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# Line 1  Line 1 
1    #
2    # Copyright (c) 2003-2006 University of Chicago and Fellowship
3    # for Interpretations of Genomes. All Rights Reserved.
4    #
5    # This file is part of the SEED Toolkit.
6    #
7    # The SEED Toolkit is free software. You can redistribute
8    # it and/or modify it under the terms of the SEED Toolkit
9    # Public License.
10    #
11    # You should have received a copy of the SEED Toolkit Public License
12    # along with this program; if not write to the University of Chicago
13    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14    # Genomes at veronika@thefig.info or download a copy from
15    # http://www.theseed.org/LICENSE.TXT.
16    #
17    
18  package Tracer;  package Tracer;
19    
20      require Exporter;      require Exporter;
21      @ISA = ('Exporter');      @ISA = ('Exporter');
22      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir);      @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);
26      use CGI;      use CGI;
27        use Cwd;
28      use FIG_Config;      use FIG_Config;
29      use PageBuilder;      use PageBuilder;
30        use Digest::MD5;
31        use File::Basename;
32        use File::Path;
33        use File::stat;
34        use LWP::UserAgent;
35        use Time::HiRes 'gettimeofday';
36        use URI::Escape;
37    
38  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
39    
40  =head2 Introduction  =head2 Tracing
41    
42  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
43  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.
44  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,
45  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
46  level is less than or equal to this package's trace level and whose category is activated will  level is less than or equal to the setup trace level and whose category is activated will
47  be written. Thus, a higher trace level on a message indicates that the message  be written. Thus, a higher trace level on a message indicates that the message
48  is less likely to be seen. A higher trace level passed to B<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
49  appear. To generate a trace message, use the following syntax.  appear.
50    
51    =head3 Putting Trace Messages in Your Code
52    
53  C<< Trace($message) if T(errors => 4); >>  To generate a trace message, use the following syntax.
54    
55        Trace($message) if T(errors => 4);
56    
57  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>
58  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
59    
60  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
61    
62  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
63    
# Line 36  Line 65 
65  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
66  active and the trace level is 2 or more.  active and the trace level is 2 or more.
67    
68  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
69    
70    In scripts, where no package name is available, the category defaults to C<main>.
71    
72  To set up tracing, you call the L</TSetup> method. The method takes as input a trace level, a list  =head3 Custom Tracing
73  of category names, and a set of options. The trace level and list of category names are  
74    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
75    the preferred method, but a knowledge of how custom tracing works can make the more modern
76    L</Emergency Tracing> easier to understand.
77    
78    To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
79    a list of category names, and a destination. The trace level and list of category names are
80  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
81    
82  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
83    
84  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
85  specifies that messages should be output as HTML paragraphs.  specifies that messages should be sent to the standard output.
86    
87  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
88  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
89  useful in a CGI environment.  useful in a CGI environment.
90    
91  C<< TSetup('3 *', 'WARN'); >>      TSetup('3 *', 'WARN');
92    
93  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
94  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
95  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
96  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
97  it easier to debug page formatting problems.  it easier to debug page formatting problems.
98    
99  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
100    a file at the same time. To trace to a file, specify the filename with an output character in front
101    of it.
102    
103        TSetup('4 SQL', ">$fileName");
104    
105    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
106    bracket.
107    
108        TSetup('3 *', "+>$fileName");
109    
110  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>.
111  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.
112  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
113  being used out in the field.  being used out in the field.
114    
115    =head3 Trace Levels
116    
117  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
118  a suggestion.  a suggestion.
119    
120  =over 4  =over 4
121    
122  =item 0 Error  =item Error 0
123    
124  Message indicates an error that may lead to incorrect results or that has stopped the  Message indicates an error that may lead to incorrect results or that has stopped the
125  application entirely.  application entirely.
126    
127  =item 1 Warning  =item Warning 1
128    
129  Message indicates something that is unexpected but that probably did not interfere  Message indicates something that is unexpected but that probably did not interfere
130  with program execution.  with program execution.
131    
132  =item 2 Notice  =item Notice 2
133    
134  Message indicates the beginning or end of a major task.  Message indicates the beginning or end of a major task.
135    
136  =item 3 Information  =item Information 3
137    
138  Message indicates a subtask. In the FIG system, a subtask generally relates to a single  Message indicates a subtask. In the FIG system, a subtask generally relates to a single
139  genome. This would be a big loop that is not expected to execute more than 500 times or so.  genome. This would be a big loop that is not expected to execute more than 500 times or so.
140    
141  =item 4 Detail  =item Detail 4
142    
143  Message indicates a low-level loop iteration.  Message indicates a low-level loop iteration.
144    
145  =back  =back
146    
147    The format of trace messages is important because some utilities analyze trace files.
148    There are three fields-- the time stamp, the category name, and the text.
149    The time stamp is between square brackets and the category name between angle brackets.
150    After the category name there is a colon (C<:>) followed by the message text.
151    If the square brackets or angle brackets are missing, then the trace management
152    utilities assume that they are encountering a set of pre-formatted lines.
153    
154    Note, however, that this formatting is done automatically by the tracing functions. You
155    only need to know about it if you want to parse a trace file.
156    
157    =head3 Emergency Tracing
158    
159    Sometimes, you need a way for tracing to happen automatically without putting parameters
160    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
161    from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.
162    Emergency tracing requires you specify a tracing key. For command-line tools, the key is
163    taken from the C<TRACING> environment variable. For web services, the key is taken from
164    a cookie. Either way, the key tells the tracing facility who you are, so that you control
165    the tracing in your environment without stepping on other users.
166    
167    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
168    generate one for you.
169    
170    You can activate and de-activate emergency tracing from the debugging control panel, as
171    well as display the trace file itself.
172    
173    To enable emergency tracing in your code, call
174    
175        ETracing($cgi)
176    
177    from a web script and
178    
179        ETracing()
180    
181    from a command-line script.
182    
183    The web script will look for the tracing key in the cookies, and the command-line
184    script will look for it in the C<TRACING> environment variable. If you are
185    using the L</StandardScript> or L</StandardSetup> methods, emergency tracing
186    will be configured automatically.
187    
188    =head3 Debugging Control Panel
189    
190    The debugging control panel provides several tools to assist in development of
191    SEED and Sprout software. You access the debugging control panel from the URL
192    C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,
193    for example, the panel access point for the development NMPDR system is
194    C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to
195    find out what the password is. From this page, you can also specify a tracing
196    key. If you don't specify a key, one will be generated for you.
197    
198    =head4 Emergency Tracing Form
199    
200    At the bottom of the debugging control panel is a form that allows you to
201    specify a trace level and tracing categories. Special and common categories
202    are listed with check boxes. You can hold your mouse over a check box to see
203    what its category does. In general, however, a category name is the same as
204    the name of the package in which the trace message occurs.
205    
206    Additional categories can be entered in an input box, delimited by spaces or commas.
207    
208    The B<Activate> button turns on Emergency tracing at the level you specify with the
209    specified categories active. The B<Terminate> button turns tracing off. The
210    B<Show File> button displays the current contents of the trace file. The tracing
211    form at the bottom of the control panel is designed for emergency tracing, so it
212    will only affect programs that call L</ETracing>, L</StandardScript>,
213    or L</StandardSetup>.
214    
215    =head4 Script Form
216    
217    The top form of the debugging control panel allows you to enter a tiny script and
218    have the output generated in a formatted table. Certain object variables are
219    predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),
220    and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.
221    
222    The last line of the script must be a scalar, but it can be a reference to a hash,
223    a list, a list of lists, and various other combinations. If you select the appropriate
224    data type in the dropdown box, the output will be formatted accordingly. The form
225    also has controls for specifying tracing. These controls override any emergency
226    tracing in effect.
227    
228    =head4 Database Query Forms
229    
230    The forms between the script form and the emergency tracing form allow you to
231    make queries against the database. The FIG query form allows simple queries against
232    a single FIG table. The Sprout query form uses the B<GetAll> method to do a
233    multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>
234    package, and it takes five parameters.
235    
236        GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
237    
238    Each of the five parameters corresponds to a text box on the query form:
239    
240    =over 4
241    
242    =item Objects
243    
244    Comma-separated list containing the names of the entity and relationship objects to be retrieved.
245    
246    =item Filter
247    
248    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
249    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
250    B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a
251    field, I<objectName> is the name of the entity or relationship object containing the field, and
252    I<number> is the 1-based position of the object in the object list. Any parameters
253    specified in the filter clause should be specified in the B<Params> field.
254    The fields in a filter clause can come from primary entity relations,
255    relationship relations, or secondary entity relations; however, all of the
256    entities and relationships involved must be included in the list of object names.
257    
258    =item Params
259    
260    List of the parameters to be substituted in for the parameters marks in the filter clause. This
261    is a comma-separated list without any quoting or escaping.
262    
263    =item fields
264    
265    Comma-separated list of the fields to be returned in each element of the list returned. Fields
266    are specified in the same manner as in the filter clause.
267    
268    =item count
269    
270    Maximum number of records to return. If omitted or 0, all available records will be returned.
271    
272    =back
273    
274    B<GetAll> automatically joins together the entities and relationships listed in the object
275    names. This simplifies the coding of the filter clause, but it means that some queries are
276    not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation
277    that has yet to be addressed.
278    
279  =cut  =cut
280    
281  # Declare the configuration variables.  # Declare the configuration variables.
# Line 156  Line 336 
336      # Presume category-based tracing until we learn otherwise.      # Presume category-based tracing until we learn otherwise.
337      $AllTrace = 0;      $AllTrace = 0;
338      # Build the category hash. Note that if we find a "*", we turn on non-category      # Build the category hash. Note that if we find a "*", we turn on non-category
339      # tracing.      # tracing. We must also clear away any pre-existing data.
340        %Categories = ( main => 1 );
341      for my $category (@categoryData) {      for my $category (@categoryData) {
342          if ($category eq '*') {          if ($category eq '*') {
343              $AllTrace = 1;              $AllTrace = 1;
344          } else {          } else {
345              $Categories{$category} = 1;              $Categories{lc $category} = 1;
346          }          }
347      }      }
348      # Now we need to process the destination information. The most important special      # Now we need to process the destination information. The most important special
# Line 174  Line 355 
355          }          }
356          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
357              open TRACEFILE, $target;              open TRACEFILE, $target;
358              print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";
359              close TRACEFILE;              close TRACEFILE;
360              $Destination = ">$target";              $Destination = ">$target";
361          } else {          } else {
# Line 187  Line 368 
368      $SetupCount++;      $SetupCount++;
369  }  }
370    
371    =head3 StandardSetup
372    
373    C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>
374    
375    This method performs standard command-line parsing and tracing setup. The return
376    values are a hash of the command-line options and a list of the positional
377    parameters. Tracing is automatically set up and the command-line options are
378    validated.
379    
380    This is a complex method that does a lot of grunt work. The parameters can
381    be more easily understood, however, once they are examined individually.
382    
383    The I<categories> parameter is the most obtuse. It is a reference to a list of
384    special-purpose tracing categories. Most tracing categories are PERL package
385    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
386    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
387    
388        ["Sprout", "SproutLoad", "ERDB"]
389    
390    This would cause trace messages in the specified three packages to appear in
391    the output. There are two special tracing categories that are automatically
392    handled by this method. In other words, if you used L</TSetup> you would need
393    to include these categories manually, but if you use this method they are turned
394    on automatically.
395    
396    =over 4
397    
398    =item SQL
399    
400    Traces SQL commands and activity.
401    
402    =item Tracer
403    
404    Traces error messages and call stacks.
405    
406    =back
407    
408    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
409    The trace level is specified using the C<-trace> command-line option. For example,
410    the following command line for C<TransactFeatures> turns on SQL tracing and runs
411    all tracing at level 3.
412    
413        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
414    
415    Standard tracing is output to the standard output and echoed to the file
416    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
417    process ID. You can also specify the C<user> parameter to put a user ID
418    instead of a process ID in the trace file name. So, for example
419    
420    The default trace level is 2. To get all messages, specify a trace level of 4.
421    For a genome-by-genome update, use 3.
422    
423        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
424    
425    would send the trace output to C<traceBruce.log> in the temporary directory.
426    
427    The I<options> parameter is a reference to a hash containing the command-line
428    options, their default values, and an explanation of what they mean. Command-line
429    options may be in the form of switches or keywords. In the case of a switch, the
430    option value is 1 if it is specified and 0 if it is not specified. In the case
431    of a keyword, the value is separated from the option name by an equal sign. You
432    can see this last in the command-line example above.
433    
434    You can specify a different default trace level by setting C<$options->{trace}>
435    prior to calling this method.
436    
437    An example at this point would help. Consider, for example, the command-line utility
438    C<TransactFeatures>. It accepts a list of positional parameters plus the options
439    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
440    the following code.
441    
442        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
443                            { safe => [0, "use database transactions"],
444                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
445                              start => [' ', "start with this genome"],
446                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
447                            "command transactionDirectory IDfile",
448                          @ARGV);
449    
450    
451    The call to C<ParseCommand> specifies the default values for the options and
452    stores the actual options in a hash that is returned as C<$options>. The
453    positional parameters are returned in C<@parameters>.
454    
455    The following is a sample command line for C<TransactFeatures>.
456    
457        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
458    
459    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
460    parameters, and would find themselves in I<@parameters> after executing the
461    above code fragment. The tracing would be set to level 2, and the categories
462    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
463    and C<DocUtils> was included because it came in within the first parameter
464    to this method. The I<$options> hash would be
465    
466        { trace => 2, sql => 0, safe => 0,
467          noAlias => 1, start => ' ', tblFiles => 0 }
468    
469    Use of C<StandardSetup> in this way provides a simple way of performing
470    standard tracing setup and command-line parsing. Note that the caller is
471    not even aware of the command-line switches C<-trace> and C<-sql>, which
472    are used by this method to control the tracing. If additional tracing features
473    need to be added in the future, they can be processed by this method without
474    upsetting the command-line utilities.
475    
476    If the C<background> option is specified on the command line, then the
477    standard and error outputs will be directed to files in the temporary
478    directory, using the same suffix as the trace file. So, if the command
479    line specified
480    
481        -user=Bruce -background
482    
483    then the trace output would go to C<traceBruce.log>, the standard output to
484    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
485    simplify starting a command in the background.
486    
487    The user name is also used as the tracing key for L</Emergency Tracing>.
488    Specifying a value of C<E> for the trace level causes emergency tracing to
489    be used instead of custom tracing. If the user name is not specified,
490    the tracing key is taken from the C<Tracing> environment variable. If there
491    is no value for that variable, the tracing key will be computed from the PID.
492    
493    Finally, if the special option C<-h> is specified, the option names will
494    be traced at level 0 and the program will exit without processing.
495    This provides a limited help capability. For example, if the user enters
496    
497        TransactFeatures -h
498    
499    he would see the following output.
500    
501        TransactFeatures [options] command transactionDirectory IDfile
502            -trace    tracing level (default E)
503            -sql      trace SQL commands
504            -safe     use database transactions
505            -noAlias  do not expect aliases in CHANGE transactions
506            -start    start with this genome
507            -tblFiles output TBL files containing the corrected IDs
508    
509    The caller has the option of modifying the tracing scheme by placing a value
510    for C<trace> in the incoming options hash. The default value can be overridden,
511    or the tracing to the standard output can be turned off by suffixing a minus
512    sign to the trace level. So, for example,
513    
514        { trace => [0, "tracing level (default 0)"],
515           ...
516    
517    would set the default trace level to 0 instead of E, while
518    
519        { trace => ["2-", "tracing level (default 2)"],
520           ...
521    
522    would set the default to 2, but trace only to the log file, not to the
523    standard output.
524    
525    The parameters to this method are as follows.
526    
527    =over 4
528    
529    =item categories
530    
531    Reference to a list of tracing category names. These should be names of
532    packages whose internal workings will need to be debugged to get the
533    command working.
534    
535    =item options
536    
537    Reference to a hash containing the legal options for the current command mapped
538    to their default values and descriptions. The user can override the defaults
539    by specifying the options as command-line switches prefixed by a hyphen.
540    Tracing-related options may be added to this hash. If the C<-h> option is
541    specified on the command line, the option descriptions will be used to
542    explain the options. To turn off tracing to the standard output, add a
543    minus sign to the value for C<trace> (see above).
544    
545    =item parmHelp
546    
547    A string that vaguely describes the positional parameters. This is used
548    if the user specifies the C<-h> option.
549    
550    =item argv
551    
552    List of command line parameters, including the option switches, which must
553    precede the positional parameters and be prefixed by a hyphen.
554    
555    =item RETURN
556    
557    Returns a list. The first element of the list is the reference to a hash that
558    maps the command-line option switches to their values. These will either be the
559    default values or overrides specified on the command line. The remaining
560    elements of the list are the position parameters, in order.
561    
562    =back
563    
564    =cut
565    
566    sub StandardSetup {
567        # Get the parameters.
568        my ($categories, $options, $parmHelp, @argv) = @_;
569        # Get the default tracing key.
570        my $tkey = EmergencyKey();
571        # Add the tracing options.
572        if (! exists $options->{trace}) {
573            $options->{trace} = ['E', "tracing level (E for emergency tracing)"];
574        }
575        $options->{sql} = [0, "turn on SQL tracing"];
576        $options->{h} = [0, "display command-line options"];
577        $options->{user} = [$tkey, "tracing key"];
578        $options->{background} = [0, "spool standard and error output"];
579        # Create a parsing hash from the options hash. The parsing hash
580        # contains the default values rather than the default value
581        # and the description. While we're at it, we'll memorize the
582        # length of the longest option name.
583        my $longestName = 0;
584        my %parseOptions = ();
585        for my $key (keys %{$options}) {
586            if (length $key > $longestName) {
587                $longestName = length $key;
588            }
589            $parseOptions{$key} = $options->{$key}->[0];
590        }
591        # Parse the command line.
592        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
593        # Get the logfile suffix.
594        my $suffix = $retOptions->{user};
595        # Check for background mode.
596        if ($retOptions->{background}) {
597            my $outFileName = "$FIG_Config::temp/out$suffix.log";
598            my $errFileName = "$FIG_Config::temp/err$suffix.log";
599            open STDOUT, ">$outFileName";
600            open STDERR, ">$errFileName";
601        }
602        # Now we want to set up tracing. First, we need to know if the user
603        # wants emergency tracing.
604        if ($retOptions->{trace} eq 'E') {
605            ETracing($retOptions->{user});
606        } else {
607            # Here the tracing is controlled from the command line.
608            my @cats = @{$categories};
609            if ($retOptions->{sql}) {
610                push @cats, "SQL";
611            }
612            # Add the default categories.
613            push @cats, "Tracer";
614            # Next, we create the category string by joining the categories.
615            my $cats = join(" ", @cats);
616            # Check to determine whether or not the caller wants to turn off tracing
617            # to the standard output.
618            my $traceLevel = $retOptions->{trace};
619            my $textOKFlag = 1;
620            if ($traceLevel =~ /^(.)-/) {
621                $traceLevel = $1;
622                $textOKFlag = 0;
623            }
624            # Now we set up the trace mode.
625            my $traceMode;
626            # Verify that we can open a file in the FIG temporary directory.
627            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
628            if (open TESTTRACE, ">$traceFileName") {
629                # Here we can trace to a file.
630                $traceMode = ">$traceFileName";
631                if ($textOKFlag) {
632                    # Echo to standard output if the text-OK flag is set.
633                    $traceMode = "+$traceMode";
634                }
635                # Close the test file.
636                close TESTTRACE;
637            } else {
638                # Here we can't trace to a file. We trace to the standard output if it's
639                # okay, and the error log otherwise.
640                if ($textOKFlag) {
641                    $traceMode = "TEXT";
642                } else {
643                    $traceMode = "WARN";
644                }
645            }
646            # Now set up the tracing.
647            TSetup("$traceLevel $cats", $traceMode);
648        }
649        # Check for the "h" option. If it is specified, dump the command-line
650        # options and exit the program.
651        if ($retOptions->{h}) {
652            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
653            print "$1 [options] $parmHelp\n";
654            for my $key (sort keys %{$options}) {
655                my $name = Pad($key, $longestName, 0, ' ');
656                my $desc = $options->{$key}->[1];
657                if ($options->{$key}->[0]) {
658                    $desc .= " (default " . $options->{$key}->[0] . ")";
659                }
660                print "  $name $desc\n";
661            }
662            exit(0);
663        }
664        # Return the parsed parameters.
665        return ($retOptions, @retParameters);
666    }
667    
668  =head3 Setups  =head3 Setups
669    
670  C<< my $count = Tracer::Setups(); >>  C<< my $count = Tracer::Setups(); >>
# Line 347  Line 825 
825    
826  =head3 OpenDir  =head3 OpenDir
827    
828  C<< my @files = OpenDir($dirName, $filtered); >>  C<< my @files = OpenDir($dirName, $filtered, $flag); >>
829    
830  Open a directory and return all the file names. This function essentially performs  Open a directory and return all the file names. This function essentially performs
831  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
832  set to TRUE, all filenames beginning with a period (C<.>) will be filtered out of  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
833  the return list. If the directory does not open, an exception is thrown. So,  or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
834  for example,  filtered out of the return list. If the directory does not open and I<$flag> is not
835    set, an exception is thrown. So, for example,
836    
837      my @files = OpenDir("/Volumes/fig/contigs", 1);      my @files = OpenDir("/Volumes/fig/contigs", 1);
838    
839  is effectively the same as  is effectively the same as
840    
841      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
842      my @files = grep { $_ !~ /^\./ } readdir(TMP);      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
843    
844  Similarly, the following code  Similarly, the following code
845    
846      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs");      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
847    
848  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
849  automatically throws an error if the directory fails to open.  automatically returns an empty list if the directory fails to open.
850    
851  =over 4  =over 4
852    
# Line 380  Line 859 
859  TRUE if files whose names begin with a period (C<.>) should be automatically removed  TRUE if files whose names begin with a period (C<.>) should be automatically removed
860  from the list, else FALSE.  from the list, else FALSE.
861    
862    =item flag
863    
864    TRUE if a failure to open is okay, else FALSE
865    
866  =back  =back
867    
868  =cut  =cut
869  #: Return Type @;  #: Return Type @;
870  sub OpenDir {  sub OpenDir {
871      # Get the parameters.      # Get the parameters.
872      my ($dirName, $filtered) = @_;      my ($dirName, $filtered, $flag) = @_;
873      # Declare the return variable.      # Declare the return variable.
874      my @retVal;      my @retVal = ();
875      # Open the directory.      # Open the directory.
876      if (opendir(my $dirHandle, $dirName)) {      if (opendir(my $dirHandle, $dirName)) {
877          # The directory opened successfully. Get the appropriate list according to the          # The directory opened successfully. Get the appropriate list according to the
878          # strictures of the filter parameter.          # strictures of the filter parameter.
879          if ($filtered) {          if ($filtered) {
880              @retVal = grep { $_ !~ /^\./ } readdir $dirHandle;              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
881          } else {          } else {
882              @retVal = readdir $dirHandle;              @retVal = readdir $dirHandle;
883          }          }
884      } else {      } elsif (! $flag) {
885          # Here the directory would not open.          # Here the directory would not open and it's considered an error.
886          Confess("Could not open directory $dirName.");          Confess("Could not open directory $dirName.");
887      }      }
888      # Return the result.      # Return the result.
# Line 650  Line 1133 
1133      # Get the timestamp.      # Get the timestamp.
1134      my $timeStamp = Now();      my $timeStamp = Now();
1135      # Format the message. Note we strip off any line terminators at the end.      # Format the message. Note we strip off any line terminators at the end.
1136      my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);      my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);
1137      # Process according to the destination.      # Process according to the destination.
1138      if ($Destination eq "TEXT") {      if ($Destination eq "TEXT") {
1139          # Write the message to the standard output.          # Write the message to the standard output.
# Line 670  Line 1153 
1153         warn $message;         warn $message;
1154      } elsif ($Destination =~ m/^>>/) {      } elsif ($Destination =~ m/^>>/) {
1155          # Write the trace message to an output file.          # Write the trace message to an output file.
1156          open TRACING, $Destination;          (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
1157          print TRACING "$formatted\n";          print TRACING "$formatted\n";
1158          close TRACING;          close TRACING;
1159          # If the Tee flag is on, echo it to the standard output.          # If the Tee flag is on, echo it to the standard output.
# Line 734  Line 1217 
1217          }          }
1218          # Save the category name.          # Save the category name.
1219          $LastCategory = $category;          $LastCategory = $category;
1220            # Convert it to lower case before we hash it.
1221            $category = lc $category;
1222          # Use the category and tracelevel to compute the result.          # Use the category and tracelevel to compute the result.
1223            if (ref $traceLevel) {
1224                Confess("Bad trace level.");
1225            } elsif (ref $TraceLevel) {
1226                Confess("Bad trace config.");
1227            }
1228          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
1229      }      }
1230      # Return the computed result.      # Return the computed result.
# Line 821  Line 1311 
1311    
1312  C<< my $codedString = Tracer::Escape($realString); >>  C<< my $codedString = Tracer::Escape($realString); >>
1313    
1314  Escape a string for use in a command length. Spaces will be replaced by C<\b>,  Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines
1315  tabs replaced by C<\t>, new-lines replaced by C<\n>, and backslashes will be  replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
1316  doubled. The effect is to exactly reverse the effect of L</UnEscape>.  result is to reverse the effect of L</UnEscape>.
1317    
1318  =over 4  =over 4
1319    
# Line 847  Line 1337 
1337      # Loop through the parameter string, looking for sequences to escape.      # Loop through the parameter string, looking for sequences to escape.
1338      while (length $realString > 0) {      while (length $realString > 0) {
1339          # Look for the first sequence to escape.          # Look for the first sequence to escape.
1340          if ($realString =~ /^(.*?)([ \n\t\\])/) {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1341              # Here we found it. The text preceding the sequence is in $1. The sequence              # Here we found it. The text preceding the sequence is in $1. The sequence
1342              # itself is in $2. First, move the clear text to the return variable.              # itself is in $2. First, move the clear text to the return variable.
1343              $retVal .= $1;              $retVal .= $1;
1344              $realString = substr $realString, (length $2 + length $1);              # Strip the processed section off the real string.
1345              # Encode the escape sequence.              $realString = substr $realString, (length $2) + (length $1);
1346                # Get the matched character.
1347              my $char = $2;              my $char = $2;
1348              $char =~ tr/ \t\n/btn/;              # If we have a CR, we are done.
1349                if ($char ne "\r") {
1350                    # It's not a CR, so encode the escape sequence.
1351                    $char =~ tr/\t\n/tn/;
1352              $retVal .= "\\" . $char;              $retVal .= "\\" . $char;
1353                }
1354          } else {          } else {
1355              # Here there are no more escape sequences. The rest of the string is              # Here there are no more escape sequences. The rest of the string is
1356              # transferred unmodified.              # transferred unmodified.
# Line 871  Line 1366 
1366    
1367  C<< my $realString = Tracer::UnEscape($codedString); >>  C<< my $realString = Tracer::UnEscape($codedString); >>
1368    
1369  Replace escape sequences with their actual equivalents. C<\b> will be replaced by a space,  Replace escape sequences with their actual equivalents. C<\t> will be replaced by
1370  C<\t> by a tab, C<\n> by a new-line character, and C<\\> by a back-slash.  a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
1371    be deleted.
1372    
1373  =over 4  =over 4
1374    
# Line 897  Line 1393 
1393      # Only proceed if the incoming string is nonempty.      # Only proceed if the incoming string is nonempty.
1394      if (defined $codedString) {      if (defined $codedString) {
1395          # Loop through the parameter string, looking for escape sequences. We can't do          # Loop through the parameter string, looking for escape sequences. We can't do
1396          # translating because it causes problems with the escaped slash. ("\\b" becomes          # translating because it causes problems with the escaped slash. ("\\t" becomes
1397          # "\ " no matter what we do.)          # "\<tab>" no matter what we do.)
1398          while (length $codedString > 0) {          while (length $codedString > 0) {
1399              # Look for the first escape sequence.              # Look for the first escape sequence.
1400              if ($codedString =~ /^(.*?)\\(\\|b|n|t)/) {              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
1401                  # Here we found it. The text preceding the sequence is in $1. The sequence                  # Here we found it. The text preceding the sequence is in $1. The sequence
1402                  # itself is in $2. First, move the clear text to the return variable.                  # itself is in $2. First, move the clear text to the return variable.
1403                  $retVal .= $1;                  $retVal .= $1;
1404                  $codedString = substr $codedString, (2 + length $1);                  $codedString = substr $codedString, (2 + length $1);
1405                  # Decode the escape sequence.                  # Get the escape value.
1406                  my $char = $2;                  my $char = $2;
1407                  $char =~ tr/\\btn/\\ \t\n/;                  # If we have a "\r", we are done.
1408                    if ($char ne 'r') {
1409                        # Here it's not an 'r', so we convert it.
1410                        $char =~ tr/\\tn/\\\t\n/;
1411                  $retVal .= $char;                  $retVal .= $char;
1412                    }
1413              } else {              } else {
1414                  # Here there are no more escape sequences. The rest of the string is                  # Here there are no more escape sequences. The rest of the string is
1415                  # transferred unmodified.                  # transferred unmodified.
# Line 1015  Line 1515 
1515      return @inputList;      return @inputList;
1516  }  }
1517    
1518    =head3 Percent
1519    
1520    C<< my $percent = Tracer::Percent($number, $base); >>
1521    
1522    Returns the percent of the base represented by the given number. If the base
1523    is zero, returns zero.
1524    
1525    =over 4
1526    
1527    =item number
1528    
1529    Percent numerator.
1530    
1531    =item base
1532    
1533    Percent base.
1534    
1535    =item RETURN
1536    
1537    Returns the percentage of the base represented by the numerator.
1538    
1539    =back
1540    
1541    =cut
1542    
1543    sub Percent {
1544        # Get the parameters.
1545        my ($number, $base) = @_;
1546        # Declare the return variable.
1547        my $retVal = 0;
1548        # Compute the percent.
1549        if ($base != 0) {
1550            $retVal = $number * 100 / $base;
1551        }
1552        # Return the result.
1553        return $retVal;
1554    }
1555    
1556  =head3 GetFile  =head3 GetFile
1557    
1558  C<< my @fileContents = Tracer::GetFile($fileName); >>  C<< my @fileContents = Tracer::GetFile($fileName); >>
1559    
1560  Return the entire contents of a file.      or
1561    
1562    C<< my $fileContents = Tracer::GetFile($fileName); >>
1563    
1564    Return the entire contents of a file. In list context, line-ends are removed and
1565    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1566    
1567  =over 4  =over 4
1568    
# Line 1030  Line 1573 
1573  =item RETURN  =item RETURN
1574    
1575  In a list context, returns the entire file as a list with the line terminators removed.  In a list context, returns the entire file as a list with the line terminators removed.
1576  In a scalar context, returns the entire file as a string.  In a scalar context, returns the entire file as a string. If an error occurs opening
1577    the file, an empty list will be returned.
1578    
1579  =back  =back
1580    
# Line 1042  Line 1586 
1586      # Declare the return variable.      # Declare the return variable.
1587      my @retVal = ();      my @retVal = ();
1588      # Open the file for input.      # Open the file for input.
1589      my $ok = open INPUTFILE, "<$fileName";      my $handle = Open(undef, "<$fileName");
     if (!$ok) {  
         # If we had an error, trace it. We will automatically return a null value.  
         Trace("Could not open \"$fileName\" for input.") if T(0);  
     } else {  
1590          # Read the whole file into the return variable, stripping off any terminator          # Read the whole file into the return variable, stripping off any terminator
1591          # characters.          # characters.
1592          my $lineCount = 0;          my $lineCount = 0;
1593          while (my $line = <INPUTFILE>) {      while (my $line = <$handle>) {
1594              $lineCount++;              $lineCount++;
1595              $line = Strip($line);              $line = Strip($line);
1596              push @retVal, $line;              push @retVal, $line;
1597          }          }
1598          # Close it.          # Close it.
1599          close INPUTFILE;      close $handle;
1600          my $actualLines = @retVal;          my $actualLines = @retVal;
     }  
1601      # Return the file's contents in the desired format.      # Return the file's contents in the desired format.
1602      if (wantarray) {      if (wantarray) {
1603          return @retVal;          return @retVal;
# Line 1067  Line 1606 
1606      }      }
1607  }  }
1608    
1609    =head3 PutFile
1610    
1611    C<< Tracer::PutFile($fileName, \@lines); >>
1612    
1613    Write out a file from a list of lines of text.
1614    
1615    =over 4
1616    
1617    =item fileName
1618    
1619    Name of the output file.
1620    
1621    =item lines
1622    
1623    Reference to a list of text lines. The lines will be written to the file in order, with trailing
1624    new-line characters. Alternatively, may be a string, in which case the string will be written without
1625    modification.
1626    
1627    =back
1628    
1629    =cut
1630    
1631    sub PutFile {
1632        # Get the parameters.
1633        my ($fileName, $lines) = @_;
1634        # Open the output file.
1635        my $handle = Open(undef, ">$fileName");
1636        if (ref $lines ne 'ARRAY') {
1637            # Here we have a scalar, so we write it raw.
1638            print $handle $lines;
1639        } else {
1640            # Write the lines one at a time.
1641            for my $line (@{$lines}) {
1642                print $handle "$line\n";
1643            }
1644        }
1645        # Close the output file.
1646        close $handle;
1647    }
1648    
1649  =head3 QTrace  =head3 QTrace
1650    
1651  C<< my $data = QTrace($format); >>  C<< my $data = QTrace($format); >>
# Line 1088  Line 1667 
1667      my ($format) = @_;      my ($format) = @_;
1668      # Create the return variable.      # Create the return variable.
1669      my $retVal = "";      my $retVal = "";
1670        # Only proceed if there is an actual queue.
1671        if (@Queue) {
1672      # Process according to the format.      # Process according to the format.
1673      if ($format =~ m/^HTML$/i) {      if ($format =~ m/^HTML$/i) {
1674          # Convert the queue into an HTML list.          # Convert the queue into an HTML list.
# Line 1103  Line 1684 
1684      }      }
1685      # Clear the queue.      # Clear the queue.
1686      @Queue = ();      @Queue = ();
1687        }
1688      # Return the formatted list.      # Return the formatted list.
1689      return $retVal;      return $retVal;
1690  }  }
# Line 1111  Line 1693 
1693    
1694  C<< Confess($message); >>  C<< Confess($message); >>
1695    
1696  Trace the call stack and abort the program with the specified message. The stack  Trace the call stack and abort the program with the specified message. When used with
 trace will only appear if the trace level for this package is 1 or more. When used with  
1697  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
1698  So, for example  So, for example
1699    
# Line 1134  Line 1715 
1715      # Get the parameters.      # Get the parameters.
1716      my ($message) = @_;      my ($message) = @_;
1717      # Trace the call stack.      # Trace the call stack.
1718      Cluck($message) if T(1);      Cluck($message);
1719      # Abort the program.      # Abort the program.
1720      croak(">>> $message");      croak(">>> $message");
1721  }  }
# Line 1144  Line 1725 
1725  C<< Assert($condition1, $condition2, ... $conditionN); >>  C<< Assert($condition1, $condition2, ... $conditionN); >>
1726    
1727  Return TRUE if all the conditions are true. This method can be used in conjunction with  Return TRUE if all the conditions are true. This method can be used in conjunction with
1728  the OR operator and the L</Confess> method, B<Assert> can function as a debugging assert.  the OR operator and the L</Confess> method as a debugging assert.
1729  So, for example  So, for example
1730    
1731  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
# Line 1265  Line 1846 
1846    
1847  =head3 AddToListMap  =head3 AddToListMap
1848    
1849  C<< Tracer::AddToListMap(\%hash, $key, $value); >>  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>
1850    
1851  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list
1852  is created for the key. Otherwise, the new value is pushed onto the list.  is created for the key. Otherwise, the new value is pushed onto the list.
# Line 1280  Line 1861 
1861    
1862  Key for which the value is to be added.  Key for which the value is to be added.
1863    
1864  =item value  =item value1, value2, ... valueN
1865    
1866  Value to add to the key's value list.  List of values to add to the key's value list.
1867    
1868  =back  =back
1869    
# Line 1290  Line 1871 
1871    
1872  sub AddToListMap {  sub AddToListMap {
1873      # Get the parameters.      # Get the parameters.
1874      my ($hash, $key, $value) = @_;      my ($hash, $key, @values) = @_;
1875      # Process according to whether or not the key already has a value.      # Process according to whether or not the key already has a value.
1876      if (! exists $hash->{$key}) {      if (! exists $hash->{$key}) {
1877          $hash->{$key} = [$value];          $hash->{$key} = [@values];
1878      } else {      } else {
1879          push @{$hash->{$key}}, $value;          push @{$hash->{$key}}, @values;
1880      }      }
1881  }  }
1882    
# Line 1303  Line 1884 
1884    
1885  C<< if (Tracer::DebugMode) { ...code... } >>  C<< if (Tracer::DebugMode) { ...code... } >>
1886    
1887  Return TRUE if debug mode has been turned on in FIG_Config, else output  Return TRUE if debug mode has been turned on, else abort.
 an error page and return FALSE.  
1888    
1889  Certain CGI scripts are too dangerous to exist in the production  Certain CGI scripts are too dangerous to exist in the production
1890  environment. This method provides a simple way to prevent them  environment. This method provides a simple way to prevent them
1891  from working unless they are explicitly turned on in the configuration  from working unless they are explicitly turned on by creating a password
1892  file by setting C<$FIG_Config::debug_mode> to 1. If debugging mode  cookie via the B<SetPassword> script.  If debugging mode
1893  is not turned on, an error web page will be output.  is not turned on, an error will occur.
1894    
1895  =cut  =cut
1896    
1897  sub DebugMode {  sub DebugMode {
1898      # Declare the return variable.      # Declare the return variable.
1899      my $retVal;      my $retVal = 0;
1900      # Check the debug configuration.      # Check the debug configuration.
1901      if ($FIG_Config::debug_mode) {      my $password = CGI::cookie("DebugMode");
1902        my $encrypted = Digest::MD5::md5_hex($password);
1903        if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1904          $retVal = 1;          $retVal = 1;
1905      } else {      } else {
1906          # Here debug mode is off, so we generate an error page.          # Here debug mode is off, so we generate an error.
1907          my $pageString = PageBuilder::Build("<Html/ErrorPage.html", {}, "Html");          Confess("Cannot use this facility without logging in.");
         print $pageString;  
1908      }      }
1909      # Return the determination indicator.      # Return the determination indicator.
1910      return $retVal;      return $retVal;
# Line 1354  Line 1935 
1935  sub Strip {  sub Strip {
1936      # Get a copy of the parameter string.      # Get a copy of the parameter string.
1937      my ($string) = @_;      my ($string) = @_;
1938      my $retVal = $string;      my $retVal = (defined $string ? $string : "");
1939      # Strip the line terminator characters.      # Strip the line terminator characters.
1940      $retVal =~ s/(\r|\n)+$//g;      $retVal =~ s/(\r|\n)+$//g;
1941      # Return the result.      # Return the result.
# Line 1385  Line 1966 
1966    
1967  =item padChar (optional)  =item padChar (optional)
1968    
1969    Character to use for padding. The default is a space.
1970    
1971  =item RETURN  =item RETURN
1972    
1973  Returns a copy of the original string with the spaces added to the specified end so  Returns a copy of the original string with the pad character added to the
1974  that it achieves the desired length.  specified end so that it achieves the desired length.
1975    
1976  =back  =back
1977    
# Line 1420  Line 2003 
2003      return $retVal;      return $retVal;
2004  }  }
2005    
2006    =head3 EOF
2007    
2008    This is a constant that is lexically greater than any useful string.
2009    
2010    =cut
2011    
2012    sub EOF {
2013        return "\xFF\xFF\xFF\xFF\xFF";
2014    }
2015    
2016    =head3 TICK
2017    
2018    C<< my @results = TICK($commandString); >>
2019    
2020    Perform a back-tick operation on a command. If this is a Windows environment, any leading
2021    dot-slash (C<./> will be removed. So, for example, if you were doing
2022    
2023        `./protein.cgi`
2024    
2025    from inside a CGI script, it would work fine in Unix, but would issue an error message
2026    in Windows complaining that C<'.'> is not a valid command. If instead you code
2027    
2028        TICK("./protein.cgi")
2029    
2030    it will work correctly in both environments.
2031    
2032    =over 4
2033    
2034    =item commandString
2035    
2036    The command string to pass to the system.
2037    
2038    =item RETURN
2039    
2040    Returns the standard output from the specified command, as a list.
2041    
2042    =back
2043    
2044    =cut
2045    #: Return Type @;
2046    sub TICK {
2047        # Get the parameters.
2048        my ($commandString) = @_;
2049        # Chop off the dot-slash if this is Windows.
2050        if ($FIG_Config::win_mode) {
2051            $commandString =~ s!^\./!!;
2052        }
2053        # Activate the command and return the result.
2054        return `$commandString`;
2055    }
2056    
2057    =head3 ScriptSetup
2058    
2059    C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>
2060    
2061    Perform standard tracing and debugging setup for scripts. The value returned is
2062    the CGI object followed by a pre-built variable hash.
2063    
2064    The C<Trace> form parameter is used to determine whether or not tracing is active and
2065    which trace modules (other than C<Tracer> itself) should be turned on. Specifying
2066    the C<CGI> trace module will trace parameter and environment information. Parameters are
2067    traced at level 3 and environment variables at level 4. To trace to a file instead of to
2068    the web page, set C<TF> to 1. At the end of the script, the client should call
2069    L</ScriptFinish> to output the web page.
2070    
2071    In some situations, it is not practical to invoke tracing via form parameters. For this
2072    situation, you can turn on emergency tracing from the debugging control panel.
2073    Tracing will then be turned on automatically for all programs that use the L</ETracing>
2074    method, which includes every program that uses this method or L</StandardSetup>.
2075    
2076    =over 4
2077    
2078    =item noTrace (optional)
2079    
2080    If specified, tracing will be suppressed. This is useful if the script wants to set up
2081    tracing manually.
2082    
2083    =item RETURN
2084    
2085    Returns a two-element list consisting of a CGI query object and a variable hash for
2086    the output page.
2087    
2088    =back
2089    
2090    =cut
2091    
2092    sub ScriptSetup {
2093        # Get the parameters.
2094        my ($noTrace) = @_;
2095        # Get the CGI query object.
2096        my $cgi = CGI->new();
2097        # Set up tracing if it's not suppressed.
2098        ETracing($cgi) unless $noTrace;
2099        # Create the variable hash.
2100        my $varHash = { results => '' };
2101        # Return the query object and variable hash.
2102        return ($cgi, $varHash);
2103    }
2104    
2105    =head3 ETracing
2106    
2107    C<< ETracing($parameter); >>
2108    
2109    Set up emergency tracing. Emergency tracing is tracing that is turned
2110    on automatically for any program that calls this method. The emergency
2111    tracing parameters are stored in a a file identified by a tracing key.
2112    If this method is called with a CGI object, then the tracing key is
2113    taken from a cookie. If it is called with no parameters, then the tracing
2114    key is taken from an environment variable. If it is called with a string,
2115    the tracing key is that string.
2116    
2117    =over 4
2118    
2119    =item parameter
2120    
2121    A parameter from which the tracing key is computed. If it is a scalar,
2122    that scalar is used as the tracing key. If it is a CGI object, the
2123    tracing key is taken from the C<IP> cookie. If it is omitted, the
2124    tracing key is taken from the C<TRACING> environment variable. If it
2125    is a CGI object and emergency tracing is not on, the C<Trace> and
2126    C<TF> parameters will be used to determine the type of tracing.
2127    
2128    =back
2129    
2130    =cut
2131    
2132    sub ETracing {
2133        # Get the parameter.
2134        my ($parameter) = @_;
2135        # Check for CGI mode.
2136        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
2137        # Default to no tracing except errors.
2138        my ($tracing, $dest) = ("0", "WARN");
2139        # Check for emergency tracing.
2140        my $tkey = EmergencyKey($parameter);
2141        my $emergencyFile = EmergencyFileName($tkey);
2142        if (-e $emergencyFile) {
2143            # We have the file. Read in the data.
2144            my @tracing = GetFile($emergencyFile);
2145            # Pull off the time limit.
2146            my $expire = shift @tracing;
2147            # Convert it to seconds.
2148            $expire *= 3600;
2149            # Check the file data.
2150            my $stat = stat($emergencyFile);
2151            my ($now) = gettimeofday;
2152            if ($now - $stat->mtime > $expire) {
2153                # Delete the expired file.
2154                unlink $emergencyFile;
2155            } else {
2156                # Emergency tracing is on. Pull off the destination and
2157                # the trace level;
2158                $dest = shift @tracing;
2159                my $level = shift @tracing;
2160                # Convert the destination to a real tracing destination.
2161                # temp directory.
2162                $dest = EmergencyTracingDest($tkey, $dest);
2163                # Insure Tracer is specified.
2164                my %moduleHash = map { $_ => 1 } @tracing;
2165                $moduleHash{Tracer} = 1;
2166                # Set the trace parameter.
2167                $tracing = join(" ", $level, sort keys %moduleHash);
2168            }
2169        } elsif (defined $cgi) {
2170            # There's no emergency tracing, but we have a CGI object, so check
2171            # for tracing from the form parameters.
2172            if ($cgi->param('Trace')) {
2173                # Here the user has requested tracing via a form.
2174                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
2175                $tracing = $cgi->param('Trace') . " Tracer";
2176            }
2177        }
2178        # Setup the tracing we've determined from all the stuff above.
2179        TSetup($tracing, $dest);
2180        # If we're a web script, trace the parameter and environment data.
2181        if (defined $cgi) {
2182            TraceParms($cgi);
2183        }
2184    }
2185    
2186    =head3 EmergencyFileName
2187    
2188    C<< my $fileName = Tracer::EmergencyFileName($tkey); >>
2189    
2190    Return the emergency tracing file name. This is the file that specifies
2191    the tracing information.
2192    
2193    =over 4
2194    
2195    =item tkey
2196    
2197    Tracing key for the current program.
2198    
2199    =item RETURN
2200    
2201    Returns the name of the file to contain the emergency tracing information.
2202    
2203    =back
2204    
2205    =cut
2206    
2207    sub EmergencyFileName {
2208        # Get the parameters.
2209        my ($tkey) = @_;
2210        # Compute the emergency tracing file name.
2211        return "$FIG_Config::temp/Emergency$tkey.txt";
2212    }
2213    
2214    =head3 EmergencyFileTarget
2215    
2216    C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>
2217    
2218    Return the emergency tracing target file name. This is the file that receives
2219    the tracing output for file-based tracing.
2220    
2221    =over 4
2222    
2223    =item tkey
2224    
2225    Tracing key for the current program.
2226    
2227    =item RETURN
2228    
2229    Returns the name of the file to contain the trace output.
2230    
2231    =back
2232    
2233    =cut
2234    
2235    sub EmergencyFileTarget {
2236        # Get the parameters.
2237        my ($tkey) = @_;
2238        # Compute the emergency tracing file name.
2239        return "$FIG_Config::temp/trace$tkey.log";
2240    }
2241    
2242    =head3 EmergencyTracingDest
2243    
2244    C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>
2245    
2246    This method converts an emergency tracing destination to a real
2247    tracing destination. The main difference is that if the
2248    destination is C<FILE> or C<APPEND>, we convert it to file
2249    output.
2250    
2251    =over 4
2252    
2253    =item tkey
2254    
2255    Tracing key for this environment.
2256    
2257    =item myDest
2258    
2259    Destination from the emergency tracing file.
2260    
2261    =item RETURN
2262    
2263    Returns a destination that can be passed into L</TSetup>.
2264    
2265    =back
2266    
2267    =cut
2268    
2269    sub EmergencyTracingDest {
2270        # Get the parameters.
2271        my ($tkey, $myDest) = @_;
2272        # Declare the return variable.
2273        my $retVal;
2274        # Process according to the destination value.
2275        if ($myDest eq 'FILE') {
2276            $retVal = ">" . EmergencyFileTarget($tkey);
2277        } elsif ($myDest eq 'APPEND') {
2278            $retVal = ">>" . EmergencyFileTarget($tkey);
2279        } else {
2280            $retVal = $myDest;
2281        }
2282        # Return the result.
2283        return $retVal;
2284    }
2285    
2286    =head3 Emergency
2287    
2288    C<< Emergency($key, $hours, $dest, $level, @modules); >>
2289    
2290    Turn on emergency tracing. This method can only be invoked over the web and is
2291    should not be called if debug mode is off. The caller specifies the duration of the
2292    emergency in hours, the desired tracing destination, the trace level,
2293    and a list of the trace modules to activate. For the length of the duration, when a
2294    program in an environment with the specified tracing key active invokes a Sprout
2295    CGI script, tracing will be turned on automatically. See L</TSetup> for more
2296    about tracing setup and L</ETracing> for more about emergency tracing.
2297    
2298    =over 4
2299    
2300    =item tkey
2301    
2302    The tracing key. This is used to identify the control file and the trace file.
2303    
2304    =item hours
2305    
2306    Number of hours to keep emergency tracing alive.
2307    
2308    =item dest
2309    
2310    Tracing destination. If no path information is specified for a file
2311    destination, it is put in the FIG temporary directory.
2312    
2313    =item level
2314    
2315    Tracing level. A higher level means more trace messages.
2316    
2317    =item modules
2318    
2319    A list of the tracing modules to activate.
2320    
2321    =back
2322    
2323    =cut
2324    
2325    sub Emergency {
2326        # Get the parameters.
2327        my ($tkey, $hours, $dest, $level, @modules) = @_;
2328        # Create the emergency file.
2329        my $specFile = EmergencyFileName($tkey);
2330        my $outHandle = Open(undef, ">$specFile");
2331        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
2332    }
2333    
2334    =head3 EmergencyKey
2335    
2336    C<< my $tkey = EmergencyKey($parameter); >>
2337    
2338    Return the Key to be used for emergency tracing. This could be an IP address,
2339     a session ID, or a user name, depending on the environment.
2340    
2341    =over 4
2342    
2343    =item parameter
2344    
2345    Parameter defining the method for finding the tracing key. If it is a scalar,
2346    then it is presumed to be the tracing key itself. If it is a CGI object, then
2347    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
2348    taken from the C<TRACING> environment variable.
2349    
2350    =item RETURN
2351    
2352    Returns the key to be used for labels in emergency tracing.
2353    
2354    =back
2355    
2356    =cut
2357    
2358    sub EmergencyKey {
2359        # Get the parameters.
2360        my ($parameter) = @_;
2361        # Declare the return variable.
2362        my $retVal;
2363        # Determine the parameter type.
2364        if (! defined $parameter) {
2365            # Here we're supposed to check the environment.
2366            $retVal = $ENV{TRACING};
2367        } else {
2368            my $ptype = ref $parameter;
2369            if ($ptype eq 'CGI') {
2370                # Here we were invoked from a web page. Look for a cookie.
2371                $retVal = $parameter->cookie('IP');
2372            } elsif (! $ptype) {
2373                # Here the key was passed in.
2374                $retVal = $parameter;
2375            }
2376        }
2377        # If no luck finding a key, use the PID.
2378        if (! defined $retVal) {
2379            $retVal = $$;
2380        }
2381        # Return the result.
2382        return $retVal;
2383    }
2384    
2385    
2386    =head3 TraceParms
2387    
2388    C<< Tracer::TraceParms($cgi); >>
2389    
2390    Trace the CGI parameters at trace level CGI => 3 and the environment variables
2391    at level CGI => 4.
2392    
2393    =over 4
2394    
2395    =item cgi
2396    
2397    CGI query object containing the parameters to trace.
2398    
2399    =back
2400    
2401    =cut
2402    
2403    sub TraceParms {
2404        # Get the parameters.
2405        my ($cgi) = @_;
2406        if (T(CGI => 3)) {
2407            # Here we want to trace the parameter data.
2408            my @names = $cgi->param;
2409            for my $parmName (sort @names) {
2410                # Note we skip the Trace parameters, which are for our use only.
2411                if ($parmName ne 'Trace' && $parmName ne 'TF') {
2412                    my @values = $cgi->param($parmName);
2413                    Trace("CGI: $parmName = " . join(", ", @values));
2414                }
2415            }
2416            # Display the request method.
2417            my $method = $cgi->request_method();
2418            Trace("Method: $method");
2419        }
2420        if (T(CGI => 4)) {
2421            # Here we want the environment data too.
2422            for my $envName (sort keys %ENV) {
2423                Trace("ENV: $envName = $ENV{$envName}");
2424            }
2425        }
2426    }
2427    
2428    =head3 ScriptFinish
2429    
2430    C<< ScriptFinish($webData, $varHash); >>
2431    
2432    Output a web page at the end of a script. Either the string to be output or the
2433    name of a template file can be specified. If the second parameter is omitted,
2434    it is assumed we have a string to be output; otherwise, it is assumed we have the
2435    name of a template file. The template should have the variable C<DebugData>
2436    specified in any form that invokes a standard script. If debugging mode is turned
2437    on, a form field will be put in that allows the user to enter tracing data.
2438    Trace messages will be placed immediately before the terminal C<BODY> tag in
2439    the output, formatted as a list.
2440    
2441    A typical standard script would loook like the following.
2442    
2443        BEGIN {
2444            # Print the HTML header.
2445            print "CONTENT-TYPE: text/html\n\n";
2446        }
2447        use Tracer;
2448        use CGI;
2449        use FIG;
2450        # ... more uses ...
2451    
2452        my ($cgi, $varHash) = ScriptSetup();
2453        eval {
2454            # ... get data from $cgi, put it in $varHash ...
2455        };
2456        if ($@) {
2457            Trace("Script Error: $@") if T(0);
2458        }
2459        ScriptFinish("Html/MyTemplate.html", $varHash);
2460    
2461    The idea here is that even if the script fails, you'll see trace messages and
2462    useful output.
2463    
2464    =over 4
2465    
2466    =item webData
2467    
2468    A string containing either the full web page to be written to the output or the
2469    name of a template file from which the page is to be constructed. If the name
2470    of a template file is specified, then the second parameter must be present;
2471    otherwise, it must be absent.
2472    
2473    =item varHash (optional)
2474    
2475    If specified, then a reference to a hash mapping variable names for a template
2476    to their values. The template file will be read into memory, and variable markers
2477    will be replaced by data in this hash reference.
2478    
2479    =back
2480    
2481    =cut
2482    
2483    sub ScriptFinish {
2484        # Get the parameters.
2485        my ($webData, $varHash) = @_;
2486        # Check for a template file situation.
2487        my $outputString;
2488        if (defined $varHash) {
2489            # Here we have a template file. We need to determine the template type.
2490            my $template;
2491            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
2492                $template = "$FIG_Config::template_url/$webData";
2493            } else {
2494                $template = "<<$webData";
2495            }
2496            $outputString = PageBuilder::Build($template, $varHash, "Html");
2497        } else {
2498            # Here the user gave us a raw string.
2499            $outputString = $webData;
2500        }
2501        # Check for trace messages.
2502        if ($Destination ne "NONE" && $TraceLevel > 0) {
2503            # We have trace messages, so we want to put them at the end of the body. This
2504            # is either at the end of the whole string or at the beginning of the BODY
2505            # end-tag.
2506            my $pos = length $outputString;
2507            if ($outputString =~ m#</body>#gi) {
2508                $pos = (pos $outputString) - 7;
2509            }
2510            # If the trace messages were queued, we unroll them. Otherwise, we display the
2511            # destination.
2512            my $traceHtml;
2513            if ($Destination eq "QUEUE") {
2514                $traceHtml = QTrace('Html');
2515            } elsif ($Destination =~ /^>>(.+)$/) {
2516                # Here the tracing output it to a file. We code it as a hyperlink so the user
2517                # can copy the file name into the clipboard easily.
2518                my $actualDest = $1;
2519                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
2520            } else {
2521                # Here we have one of the special destinations.
2522                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
2523            }
2524            substr $outputString, $pos, 0, $traceHtml;
2525        }
2526        # Write the output string.
2527        print $outputString;
2528    }
2529    
2530    =head3 Insure
2531    
2532    C<< Insure($dirName); >>
2533    
2534    Insure a directory is present.
2535    
2536    =over 4
2537    
2538    =item dirName
2539    
2540    Name of the directory to check. If it does not exist, it will be created.
2541    
2542    =back
2543    
2544    =cut
2545    
2546    sub Insure {
2547        my ($dirName) = @_;
2548        if (! -d $dirName) {
2549            Trace("Creating $dirName directory.") if T(2);
2550            eval { mkpath $dirName; };
2551            if ($@) {
2552                Confess("Error creating $dirName: $@");
2553            }
2554        }
2555    }
2556    
2557    =head3 ChDir
2558    
2559    C<< ChDir($dirName); >>
2560    
2561    Change to the specified directory.
2562    
2563    =over 4
2564    
2565    =item dirName
2566    
2567    Name of the directory to which we want to change.
2568    
2569    =back
2570    
2571    =cut
2572    
2573    sub ChDir {
2574        my ($dirName) = @_;
2575        if (! -d $dirName) {
2576            Confess("Cannot change to directory $dirName: no such directory.");
2577        } else {
2578            Trace("Changing to directory $dirName.") if T(4);
2579            my $okFlag = chdir $dirName;
2580            if (! $okFlag) {
2581                Confess("Error switching to directory $dirName.");
2582            }
2583        }
2584    }
2585    
2586    =head3 SendSMS
2587    
2588    C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>
2589    
2590    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
2591    user name, password, and API ID for the relevant account in the hash reference variable
2592    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
2593    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
2594    is C<2561022>, then the FIG_Config file must contain
2595    
2596        $phone =  { user => 'BruceTheHumanPet',
2597                    password => 'silly',
2598                    api_id => '2561022' };
2599    
2600    The original purpose of this method was to insure Bruce would be notified immediately when the
2601    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
2602    when you call this method.
2603    
2604    The message ID will be returned if successful, and C<undef> if an error occurs.
2605    
2606    =over 4
2607    
2608    =item phoneNumber
2609    
2610    Phone number to receive the message, in international format. A United States phone number
2611    would be prefixed by "1". A British phone number would be prefixed by "44".
2612    
2613    =item msg
2614    
2615    Message to send to the specified phone.
2616    
2617    =item RETURN
2618    
2619    Returns the message ID if successful, and C<undef> if the message could not be sent.
2620    
2621    =back
2622    
2623    =cut
2624    
2625    sub SendSMS {
2626        # Get the parameters.
2627        my ($phoneNumber, $msg) = @_;
2628        # Declare the return variable. If we do not change it, C<undef> will be returned.
2629        my $retVal;
2630        # Only proceed if we have phone support.
2631        if (! defined $FIG_Config::phone) {
2632            Trace("Phone support not present in FIG_Config.") if T(1);
2633        } else {
2634            # Get the phone data.
2635            my $parms = $FIG_Config::phone;
2636            # Get the Clickatell URL.
2637            my $url = "http://api.clickatell.com/http/";
2638            # Create the user agent.
2639            my $ua = LWP::UserAgent->new;
2640            # Request a Clickatell session.
2641            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
2642                                         password => $parms->{password},
2643                                         api_id => $parms->{api_id},
2644                                         to => $phoneNumber,
2645                                         text => $msg});
2646            # Check for an error.
2647            if (! $resp->is_success) {
2648                Trace("Alert failed.") if T(1);
2649            } else {
2650                # Get the message ID.
2651                my $rstring = $resp->content;
2652                if ($rstring =~ /^ID:\s+(.*)$/) {
2653                    $retVal = $1;
2654                } else {
2655                    Trace("Phone attempt failed with $rstring") if T(1);
2656                }
2657            }
2658        }
2659        # Return the result.
2660        return $retVal;
2661    }
2662    
2663    =head3 CommaFormat
2664    
2665    C<< my $formatted = Tracer::CommaFormat($number); >>
2666    
2667    Insert commas into a number.
2668    
2669    =over 4
2670    
2671    =item number
2672    
2673    A sequence of digits.
2674    
2675    =item RETURN
2676    
2677    Returns the same digits with commas strategically inserted.
2678    
2679    =back
2680    
2681    =cut
2682    
2683    sub CommaFormat {
2684        # Get the parameters.
2685        my ($number) = @_;
2686        # Pad the length up to a multiple of three.
2687        my $padded = "$number";
2688        $padded = " " . $padded while length($padded) % 3 != 0;
2689        # This is a fancy PERL trick. The parentheses in the SPLIT pattern
2690        # cause the delimiters to be included in the output stream. The
2691        # GREP removes the empty strings in between the delimiters.
2692        my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
2693        # Clean out the spaces.
2694        $retVal =~ s/ //g;
2695        # Return the result.
2696        return $retVal;
2697    }
2698    =head3 SetPermissions
2699    
2700    C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>
2701    
2702    Set the permissions for a directory and all the files and folders inside it.
2703    In addition, the group ownership will be changed to the specified value.
2704    
2705    This method is more vulnerable than most to permission and compatability
2706    problems, so it does internal error recovery.
2707    
2708    =over 4
2709    
2710    =item dirName
2711    
2712    Name of the directory to process.
2713    
2714    =item group
2715    
2716    Name of the group to be assigned.
2717    
2718    =item mask
2719    
2720    Permission mask. Bits that are C<1> in this mask will be ORed into the
2721    permission bits of any file or directory that does not already have them
2722    set to 1.
2723    
2724    =item otherMasks
2725    
2726    Map of search patterns to permission masks. If a directory name matches
2727    one of the patterns, that directory and all its members and subdirectories
2728    will be assigned the new pattern. For example, the following would
2729    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2730    
2731        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2732    
2733    The list is ordered, so the following would use 0777 for C<tmp1> and
2734    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2735    
2736        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2737                                                       '^tmp' => 0666);
2738    
2739    Note that the pattern matches are all case-insensitive, and only directory
2740    names are matched, not file names.
2741    
2742    =back
2743    
2744    =cut
2745    
2746    sub SetPermissions {
2747        # Get the parameters.
2748        my ($dirName, $group, $mask, @otherMasks) = @_;
2749        # Set up for error recovery.
2750        eval {
2751            # Switch to the specified directory.
2752            ChDir($dirName);
2753            # Get the group ID.
2754            my $gid = getgrnam($group);
2755            # Get the mask for tracing.
2756            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2757            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(2);
2758            my $fixCount = 0;
2759            my $lookCount = 0;
2760            # @dirs will be a stack of directories to be processed.
2761            my @dirs = (getcwd());
2762            while (scalar(@dirs) > 0) {
2763                # Get the current directory.
2764                my $dir = pop @dirs;
2765                # Check for a match to one of the specified directory names. To do
2766                # that, we need to pull the individual part of the name off of the
2767                # whole path.
2768                my $simpleName = $dir;
2769                if ($dir =~ m!/([^/]+)$!) {
2770                    $simpleName = $1;
2771                }
2772                Trace("Simple directory name for $dir is $simpleName.") if T(4);
2773                # Search for a match.
2774                my $match = 0;
2775                my $i;
2776                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2777                    my $pattern = $otherMasks[$i];
2778                    if ($simpleName =~ /$pattern/i) {
2779                        $match = 1;
2780                    }
2781                }
2782                # Check for a match. Note we use $i-1 because the loop added 2
2783                # before terminating due to the match.
2784                if ($match && $otherMasks[$i-1] != $mask) {
2785                    # This directory matches one of the incoming patterns, and it's
2786                    # a different mask, so we process it recursively with that mask.
2787                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2788                } else {
2789                    # Here we can process normally. Get all of the non-hidden members.
2790                    my @submems = OpenDir($dir, 1);
2791                    for my $submem (@submems) {
2792                        # Get the full name.
2793                        my $thisMem = "$dir/$submem";
2794                        Trace("Checking member $thisMem.") if T(4);
2795                        $lookCount++;
2796                        if ($lookCount % 1000 == 0) {
2797                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(3);
2798                        }
2799                        # Fix the group.
2800                        chown -1, $gid, $thisMem;
2801                        # Insure this member is not a symlink.
2802                        if (! -l $thisMem) {
2803                            # Get its info.
2804                            my $fileInfo = stat $thisMem;
2805                            # Only proceed if we got the info. Otherwise, it's a hard link
2806                            # and we want to skip it anyway.
2807                            if ($fileInfo) {
2808                                my $fileMode = $fileInfo->mode;
2809                                if (($fileMode & $mask) != $mask) {
2810                                    # Fix this member.
2811                                    $fileMode |= $mask;
2812                                    chmod $fileMode, $thisMem;
2813                                    $fixCount++;
2814                                }
2815                                # If it's a subdirectory, stack it.
2816                                if (-d $thisMem) {
2817                                    push @dirs, $thisMem;
2818                                }
2819                            }
2820                        }
2821                    }
2822                }
2823            }
2824            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(2);
2825        };
2826        # Check for an error.
2827        if ($@) {
2828            Confess("SetPermissions error: $@");
2829        }
2830    }
2831    
2832    =head3 CompareLists
2833    
2834    C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>
2835    
2836    Compare two lists of tuples, and return a hash analyzing the differences. The lists
2837    are presumed to be sorted alphabetically by the value in the $keyIndex column.
2838    The return value contains a list of items that are only in the new list
2839    (inserted) and only in the old list (deleted).
2840    
2841    =over 4
2842    
2843    =item newList
2844    
2845    Reference to a list of new tuples.
2846    
2847    =item oldList
2848    
2849    Reference to a list of old tuples.
2850    
2851    =item keyIndex (optional)
2852    
2853    Index into each tuple of its key field. The default is 0.
2854    
2855    =item RETURN
2856    
2857    Returns a 2-tuple consisting of a reference to the list of items that are only in the new
2858    list (inserted) followed by a reference to the list of items that are only in the old
2859    list (deleted).
2860    
2861    =back
2862    
2863    =cut
2864    
2865    sub CompareLists {
2866        # Get the parameters.
2867        my ($newList, $oldList, $keyIndex) = @_;
2868        if (! defined $keyIndex) {
2869            $keyIndex = 0;
2870        }
2871        # Declare the return variables.
2872        my ($inserted, $deleted) = ([], []);
2873        # Loop through the two lists simultaneously.
2874        my ($newI, $oldI) = (0, 0);
2875        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
2876        while ($newI < $newN || $oldI < $oldN) {
2877            # Get the current object in each list. Note that if one
2878            # of the lists is past the end, we'll get undef.
2879            my $newItem = $newList->[$newI];
2880            my $oldItem = $oldList->[$oldI];
2881            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
2882                # The old item is not in the new list, so mark it deleted.
2883                push @{$deleted}, $oldItem;
2884                $oldI++;
2885            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
2886                # The new item is not in the old list, so mark it inserted.
2887                push @{$inserted}, $newItem;
2888                $newI++;
2889            } else {
2890                # The item is in both lists, so push forward.
2891                $oldI++;
2892                $newI++;
2893            }
2894        }
2895        # Return the result.
2896        return ($inserted, $deleted);
2897    }
2898    
2899    =head3 GetLine
2900    
2901    C<< my @data = Tracer::GetLine($handle); >>
2902    
2903    Read a line of data from a tab-delimited file.
2904    
2905    =over 4
2906    
2907    =item handle
2908    
2909    Open file handle from which to read.
2910    
2911    =item RETURN
2912    
2913    Returns a list of the fields in the record read. The fields are presumed to be
2914    tab-delimited. If we are at the end of the file, then an empty list will be
2915    returned. If an empty line is read, a single list item consisting of a null
2916    string will be returned.
2917    
2918    =back
2919    
2920    =cut
2921    
2922    sub GetLine {
2923        # Get the parameters.
2924        my ($handle) = @_;
2925        # Declare the return variable.
2926        my @retVal = ();
2927        # Read from the file.
2928        my $line = <$handle>;
2929        # Only proceed if we found something.
2930        if (defined $line) {
2931            # Remove the new-line.
2932            chomp $line;
2933            # If the line is empty, return a single empty string; otherwise, parse
2934            # it into fields.
2935            if ($line eq "") {
2936                push @retVal, "";
2937            } else {
2938                push @retVal, split /\t/,$line;
2939            }
2940        }
2941        # Return the result.
2942        return @retVal;
2943    }
2944    
2945    =head3 PutLine
2946    
2947    C<< Tracer::PutLine($handle, \@fields); >>
2948    
2949    Write a line of data to a tab-delimited file. The specified field values will be
2950    output in tab-separated form, with a trailing new-line.
2951    
2952    =over 4
2953    
2954    =item handle
2955    
2956    Output file handle.
2957    
2958    =item fields
2959    
2960    List of field values.
2961    
2962    =back
2963    
2964    =cut
2965    
2966    sub PutLine {
2967        # Get the parameters.
2968        my ($handle, $fields) = @_;
2969        # Write the data.
2970        print $handle join("\t", @{$fields}) . "\n";
2971    }
2972    
2973    =head3 GenerateURL
2974    
2975    C<< my $queryUrl = Tracer::GenerateURL($page, %parameters); >>
2976    
2977    Generate a GET-style URL for the specified page with the specified parameter
2978    names and values. The values will be URL-escaped automatically. So, for
2979    example
2980    
2981        Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
2982    
2983    would return
2984    
2985        form.cgi?type=1&string=%22high%20pass%22%20or%20highway
2986    
2987    =over 4
2988    
2989    =item page
2990    
2991    Page URL.
2992    
2993    =item parameters
2994    
2995    Hash mapping parameter names to parameter values.
2996    
2997    =item RETURN
2998    
2999    Returns a GET-style URL that goes to the specified page and passes in the
3000    specified parameters and values.
3001    
3002    =back
3003    
3004    =cut
3005    
3006    sub GenerateURL {
3007        # Get the parameters.
3008        my ($page, %parameters) = @_;
3009        # Prime the return variable with the page URL.
3010        my $retVal = $page;
3011        # Loop through the parameters, creating parameter elements in a list.
3012        my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3013        # If the list is nonempty, tack it on.
3014        if (@parmList) {
3015            $retVal .= "?" . join("&", @parmList);
3016        }
3017        # Return the result.
3018        return $retVal;
3019    }
3020    
3021  1;  1;

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