return variable.      # Attempt to open the file.
2094      my $retVal = 0;      my $rv = open $fileHandle, $fileSpec;
2095      # Compute the percent.      # If the open failed, generate an error message.
2096      if ($base != 0) {      if (! $rv) {
2097          $retVal = $number * 100 / $base;          # Save the system error message.
2098            my $sysMessage = $!;
2099            # See if we need a default message.
2100            if (!$message) {
2101                # Clean any obvious mode characters and leading spaces from the
2102                # filename.
2103                my ($fileName) = FindNamePart($fileSpec);
2104                $message = "Could not open \"$fileName\"";
2105      }      }
2106      # Return the result.          # Terminate with an error using the supplied message and the
2107      return $retVal;          # error message from the file system.
2108            Confess("$message: $!");
2109        }
2110        # Return the file handle.
2111        return $fileHandle;
2112  }  }
2113    
2114  =head3 GetFile  =head3 FindNamePart
2115    
2116  C<< my @fileContents = Tracer::GetFile($fileName); >>      my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2117    
2118      or  Extract the portion of a file specification that contains the file name.
2119    
2120  C<< my $fileContents = Tracer::GetFile($fileName); >>  A file specification is the string passed to an C<open> call. It specifies the file
2121    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2122    method assumes that the file name is whatever follows the first angle bracket
2123    sequence.  So, for example, in the following strings the file name is
2124    C</usr/fig/myfile.txt>.
2125    
2126  Return the entire contents of a file. In list context, line-ends are removed and      >>/usr/fig/myfile.txt
2127  each line is a list element. In scalar context, line-ends are replaced by C<\n>.      </usr/fig/myfile.txt
2128        | sort -u > /usr/fig/myfile.txt
2129    
2130    If the method cannot find a file name using its normal methods, it will return the
2131    whole incoming string.
2132    
2133  =over 4  =over 4
2134    
2135  =item fileName  =item fileSpec
2136    
2137  Name of the file to read.  File specification string from which the file name is to be extracted.
2138    
2139  =item RETURN  =item RETURN
2140    
2141  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
2142  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
2143  the file, an empty list will be returned.  methods. The second element contains the start position of the file name portion and
2144    the third element contains the length.
2145    
2146  =back  =back
2147    
2148  =cut  =cut
2149    #: Return Type $;
2150  sub GetFile {  sub FindNamePart {
2151      # Get the parameters.      # Get the parameters.
2152      my ($fileName) = @_;      my ($fileSpec) = @_;
2153      # Declare the return variable.      # Default to the whole input string.
2154      my @retVal = ();      my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2155      # Open the file for input.      # Parse out the file name if we can.
2156      my $handle = Open(undef, "<$fileName");      if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2157      # Read the whole file into the return variable, stripping off any terminator          $retVal = $2;
2158      # characters.          $len = length $retVal;
2159      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 $actualLines = @retVal;  
     # Return the file's contents in the desired format.  
     if (wantarray) {  
         return @retVal;  
     } else {  
         return join "\n", @retVal;  
2160      }      }
2161        # Return the result.
2162        return ($retVal, $pos, $len);
2163  }  }
2164    
2165  =head3 PutFile  =head3 OpenDir
   
 C<< Tracer::PutFile($fileName, \@lines); >>  
2166    
2167  Write out a file from a list of lines of text.      my @files = OpenDir($dirName, $filtered, $flag);
2168    
2169  =over 4  Open a directory and return all the file names. This function essentially performs
2170    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2171    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2172    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2173    filtered out of the return list. If the directory does not open and I<$flag> is not
2174    set, an exception is thrown. So, for example,
2175    
2176  =item fileName      my @files = OpenDir("/Volumes/fig/contigs", 1);
2177    
2178  Name of the output file.  is effectively the same as
2179    
2180  =item lines      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2181        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2182    
2183  Reference to a list of text lines. The lines will be written to the file in order, with trailing  Similarly, the following code
 new-line characters. Alternatively, may be a string, in which case the string will be written without  
 modification.  
2184    
2185  =back      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2186    
2187  =cut  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2188    automatically returns an empty list if the directory fails to open.
2189    
2190  sub PutFile {  =over 4
     # Get the parameters.  
     my ($fileName, $lines) = @_;  
     # Open the output file.  
     my $handle = Open(undef, ">$fileName");  
     if (ref $lines ne 'ARRAY') {  
         # Here we have a scalar, so we write it raw.  
         print $handle $lines;  
     } else {  
         # Write the lines one at a time.  
         for my $line (@{$lines}) {  
             print $handle "$line\n";  
         }  
     }  
     # Close the output file.  
     close $handle;  
 }  
2191    
2192  =head3 QTrace  =item dirName
2193    
2194  C<< my $data = QTrace($format); >>  Name of the directory to open.
2195    
2196  Return the queued trace data in the specified format.  =item filtered
2197    
2198  =over 4  TRUE if files whose names begin with a period (C<.>) should be automatically removed
2199    from the list, else FALSE.
2200    
2201  =item format  =item flag
2202    
2203  C<html> to format the data as an HTML list, C<text> to format it as straight text.  TRUE if a failure to open is okay, else FALSE
2204    
2205  =back  =back
2206    
2207  =cut  =cut
2208    #: Return Type @;
2209  sub QTrace {  sub OpenDir {
2210      # Get the parameter.      # Get the parameters.
2211      my ($format) = @_;      my ($dirName, $filtered, $flag) = @_;
2212      # Create the return variable.      # Declare the return variable.
2213      my $retVal = "";      my @retVal = ();
2214      # Only proceed if there is an actual queue.      # Open the directory.
2215      if (@Queue) {      if (opendir(my $dirHandle, $dirName)) {
2216          # Process according to the format.          # The directory opened successfully. Get the appropriate list according to the
2217          if ($format =~ m/^HTML$/i) {          # strictures of the filter parameter.
2218              # Convert the queue into an HTML list.          if ($filtered) {
2219              $retVal = "<ul>\n";              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2220              for my $line (@Queue) {          } else {
2221                  my $escapedLine = CGI::escapeHTML($line);              @retVal = readdir $dirHandle;
                 $retVal .= "<li>$escapedLine</li>\n";  
             }  
             $retVal .= "</ul>\n";  
         } elsif ($format =~ m/^TEXT$/i) {  
             # Convert the queue into a list of text lines.  
             $retVal = join("\n", @Queue) . "\n";  
2222          }          }
2223          # Clear the queue.      } elsif (! $flag) {
2224          @Queue = ();          # Here the directory would not open and it's considered an error.
2225            Confess("Could not open directory $dirName.");
2226      }      }
2227      # Return the formatted list.      # Return the result.
2228      return $retVal;      return @retVal;
2229  }  }
2230    
 =head3 Confess  
   
 C<< Confess($message); >>  
2231    
2232  Trace the call stack and abort the program with the specified message. When used with  =head3 Insure
 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  
 So, for example  
2233    
2234  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>      Insure($dirName, $chmod);
2235    
2236  Will abort the program with a stack trace if the value of C<$recNum> is negative.  Insure a directory is present.
2237    
2238  =over 4  =over 4
2239    
2240  =item message  =item dirName
   
 Message to include in the trace.  
   
 =back  
   
 =cut  
   
 sub Confess {  
     # Get the parameters.  
     my ($message) = @_;  
     # Trace the call stack.  
     Cluck($message);  
     # Abort the program.  
     croak(">>> $message");  
 }  
   
 =head3 Assert  
2241    
2242  C<< Assert($condition1, $condition2, ... $conditionN); >>  Name of the directory to check. If it does not exist, it will be created.
2243    
2244  Return TRUE if all the conditions are true. This method can be used in conjunction with  =item chmod (optional)
 the OR operator and the L</Confess> method as a debugging assert.  
 So, for example  
2245    
2246  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  Security privileges to be given to the directory if it is created.
2247    
2248  Will abort the program with a stack trace if the value of C<$recNum> is negative.  =back
2249    
2250  =cut  =cut
2251  sub Assert {  
2252      my $retVal = 1;  sub Insure {
2253      LOOP: for my $condition (@_) {      my ($dirName, $chmod) = @_;
2254          if (! $condition) {      if (! -d $dirName) {
2255              $retVal = 0;          Trace("Creating $dirName directory.") if T(2);
2256              last LOOP;          eval {
2257                mkpath $dirName;
2258                # If we have permissions specified, set them here.
2259                if (defined($chmod)) {
2260                    chmod $chmod, $dirName;
2261                }
2262            };
2263            if ($@) {
2264                Confess("Error creating $dirName: $@");
2265          }          }
2266      }      }
     return $retVal;  
2267  }  }
2268    
2269  =head3 Cluck  =head3 ChDir
   
 C<< Cluck($message); >>  
   
 Trace the call stack. Note that for best results, you should qualify the call with a  
 trace condition. For example,  
2270    
2271  C<< Cluck("Starting record parse.") if T(3); >>      ChDir($dirName);
2272    
2273  will only trace the stack if the trace level for the package is 3 or more.  Change to the specified directory.
2274    
2275  =over 4  =over 4
2276    
2277  =item message  =item dirName
2278    
2279  Message to include in the trace.  Name of the directory to which we want to change.
2280    
2281  =back  =back
2282    
2283  =cut  =cut
2284    
2285  sub Cluck {  sub ChDir {
2286      # Get the parameters.      my ($dirName) = @_;
2287      my ($message) = @_;      if (! -d $dirName) {
2288      # Trace what's happening.          Confess("Cannot change to directory $dirName: no such directory.");
2289      Trace("Stack trace for event: $message");      } else {
2290      my $confession = longmess($message);          Trace("Changing to directory $dirName.") if T(File => 4);
2291      # Convert the confession to a series of trace messages. Note we skip any          my $okFlag = chdir $dirName;
2292      # messages relating to calls into Tracer.          if (! $okFlag) {
2293      for my $line (split /\s*\n/, $confession) {              Confess("Error switching to directory $dirName.");
2294          Trace($line) if ($line !~ /Tracer\.pm/);          }
2295      }      }
2296  }  }
2297    
2298  =head3 Min  =head3 SetPermissions
2299    
2300  C<< my $min = Min($value1, $value2, ... $valueN); >>      Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2301    
2302  Return the minimum argument. The arguments are treated as numbers.  Set the permissions for a directory and all the files and folders inside it.
2303    In addition, the group ownership will be changed to the specified value.
2304    
2305    This method is more vulnerable than most to permission and compatability
2306    problems, so it does internal error recovery.
2307    
2308  =over 4  =over 4
2309    
2310  =item $value1, $value2, ... $valueN  =item dirName
2311    
2312  List of numbers to compare.  Name of the directory to process.
2313    
2314  =item RETURN  =item group
2315    
2316  Returns the lowest number in the list.  Name of the group to be assigned.
2317    
2318    =item mask
2319    
2320    Permission mask. Bits that are C<1> in this mask will be ORed into the
2321    permission bits of any file or directory that does not already have them
2322    set to 1.
2323    
2324    =item otherMasks
2325    
2326    Map of search patterns to permission masks. If a directory name matches
2327    one of the patterns, that directory and all its members and subdirectories
2328    will be assigned the new pattern. For example, the following would
2329    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2330    
2331        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2332    
2333    The list is ordered, so the following would use 0777 for C<tmp1> and
2334    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2335    
2336        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2337                                                       '^tmp' => 0666);
2338    
2339    Note that the pattern matches are all case-insensitive, and only directory
2340    names are matched, not file names.
2341    
2342  =back  =back
2343    
2344  =cut  =cut
2345    
2346  sub Min {  sub SetPermissions {
2347      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2348      my ($retVal, @values) = @_;      my ($dirName, $group, $mask, @otherMasks) = @_;
2349      # Loop through the remaining parameters, looking for the lowest.      # Set up for error recovery.
2350      for my $value (@values) {      eval {
2351          if ($value < $retVal) {          # Switch to the specified directory.
2352              $retVal = $value;          ChDir($dirName);
2353            # Get the group ID.
2354            my $gid = getgrnam($group);
2355            # Get the mask for tracing.
2356            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2357            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2358            my $fixCount = 0;
2359            my $lookCount = 0;
2360            # @dirs will be a stack of directories to be processed.
2361            my @dirs = (getcwd());
2362            while (scalar(@dirs) > 0) {
2363                # Get the current directory.
2364                my $dir = pop @dirs;
2365                # Check for a match to one of the specified directory names. To do
2366                # that, we need to pull the individual part of the name off of the
2367                # whole path.
2368                my $simpleName = $dir;
2369                if ($dir =~ m!/([^/]+)$!) {
2370                    $simpleName = $1;
2371                }
2372                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2373                # Search for a match.
2374                my $match = 0;
2375                my $i;
2376                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2377                    my $pattern = $otherMasks[$i];
2378                    if ($simpleName =~ /$pattern/i) {
2379                        $match = 1;
2380          }          }
2381      }      }
2382      # Return the minimum found.              # Check for a match. Note we use $i-1 because the loop added 2
2383      return $retVal;              # before terminating due to the match.
2384                if ($match && $otherMasks[$i-1] != $mask) {
2385                    # This directory matches one of the incoming patterns, and it's
2386                    # a different mask, so we process it recursively with that mask.
2387                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2388                } else {
2389                    # Here we can process normally. Get all of the non-hidden members.
2390                    my @submems = OpenDir($dir, 1);
2391                    for my $submem (@submems) {
2392                        # Get the full name.
2393                        my $thisMem = "$dir/$submem";
2394                        Trace("Checking member $thisMem.") if T(4);
2395                        $lookCount++;
2396                        if ($lookCount % 1000 == 0) {
2397                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2398                        }
2399                        # Fix the group.
2400                        chown -1, $gid, $thisMem;
2401                        # Insure this member is not a symlink.
2402                        if (! -l $thisMem) {
2403                            # Get its info.
2404                            my $fileInfo = stat $thisMem;
2405                            # Only proceed if we got the info. Otherwise, it's a hard link
2406                            # and we want to skip it anyway.
2407                            if ($fileInfo) {
2408                                my $fileMode = $fileInfo->mode;
2409                                if (($fileMode & $mask) != $mask) {
2410                                    # Fix this member.
2411                                    $fileMode |= $mask;
2412                                    chmod $fileMode, $thisMem;
2413                                    $fixCount++;
2414                                }
2415                                # If it's a subdirectory, stack it.
2416                                if (-d $thisMem) {
2417                                    push @dirs, $thisMem;
2418                                }
2419                            }
2420                        }
2421                    }
2422                }
2423            }
2424            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2425        };
2426        # Check for an error.
2427        if ($@) {
2428            Confess("SetPermissions error: $@");
2429        }
2430  }  }
2431    
2432  =head3 Max  =head3 GetLine
2433    
2434  C<< my $max = Max($value1, $value2, ... $valueN); >>      my @data = Tracer::GetLine($handle);
2435    
2436  Return the maximum argument. The arguments are treated as numbers.  Read a line of data from a tab-delimited file.
2437    
2438  =over 4  =over 4
2439    
2440  =item $value1, $value2, ... $valueN  =item handle
2441    
2442  List of numbers to compare.  Open file handle from which to read.
2443    
2444  =item RETURN  =item RETURN
2445    
2446  Returns the highest number in the list.  Returns a list of the fields in the record read. The fields are presumed to be
2447    tab-delimited. If we are at the end of the file, then an empty list will be
2448    returned. If an empty line is read, a single list item consisting of a null
2449    string will be returned.
2450    
2451  =back  =back
2452    
2453  =cut  =cut
2454    
2455  sub Max {  sub GetLine {
2456      # Get the parameters. Note that we prime the return value with the first parameter.      # Get the parameters.
2457      my ($retVal, @values) = @_;      my ($handle) = @_;
2458      # Loop through the remaining parameters, looking for the highest.      # Declare the return variable.
2459      for my $value (@values) {      my @retVal = ();
2460          if ($value > $retVal) {      Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2461              $retVal = $value;      # Read from the file.
2462        my $line = <$handle>;
2463        # Only proceed if we found something.
2464        if (defined $line) {
2465            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2466            # upload control and have a nonstandard EOL combination.
2467            $line =~ s/(\r|\n)+$//;
2468            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2469            if (T(File => 4)) {
2470                my $escapedLine = $line;
2471                $escapedLine =~ s/\n/\\n/g;
2472                $escapedLine =~ s/\r/\\r/g;
2473                $escapedLine =~ s/\t/\\t/g;
2474                Trace("Line read: -->$escapedLine<--");
2475            }
2476            # If the line is empty, return a single empty string; otherwise, parse
2477            # it into fields.
2478            if ($line eq "") {
2479                push @retVal, "";
2480            } else {
2481                push @retVal, split /\t/,$line;
2482          }          }
2483        } else {
2484            # Trace the reason the read failed.
2485            Trace("End of file: $!") if T(File => 3);
2486      }      }
2487      # Return the maximum found.      # Return the result.
2488      return $retVal;      return @retVal;
2489  }  }
2490    
2491  =head3 AddToListMap  =head3 PutLine
2492    
2493  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>      Tracer::PutLine($handle, \@fields, $eol);
2494    
2495  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Write a line of data to a tab-delimited file. The specified field values will be
2496  is created for the key. Otherwise, the new value is pushed onto the list.  output in tab-separated form, with a trailing new-line.
2497    
2498  =over 4  =over 4
2499    
2500  =item hash  =item handle
2501    
2502  Reference to the target hash.  Output file handle.
2503    
2504  =item key  =item fields
2505    
2506  Key for which the value is to be added.  List of field values.
2507    
2508  =item value1, value2, ... valueN  =item eol (optional)
2509    
2510  List of values to add to the key's value list.  End-of-line character (default is "\n").
2511    
2512  =back  =back
2513    
2514  =cut  =cut
2515    
2516  sub AddToListMap {  sub PutLine {
2517      # Get the parameters.      # Get the parameters.
2518      my ($hash, $key, @values) = @_;      my ($handle, $fields, $eol) = @_;
2519      # Process according to whether or not the key already has a value.      # Write the data.
2520      if (! exists $hash->{$key}) {      print $handle join("\t", @{$fields}) . ($eol || "\n");
         $hash->{$key} = [@values];  
     } else {  
         push @{$hash->{$key}}, @values;  
     }  
2521  }  }
2522    
 =head3 DebugMode  
   
 C<< if (Tracer::DebugMode) { ...code... } >>  
   
 Return TRUE if debug mode has been turned on, else output an error  
 page and return FALSE.  
2523    
 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.  
   
 =cut  
   
 sub DebugMode {  
     # 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;  
 }  
2524    
2525  =head3 Strip  =head2 Other Useful Methods
2526    
2527  C<< my $string = Tracer::Strip($line); >>  =head3 ParseParm
2528    
2529  Strip all line terminators off a string. This is necessary when dealing with files      my $listValue = Tracer::ParseParm($string);
2530  that may have been transferred back and forth several times among different  
2531  operating environments.  Convert a parameter into a list reference. If the parameter is undefined,
2532    an undefined value will be returned. Otherwise, it will be parsed as a
2533    comma-separated list of values.
2534    
2535  =over 4  =over 4
2536    
2537  =item line  =item string
2538    
2539  Line of text to be stripped.  Incoming string.
2540    
2541  =item RETURN  =item RETURN
2542    
2543  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
2544    was undefined.
2545    
2546  =back  =back
2547    
2548  =cut  =cut
2549    
2550  sub Strip {  sub ParseParm {
2551      # Get a copy of the parameter string.      # Get the parameters.
2552      my ($string) = @_;      my ($string) = @_;
2553      my $retVal = (defined $string ? $string : "");      # Declare the return variable.
2554      # Strip the line terminator characters.      my $retVal;
2555      $retVal =~ s/(\r|\n)+$//g;      # Check for data.
2556        if (defined $string) {
2557            # We have some, so split it into a list.
2558            $retVal = [ split /\s*,\s*/, $string];
2559        }
2560      # Return the result.      # Return the result.
2561      return $retVal;      return $retVal;
2562  }  }
2563    
 =head3 Pad  
2564    
 C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>  
2565    
 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.  
2566    
2567  =over 4  =head3 Now
2568    
2569  =item string      my $string = Tracer::Now();
2570    
2571  String to be padded.  Return a displayable time stamp containing the local time.
2572    
2573  =item len  =cut
2574    
2575  Desired length of the padded string.  sub Now {
2576        my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
2577        my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2578                     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2579        return $retVal;
2580    }
2581    
2582  =item left (optional)  # Pad a number to 2 digits.
2583    sub _p2 {
2584        my ($value) = @_;
2585        $value = "0$value" if ($value < 10);
2586        return $value;
2587    }
2588    
2589  TRUE if the string is to be left-padded; otherwise it will be padded on the right.  =head3 Escape
2590    
2591  =item padChar (optional)      my $codedString = Tracer::Escape($realString);
2592    
2593  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
2594    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2595    result is to reverse the effect of L</UnEscape>.
2596    
2597    =over 4
2598    
2599    =item realString
2600    
2601    String to escape.
2602    
2603  =item RETURN  =item RETURN
2604    
2605  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.  
2606    
2607  =back  =back
2608    
2609  =cut  =cut
2610    
2611  sub Pad {  sub Escape {
2612      # Get the parameters.      # Get the parameter.
2613      my ($string, $len, $left, $padChar) = @_;      my ($realString) = @_;
2614      # Compute the padding character.      # Initialize the return variable.
2615      if (! defined $padChar) {      my $retVal = "";
2616          $padChar = " ";      # Loop through the parameter string, looking for sequences to escape.
2617        while (length $realString > 0) {
2618            # Look for the first sequence to escape.
2619            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2620                # Here we found it. The text preceding the sequence is in $1. The sequence
2621                # itself is in $2. First, move the clear text to the return variable.
2622                $retVal .= $1;
2623                # Strip the processed section off the real string.
2624                $realString = substr $realString, (length $2) + (length $1);
2625                # Get the matched character.
2626                my $char = $2;
2627                # If we have a CR, we are done.
2628                if ($char ne "\r") {
2629                    # It's not a CR, so encode the escape sequence.
2630                    $char =~ tr/\t\n/tn/;
2631                    $retVal .= "\\" . $char;
2632      }      }
     # 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;  
2633          } else {          } else {
2634              $retVal .= $pad;              # Here there are no more escape sequences. The rest of the string is
2635                # transferred unmodified.
2636                $retVal .= $realString;
2637                $realString = "";
2638          }          }
2639      }      }
2640      # Return the result.      # Return the result.
2641      return $retVal;      return $retVal;
2642  }  }
2643    
2644  =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  
2645    
2646      TICK("./protein.cgi")      my $realString = Tracer::UnEscape($codedString);
2647    
2648  it will work correctly in both environments.  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2649    a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2650    be deleted.
2651    
2652  =over 4  =over 4
2653    
2654  =item commandString  =item codedString
2655    
2656  The command string to pass to the system.  String to un-escape.
2657    
2658  =item RETURN  =item RETURN
2659    
2660  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
2661    values.
2662    
2663  =back  =back
2664    
2665  =cut  =cut
2666  #: Return Type @;  
2667  sub TICK {  sub UnEscape {
2668      # Get the parameters.      # Get the parameter.
2669      my ($commandString) = @_;      my ($codedString) = @_;
2670      # Chop off the dot-slash if this is Windows.      # Initialize the return variable.
2671      if ($FIG_Config::win_mode) {      my $retVal = "";
2672          $commandString =~ s!^\./!!;      # Only proceed if the incoming string is nonempty.
2673        if (defined $codedString) {
2674            # Loop through the parameter string, looking for escape sequences. We can't do
2675            # translating because it causes problems with the escaped slash. ("\\t" becomes
2676            # "\<tab>" no matter what we do.)
2677            while (length $codedString > 0) {
2678                # Look for the first escape sequence.
2679                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2680                    # Here we found it. The text preceding the sequence is in $1. The sequence
2681                    # itself is in $2. First, move the clear text to the return variable.
2682                    $retVal .= $1;
2683                    $codedString = substr $codedString, (2 + length $1);
2684                    # Get the escape value.
2685                    my $char = $2;
2686                    # If we have a "\r", we are done.
2687                    if ($char ne 'r') {
2688                        # Here it's not an 'r', so we convert it.
2689                        $char =~ tr/\\tn/\\\t\n/;
2690                        $retVal .= $char;
2691      }      }
2692      # Activate the command and return the result.              } else {
2693      return `$commandString`;                  # Here there are no more escape sequences. The rest of the string is
2694                    # transferred unmodified.
2695                    $retVal .= $codedString;
2696                    $codedString = "";
2697                }
2698            }
2699        }
2700        # Return the result.
2701        return $retVal;
2702  }  }
2703    
2704  =head3 ScriptSetup  =head3 Percent
   
 C<< my ($query, $varHash) = ScriptSetup(); >>  
   
 Perform standard tracing and debugging setup for scripts. The value returned is  
 the CGI object followed by a pre-built variable hash.  
2705    
2706  The C<Trace> query parameter is used to determine whether or not tracing is active and      my $percent = Tracer::Percent($number, $base);
 which trace modules (other than C<Tracer> and C<FIG>) should be turned on. Specifying  
 the C<CGI> trace module will trace parameter and environment information. Parameters are  
 traced at level 3 and environment variables at level 4. At the end of the script, the  
 client should call L</ScriptFinish> to output the web page.  
2707    
2708  =cut  Returns the percent of the base represented by the given number. If the base
2709    is zero, returns zero.
2710    
2711  sub ScriptSetup {  =over 4
     # 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.  
         my $ttype = ($query->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");  
         TSetup($query->param('Trace') . " FIG Tracer", $ttype);  
         # Trace the parameter and environment data.  
         TraceParms($query);  
     } 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 $varHash = { DebugData => '' };  
     # Return the query object and variable hash.  
     return ($query, $varHash);  
 }  
2712    
2713  =head3 TraceParms  =item number
2714    
2715  C<< Tracer::TraceParms($query); >>  Percent numerator.
2716    
2717  Trace the CGI parameters at trace level CGI => 3 and the environment variables  =item base
 at level CGI => 4.  
2718    
2719  =over 4  Percent base.
2720    
2721  =item query  =item RETURN
2722    
2723  CGI query object containing the parameters to trace.  Returns the percentage of the base represented by the numerator.
2724    
2725  =back  =back
2726    
2727  =cut  =cut
2728    
2729  sub TraceParms {  sub Percent {
2730      # Get the parameters.      # Get the parameters.
2731      my ($query) = @_;      my ($number, $base) = @_;
2732      if (T(CGI => 3)) {      # Declare the return variable.
2733          # Here we want to trace the parameter data.      my $retVal = 0;
2734          my @names = $query->param;      # Compute the percent.
2735          for my $parmName (sort @names) {      if ($base != 0) {
2736              # Note we skip "Trace", which is for our use only.          $retVal = $number * 100 / $base;
             if ($parmName ne 'Trace') {  
                 my @values = $query->param($parmName);  
                 Trace("CGI: $parmName = " . join(", ", @values));  
             }  
         }  
         # Now output a GET-style URL for this query.  
         my $getURL = $query->url(-relative => 1, -query => 1);  
         # Strip out the Trace parameters.  
         $getURL =~ s/Trace=\d[^;&]+[;&]//;  
         $getURL =~ s/TF=\d[;&]//;  
         # Output the URL.  
         Trace("URL: ../FIG/$getURL");  
         # Display the request method.  
         my $method = $query->request_method();  
         Trace("Method: $method");  
     }  
     if (T(CGI => 4)) {  
         # Here we want the environment data too.  
         for my $envName (sort keys %ENV) {  
             Trace("ENV: $envName = $ENV{$envName}");  
         }  
     }  
2737  }  }
2738        # Return the result.
2739  =head3 ScriptFinish      return $retVal;
   
 C<< ScriptFinish($webData, $varHash); >>  
   
 Output a web page at the end of a script. Either the string to be output or the  
 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.  
   
 A typical standard script would loook like the following.  
   
     BEGIN {  
         # Print the HTML header.  
         print "CONTENT-TYPE: text/html\n\n";  
2740      }      }
     use Tracer;  
     use CGI;  
     use FIG;  
     # ... more uses ...  
2741    
2742      my ($query, $varHash) = ScriptSetup();  =head3 Min
     eval {  
         # ... get data from $query, put it in $varHash ...  
     };  
     if ($@) {  
         Trace("Script Error: $@") if T(0);  
     }  
     ScriptFinish("Html/MyTemplate.html", $varHash);  
2743    
2744  The idea here is that even if the script fails, you'll see trace messages and      my $min = Min($value1, $value2, ... $valueN);
2745  useful output.  
2746    Return the minimum argument. The arguments are treated as numbers.
2747    
2748  =over 4  =over 4
2749    
2750  =item webData  =item $value1, $value2, ... $valueN
2751    
2752  A string containing either the full web page to be written to the output or the  List of numbers to compare.
 name of a template file from which the page is to be constructed. If the name  
 of a template file is specified, then the second parameter must be present;  
 otherwise, it must be absent.  
2753    
2754  =item varHash (optional)  =item RETURN
2755    
2756  If specified, then a reference to a hash mapping variable names for a template  Returns the lowest number in the list.
 to their values. The template file will be read into memory, and variable markers  
 will be replaced by data in this hash reference.  
2757    
2758  =back  =back
2759    
2760  =cut  =cut
2761    
2762  sub ScriptFinish {  sub Min {
2763      # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
2764      my ($webData, $varHash) = @_;      my ($retVal, @values) = @_;
2765      # Check for a template file situation.      # Loop through the remaining parameters, looking for the lowest.
2766      my $outputString;      for my $value (@values) {
2767      if (defined $varHash) {          if ($value < $retVal) {
2768          # Here we have a template file. We need to determine the template type.              $retVal = $value;
         my $template;  
         if ($FIG_Config::template_url && $webData =~ /\.php$/) {  
             $template = "$FIG_Config::template_url/$webData";  
         } else {  
             $template = "<<$webData";  
         }  
         $outputString = PageBuilder::Build($template, $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;  
2769          }          }
         substr $outputString, $pos, 0, QTrace('Html');  
2770      }      }
2771      # Write the output string.      # Return the minimum found.
2772      print $outputString;      return $retVal;
2773  }  }
2774    
2775  =head3 Insure  =head3 Max
2776    
2777  C<< Insure($dirName); >>      my $max = Max($value1, $value2, ... $valueN);
2778    
2779  Insure a directory is present.  Return the maximum argument. The arguments are treated as numbers.
2780    
2781  =over 4  =over 4
2782    
2783  =item dirName  =item $value1, $value2, ... $valueN
2784    
2785  Name of the directory to check. If it does not exist, it will be created.  List of numbers to compare.
2786    
2787    =item RETURN
2788    
2789    Returns the highest number in the list.
2790    
2791  =back  =back
2792    
2793  =cut  =cut
2794    
2795  sub Insure {  sub Max {
2796      my ($dirName) = @_;      # Get the parameters. Note that we prime the return value with the first parameter.
2797      if (! -d $dirName) {      my ($retVal, @values) = @_;
2798          Trace("Creating $dirName directory.") if T(2);      # Loop through the remaining parameters, looking for the highest.
2799          eval { mkpath $dirName; };      for my $value (@values) {
2800          if ($@) {          if ($value > $retVal) {
2801              Confess("Error creating $dirName: $@");              $retVal = $value;
2802          }          }
2803      }      }
2804        # Return the maximum found.
2805        return $retVal;
2806  }  }
2807    
2808  =head3 ChDir  =head3 DebugMode
2809    
2810  C<< ChDir($dirName); >>      if (Tracer::DebugMode) { ...code... }
2811    
2812  Change to the specified directory.  Return TRUE if debug mode has been turned on, else abort.
2813    
2814    Certain CGI scripts are too dangerous to exist in the production
2815    environment. This method provides a simple way to prevent them
2816    from working unless they are explicitly turned on by creating a password
2817    cookie via the B<SetPassword> script.  If debugging mode
2818    is not turned on, an error will occur.
2819    
2820    =cut
2821    
2822    sub DebugMode {
2823        # Declare the return variable.
2824        my $retVal = 0;
2825        # Check the debug configuration.
2826        my $password = CGI::cookie("DebugMode");
2827        my $encrypted = Digest::MD5::md5_hex($password);
2828        if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
2829            $retVal = 1;
2830        } else {
2831            # Here debug mode is off, so we generate an error.
2832            Confess("Cannot use this facility without logging in.");
2833        }
2834        # Return the determination indicator.
2835        return $retVal;
2836    }
2837    
2838    =head3 Strip
2839    
2840        my $string = Tracer::Strip($line);
2841    
2842    Strip all line terminators off a string. This is necessary when dealing with files
2843    that may have been transferred back and forth several times among different
2844    operating environments.
2845    
2846  =over 4  =over 4
2847    
2848  =item dirName  =item line
2849    
2850  Name of the directory to which we want to change.  Line of text to be stripped.
2851    
2852    =item RETURN
2853    
2854    The same line of text with all the line-ending characters chopped from the end.
2855    
2856  =back  =back
2857    
2858  =cut  =cut
2859    
2860  sub ChDir {  sub Strip {
2861      my ($dirName) = @_;      # Get a copy of the parameter string.
2862      if (! -d $dirName) {      my ($string) = @_;
2863          Confess("Cannot change to directory $dirName: no such directory.");      my $retVal = (defined $string ? $string : "");
2864      } else {      # Strip the line terminator characters.
2865          Trace("Changing to directory $dirName.") if T(4);      $retVal =~ s/(\r|\n)+$//g;
2866          my $okFlag = chdir $dirName;      # Return the result.
2867          if (! $okFlag) {      return $retVal;
             Confess("Error switching to directory $dirName.");  
         }  
     }  
2868  }  }
2869    
2870  =head3 SendSMS  =head3 Pad
2871    
2872  C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
2873    
2874  Send a text message to a phone number using Clickatell. The FIG_Config file must contain the  Pad a string to a specified length. The pad character will be a
2875  user name, password, and API ID for the relevant account in the hash reference variable  space, and the padding will be on the right side unless specified
2876  I<$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  
2877    
2878      $phone =  { user => 'BruceTheHumanPet',  =over 4
                 password => 'silly',  
                 api_id => '2561022' };  
2879    
2880  The original purpose of this method was to insure Bruce would be notified immediately when the  =item string
 Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately  
 when you call this method.  
2881    
2882  The message ID will be returned if successful, and C<undef> if an error occurs.  String to be padded.
2883    
2884  =over 4  =item len
2885    
2886  =item phoneNumber  Desired length of the padded string.
2887    
2888  Phone number to receive the message, in international format. A United States phone number  =item left (optional)
 would be prefixed by "1". A British phone number would be prefixed by "44".  
2889    
2890  =item msg  TRUE if the string is to be left-padded; otherwise it will be padded on the right.
2891    
2892  Message to send to the specified phone.  =item padChar (optional)
2893    
2894    Character to use for padding. The default is a space.
2895    
2896  =item RETURN  =item RETURN
2897    
2898  Returns the message ID if successful, and C<undef> if the message could not be sent.  Returns a copy of the original string with the pad character added to the
2899    specified end so that it achieves the desired length.
2900    
2901  =back  =back
2902    
2903  =cut  =cut
2904    
2905  sub SendSMS {  sub Pad {
2906      # Get the parameters.      # Get the parameters.
2907      my ($phoneNumber, $msg) = @_;      my ($string, $len, $left, $padChar) = @_;
2908      # Declare the return variable. If we do not change it, C<undef> will be returned.      # Compute the padding character.
2909      my $retVal;      if (! defined $padChar) {
2910      # Only proceed if we have phone support.          $padChar = " ";
2911      if (! defined $FIG_Config::phone) {      }
2912          Trace("Phone support not present in FIG_Config.") if T(1);      # Compute the number of spaces needed.
2913      } else {      my $needed = $len - length $string;
2914          # Get the phone data.      # Copy the string into the return variable.
2915          my $parms = $FIG_Config::phone;      my $retVal = $string;
2916          # Get the Clickatell URL.      # Only proceed if padding is needed.
2917          my $url = "http://api.clickatell.com/http/";      if ($needed > 0) {
2918          # Create the user agent.          # Create the pad string.
2919          my $ua = LWP::UserAgent->new;          my $pad = $padChar x $needed;
2920          # Request a Clickatell session.          # Affix it to the return value.
2921          my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},          if ($left) {
2922                                       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;  
2923              } else {              } else {
2924                  Trace("Phone attempt failed with $rstring") if T(1);              $retVal .= $pad;
2925            }
2926              }              }
2927        # Return the result.
2928        return $retVal;
2929    }
2930    
2931    =head3 EOF
2932    
2933    This is a constant that is lexically greater than any useful string.
2934    
2935    =cut
2936    
2937    sub EOF {
2938        return "\xFF\xFF\xFF\xFF\xFF";
2939          }          }
2940    
2941    =head3 TICK
2942    
2943        my @results = TICK($commandString);
2944    
2945    Perform a back-tick operation on a command. If this is a Windows environment, any leading
2946    dot-slash (C<./> will be removed. So, for example, if you were doing
2947    
2948        `./protein.cgi`
2949    
2950    from inside a CGI script, it would work fine in Unix, but would issue an error message
2951    in Windows complaining that C<'.'> is not a valid command. If instead you code
2952    
2953        TICK("./protein.cgi")
2954    
2955    it will work correctly in both environments.
2956    
2957    =over 4
2958    
2959    =item commandString
2960    
2961    The command string to pass to the system.
2962    
2963    =item RETURN
2964    
2965    Returns the standard output from the specified command, as a list.
2966    
2967    =back
2968    
2969    =cut
2970    #: Return Type @;
2971    sub TICK {
2972        # Get the parameters.
2973        my ($commandString) = @_;
2974        # Chop off the dot-slash if this is Windows.
2975        if ($FIG_Config::win_mode) {
2976            $commandString =~ s!^\./!!;
2977      }      }
2978      # Return the result.      # Activate the command and return the result.
2979      return $retVal;      return `$commandString`;
2980  }  }
2981    
2982    
2983  =head3 CommaFormat  =head3 CommaFormat
2984    
2985  C<< my $formatted = Tracer::CommaFormat($number); >>      my $formatted = Tracer::CommaFormat($number);
2986    
2987  Insert commas into a number.  Insert commas into a number.
2988    
# Line 2234  Line 3015 
3015      # Return the result.      # Return the result.
3016      return $retVal;      return $retVal;
3017  }  }
 =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>.  
3018    
     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: $@");  
     }  
 }  
3019    
3020  =head3 CompareLists  =head3 CompareLists
3021    
3022  C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>      my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3023    
3024  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
3025  are presumed to be sorted alphabetically by the value in the $keyIndex column.  are presumed to be sorted alphabetically by the value in the $keyIndex column.
# Line 2435  Line 3084 
3084      return ($inserted, $deleted);      return ($inserted, $deleted);
3085  }  }
3086    
3087  =head3 GetLine  =head3 GenerateURL
3088    
3089  C<< my @data = Tracer::GetLine($handle); >>      my $queryUrl = Tracer::GenerateURL($page, %parameters);
3090    
3091  Read a line of data from a tab-delimited file.  Generate a GET-style URL for the specified page with the specified parameter
3092    names and values. The values will be URL-escaped automatically. So, for
3093    example
3094    
3095        Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3096    
3097    would return
3098    
3099        form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3100    
3101  =over 4  =over 4
3102    
3103  =item handle  =item page
3104    
3105  Open file handle from which to read.  Page URL.
3106    
3107    =item parameters
3108    
3109    Hash mapping parameter names to parameter values.
3110    
3111  =item RETURN  =item RETURN
3112    
3113  Returns a list of the fields in the record read. The fields are presumed to be  Returns a GET-style URL that goes to the specified page and passes in the
3114  tab-delimited. If we are at the end of the file, then an empty list will be  specified parameters and values.
 returned. If an empty line is read, a single list item consisting of a null  
 string will be returned.  
3115    
3116  =back  =back
3117    
3118  =cut  =cut
3119    
3120  sub GetLine {  sub GenerateURL {
3121      # Get the parameters.      # Get the parameters.
3122      my ($handle) = @_;      my ($page, %parameters) = @_;
3123      # Declare the return variable.      # Prime the return variable with the page URL.
3124      my @retVal = ();      my $retVal = $page;
3125      # Read from the file.      # Loop through the parameters, creating parameter elements in a list.
3126      my $line = <$handle>;      my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3127      # Only proceed if we found something.      # If the list is nonempty, tack it on.
3128      if (defined $line) {      if (@parmList) {
3129          # Remove the new-line.          $retVal .= "?" . join(";", @parmList);
         chomp $line;  
         # If the line is empty, return a single empty string; otherwise, parse  
         # it into fields.  
         if ($line eq "") {  
             push @retVal, "";  
         } else {  
             push @retVal, split /\t/,$line;  
         }  
3130      }      }
3131      # Return the result.      # Return the result.
3132      return @retVal;      return $retVal;
3133  }  }
3134    
3135  =head3 PutLine  =head3 ApplyURL
3136    
3137  C<< Tracer::PutLine($handle, \@fields); >>      Tracer::ApplyURL($table, $target, $url);
3138    
3139  Write a line of data to a tab-delimited file. The specified field values will be  Run through a two-dimensional table (or more accurately, a list of lists), converting the
3140  output in tab-separated form, with a trailing new-line.  I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3141    URL column will be deleted by this process and the target column will be HTML-escaped.
3142    
3143    This provides a simple way to process the results of a database query into something
3144    displayable by combining a URL with text.
3145    
3146  =over 4  =over 4
3147    
3148  =item handle  =item table
3149    
3150  Output file handle.  Reference to a list of lists. The elements in the containing list will be updated by
3151    this method.
3152    
3153  =item fields  =item target
3154    
3155  List of field values.  The index of the column to be converted into HTML.
3156    
3157    =item url
3158    
3159    The index of the column containing the URL. Note that the URL must have a recognizable
3160    C<http:> at the beginning.
3161    
3162  =back  =back
3163    
3164  =cut  =cut
3165    
3166  sub PutLine {  sub ApplyURL {
3167      # Get the parameters.      # Get the parameters.
3168      my ($handle, $fields) = @_;      my ($table, $target, $url) = @_;
3169      # Write the data.      # Loop through the table.
3170      print $handle join("\t", @{$fields}) . "\n";      for my $row (@{$table}) {
3171            # Apply the URL to the target cell.
3172            $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3173            # Delete the URL from the row.
3174            delete $row->[$url];
3175        }
3176  }  }
3177    
3178  =head3 GenerateURL  =head3 CombineURL
3179    
3180  C<< my $queryUrl = Tracer::GenerateURL($page, %parameters); >>      my $combinedHtml = Tracer::CombineURL($text, $url);
3181    
3182  Generate a GET-style URL for the specified page with the specified parameter  This method will convert the specified text into HTML hyperlinked to the specified
3183  names and values. The values will be URL-escaped automatically. So, for  URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3184  example  is defined and begins with an C<http:> header.
3185    
3186      Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")  =over 4
3187    
3188  would return  =item text
3189    
3190    Text to return. This will be HTML-escaped automatically.
3191    
3192    =item url
3193    
3194    A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3195    will be returned without any hyperlinking.
3196    
3197    =item RETURN
3198    
3199    Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3200    doesn't look right, the HTML-escaped text will be returned without any further
3201    modification.
3202    
3203      form.cgi?type=1&string=%22high%20pass%22%20or%20highway  =back
3204    
3205    =cut
3206    
3207    sub CombineURL {
3208        # Get the parameters.
3209        my ($text, $url) = @_;
3210        # Declare the return variable.
3211        my $retVal = CGI::escapeHTML($text);
3212        # Verify the URL.
3213        if (defined($url) && $url =~ m!http://!i) {
3214            # It's good, so we apply it to the text.
3215            $retVal = "<a href=\"$url\">$retVal</a>";
3216        }
3217        # Return the result.
3218        return $retVal;
3219    }
3220    
3221    =head3 Cmp
3222    
3223        my $cmp = Tracer::Cmp($a, $b);
3224    
3225    This method performs a universal sort comparison. Each value coming in is
3226    separated into a leading text part and a trailing number part. The text
3227    part is string compared, and if both parts are equal, then the number
3228    parts are compared numerically. A stream of just numbers or a stream of
3229    just strings will sort correctly, and a mixed stream will sort with the
3230    numbers first. Strings with a label and a number will sort in the
3231    expected manner instead of lexically.
3232    
3233  =over 4  =over 4
3234    
3235  =item page  =item a
3236    
3237  Page URL.  First item to compare.
3238    
3239  =item parameters  =item b
3240    
3241  Hash mapping parameter names to parameter values.  Second item to compare.
3242    
3243  =item RETURN  =item RETURN
3244    
3245  Returns a GET-style URL that goes to the specified page and passes in the  Returns a negative number if the first item should sort first (is less), a positive
3246  specified parameters and values.  number if the first item should sort second (is greater), and a zero if the items are
3247    equal.
3248    
3249  =back  =back
3250    
3251  =cut  =cut
3252    
3253  sub GenerateURL {  sub Cmp {
3254      # Get the parameters.      # Get the parameters.
3255      my ($page, %parameters) = @_;      my ($a, $b) = @_;
3256      # Prime the return variable with the page URL.      # Declare the return value.
3257      my $retVal = $page;      my $retVal;
3258      # Loop through the parameters, creating parameter elements in a list.      # Check for nulls.
3259      my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;      if (! defined($a)) {
3260      # If the list is nonempty, tack it on.          $retVal = (! defined($b) ? 0 : -1);
3261      if (@parmList) {      } elsif (! defined($b)) {
3262          $retVal .= "?" . join("&", @parmList);          $retVal = 1;
3263        } else {
3264            # Here we have two real values. Parse the two strings.
3265            $a =~ /^(\D*)(\d*)$/;
3266            my $aParsed = [$1, $2];
3267            $b =~ /^(\D*)(\d*)$/;
3268            my $bParsed = [$1, $2];
3269            # Compare the string parts.
3270            $retVal = $aParsed->[0] cmp $bParsed->[0];
3271            if (! $retVal) {
3272                $retVal = $aParsed->[1] <=> $bParsed->[1];
3273            }
3274      }      }
3275      # Return the result.      # Return the result.
3276      return $retVal;      return $retVal;
3277  }  }
3278    
3279    
3280  1;  1;

Legend:
Removed from v.1.67  
changed lines
  Added in v.1.93

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3