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revision 1.23, Tue Sep 13 05:36:12 2005 UTC revision 1.90, Mon Jul 16 19:44:02 2007 UTC
# 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 TICK);      @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;      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        use Time::Local;
38    
39  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
40    
41  =head2 Introduction  =head2 Tracing
42    
43  This package provides simple tracing for debugging and reporting purposes. To use it simply call the  This package provides simple tracing for debugging and reporting purposes. To use it simply call the
44  L</TSetup> method to set the options and call L</Trace> to write out trace messages. Each trace  L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
45  message has a I<trace level> and I<category> associated with it. In addition, the tracing package itself  L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
46  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace  each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
47  level is less than or equal to this package's trace level and whose category is activated will  level is less than or equal to the setup trace level and whose category is activated will
48  be written. Thus, a higher trace level on a message indicates that the message  be written. Thus, a higher trace level on a message indicates that the message
49  is less likely to be seen. A higher trace level passed to B<TSetup> means more trace messages will  is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
50  appear. To generate a trace message, use the following syntax.  appear.
51    
52    =head3 Putting Trace Messages in Your Code
53    
54  C<< Trace($message) if T(errors => 4); >>  To generate a trace message, use the following syntax.
55    
56        Trace($message) if T(errors => 4);
57    
58  This statement will produce a trace message if the trace level is 4 or more and the C<errors>  This statement will produce a trace message if the trace level is 4 or more and the C<errors>
59  category is active. Note that the special category C<main> is always active, so  category is active. There is a special category C<main> that is always active, so
60    
61  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
62    
63  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
64    
# Line 37  Line 66 
66  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
67  active and the trace level is 2 or more.  active and the trace level is 2 or more.
68    
69  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
70    
71    In scripts, where no package name is available, the category defaults to C<main>.
72    
73  To set up tracing, you call the L</TSetup> method. The method takes as input a trace level, a list  =head3 Custom Tracing
74  of category names, and a set of options. The trace level and list of category names are  
75    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
76    the preferred method, but a knowledge of how custom tracing works can make the more modern
77    L</Emergency Tracing> easier to understand.
78    
79    To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
80    a list of category names, and a destination. The trace level and list of category names are
81  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
82    
83  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
84    
85  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
86  specifies that messages should be output as HTML paragraphs.  specifies that messages should be sent to the standard output.
87    
88  To turn on tracing for ALL categories, use an asterisk. The call below sets every category to  To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
89  level 3 and writes the output to the standard error output. This sort of thing might be  level 3 and writes the output to the standard error output. This sort of thing might be
90  useful in a CGI environment.  useful in a CGI environment.
91    
92  C<< TSetup('3 *', 'WARN'); >>      TSetup('3 *', 'WARN');
93    
94  In addition to HTML and file output for trace messages, you can specify that the trace messages  In addition standard error and file output for trace messages, you can specify that the trace messages
95  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
96  is useful if you are building a web page. Instead of having the trace messages interspersed with  is useful if you are building a web page. Instead of having the trace messages interspersed with
97  the page output, they can be gathered together and displayed at the end of the page. This makes  the page output, they can be gathered together and displayed at the end of the page. This makes
98  it easier to debug page formatting problems.  it easier to debug page formatting problems.
99    
100  Finally, you can specify that all trace messages be emitted as warnings.  Finally, you can specify that all trace messages be emitted to a file, or the standard output and
101    a file at the same time. To trace to a file, specify the filename with an output character in front
102    of it.
103    
104        TSetup('4 SQL', ">$fileName");
105    
106    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
107    bracket.
108    
109        TSetup('3 *', "+>$fileName");
110    
111  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
112  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
113  Thus, debugging information is available and easily retrieved even when the application is  Thus, debugging information is available and easily retrieved even when the application is
114  being used out in the field.  being used out in the field.
115    
116    =head3 Trace Levels
117    
118  There is no hard and fast rule on how to use trace levels. The following is therefore only  There is no hard and fast rule on how to use trace levels. The following is therefore only
119  a suggestion.  a suggestion.
120    
121  =over 4  =over 4
122    
123  =item 0 Error  =item Error 0
124    
125  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
126  application entirely.  application entirely.
127    
128  =item 1 Warning  =item Warning 1
129    
130  Message indicates something that is unexpected but that probably did not interfere  Message indicates something that is unexpected but that probably did not interfere
131  with program execution.  with program execution.
132    
133  =item 2 Notice  =item Notice 2
134    
135  Message indicates the beginning or end of a major task.  Message indicates the beginning or end of a major task.
136    
137  =item 3 Information  =item Information 3
138    
139  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
140  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.
141    
142  =item 4 Detail  =item Detail 4
143    
144  Message indicates a low-level loop iteration.  Message indicates a low-level loop iteration.
145    
146  =back  =back
147    
148    The format of trace messages is important because some utilities analyze trace files.
149    There are three fields-- the time stamp, the category name, and the text.
150    The time stamp is between square brackets and the category name between angle brackets.
151    After the category name there is a colon (C<:>) followed by the message text.
152    If the square brackets or angle brackets are missing, then the trace management
153    utilities assume that they are encountering a set of pre-formatted lines.
154    
155    Note, however, that this formatting is done automatically by the tracing functions. You
156    only need to know about it if you want to parse a trace file.
157    
158    =head3 Emergency Tracing
159    
160    Sometimes, you need a way for tracing to happen automatically without putting parameters
161    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
162    from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.
163    Emergency tracing requires you specify a tracing key. For command-line tools, the key is
164    taken from the C<TRACING> environment variable. For web services, the key is taken from
165    a cookie. Either way, the key tells the tracing facility who you are, so that you control
166    the tracing in your environment without stepping on other users.
167    
168    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
169    generate one for you.
170    
171    You can activate and de-activate emergency tracing from the debugging control panel, as
172    well as display the trace file itself.
173    
174    To enable emergency tracing in your code, call
175    
176        ETracing($cgi)
177    
178    from a web script and
179    
180        ETracing()
181    
182    from a command-line script.
183    
184    The web script will look for the tracing key in the cookies, and the command-line
185    script will look for it in the C<TRACING> environment variable. If you are
186    using the L</StandardScript> or L</StandardSetup> methods, emergency tracing
187    will be configured automatically.
188    
189    NOTE: to configure emergency tracing from the command line instead of the Debugging
190    Control Panel (see below), use the C<trace.pl> script.
191    
192    =head3 Debugging Control Panel
193    
194    The debugging control panel provides several tools to assist in development of
195    SEED and Sprout software. You access the debugging control panel from the URL
196    C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,
197    for example, the panel access point for the development NMPDR system is
198    C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to
199    find out what the password is. From this page, you can also specify a tracing
200    key. If you don't specify a key, one will be generated for you.
201    
202    =head4 Emergency Tracing Form
203    
204    At the bottom of the debugging control panel is a form that allows you to
205    specify a trace level and tracing categories. Special and common categories
206    are listed with check boxes. You can hold your mouse over a check box to see
207    what its category does. In general, however, a category name is the same as
208    the name of the package in which the trace message occurs.
209    
210    Additional categories can be entered in an input box, delimited by spaces or commas.
211    
212    The B<Activate> button turns on Emergency tracing at the level you specify with the
213    specified categories active. The B<Terminate> button turns tracing off. The
214    B<Show File> button displays the current contents of the trace file. The tracing
215    form at the bottom of the control panel is designed for emergency tracing, so it
216    will only affect programs that call L</ETracing>, L</StandardScript>,
217    or L</StandardSetup>.
218    
219    =head4 Script Form
220    
221    The top form of the debugging control panel allows you to enter a tiny script and
222    have the output generated in a formatted table. Certain object variables are
223    predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),
224    and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.
225    
226    The last line of the script must be a scalar, but it can be a reference to a hash,
227    a list, a list of lists, and various other combinations. If you select the appropriate
228    data type in the dropdown box, the output will be formatted accordingly. The form
229    also has controls for specifying tracing. These controls override any emergency
230    tracing in effect.
231    
232    =head4 Database Query Forms
233    
234    The forms between the script form and the emergency tracing form allow you to
235    make queries against the database. The FIG query form allows simple queries against
236    a single FIG table. The Sprout query form uses the B<GetAll> method to do a
237    multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>
238    package, and it takes five parameters.
239    
240        GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
241    
242    Each of the five parameters corresponds to a text box on the query form:
243    
244    =over 4
245    
246    =item Objects
247    
248    Comma-separated list containing the names of the entity and relationship objects to be retrieved.
249    
250    =item Filter
251    
252    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
253    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
254    B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a
255    field, I<objectName> is the name of the entity or relationship object containing the field, and
256    I<number> is the 1-based position of the object in the object list. Any parameters
257    specified in the filter clause should be specified in the B<Params> field.
258    The fields in a filter clause can come from primary entity relations,
259    relationship relations, or secondary entity relations; however, all of the
260    entities and relationships involved must be included in the list of object names.
261    
262    =item Params
263    
264    List of the parameters to be substituted in for the parameters marks in the filter clause. This
265    is a comma-separated list without any quoting or escaping.
266    
267    =item fields
268    
269    Comma-separated list of the fields to be returned in each element of the list returned. Fields
270    are specified in the same manner as in the filter clause.
271    
272    =item count
273    
274    Maximum number of records to return. If omitted or 0, all available records will be returned.
275    
276    =back
277    
278    B<GetAll> automatically joins together the entities and relationships listed in the object
279    names. This simplifies the coding of the filter clause, but it means that some queries are
280    not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation
281    that has yet to be addressed.
282    
283  =cut  =cut
284    
285  # Declare the configuration variables.  # Declare the configuration variables.
# Line 157  Line 340 
340      # Presume category-based tracing until we learn otherwise.      # Presume category-based tracing until we learn otherwise.
341      $AllTrace = 0;      $AllTrace = 0;
342      # 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
343      # tracing.      # tracing. We must also clear away any pre-existing data.
344        %Categories = ( main => 1 );
345      for my $category (@categoryData) {      for my $category (@categoryData) {
346          if ($category eq '*') {          if ($category eq '*') {
347              $AllTrace = 1;              $AllTrace = 1;
# Line 175  Line 359 
359          }          }
360          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
361              open TRACEFILE, $target;              open TRACEFILE, $target;
362              print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";
363              close TRACEFILE;              close TRACEFILE;
364              $Destination = ">$target";              $Destination = ">$target";
365          } else {          } else {
# Line 188  Line 372 
372      $SetupCount++;      $SetupCount++;
373  }  }
374    
375    =head3 StandardSetup
376    
377    C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>
378    
379    This method performs standard command-line parsing and tracing setup. The return
380    values are a hash of the command-line options and a list of the positional
381    parameters. Tracing is automatically set up and the command-line options are
382    validated.
383    
384    This is a complex method that does a lot of grunt work. The parameters can
385    be more easily understood, however, once they are examined individually.
386    
387    The I<categories> parameter is the most obtuse. It is a reference to a list of
388    special-purpose tracing categories. Most tracing categories are PERL package
389    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
390    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
391    
392        ["Sprout", "SproutLoad", "ERDB"]
393    
394    This would cause trace messages in the specified three packages to appear in
395    the output. There are two special tracing categories that are automatically
396    handled by this method. In other words, if you used L</TSetup> you would need
397    to include these categories manually, but if you use this method they are turned
398    on automatically.
399    
400    =over 4
401    
402    =item SQL
403    
404    Traces SQL commands and activity.
405    
406    =item Tracer
407    
408    Traces error messages and call stacks.
409    
410    =back
411    
412    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
413    The trace level is specified using the C<-trace> command-line option. For example,
414    the following command line for C<TransactFeatures> turns on SQL tracing and runs
415    all tracing at level 3.
416    
417        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
418    
419    Standard tracing is output to the standard output and echoed to the file
420    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
421    process ID. You can also specify the C<user> parameter to put a user ID
422    instead of a process ID in the trace file name. So, for example
423    
424    The default trace level is 2. To get all messages, specify a trace level of 4.
425    For a genome-by-genome update, use 3.
426    
427        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
428    
429    would send the trace output to C<traceBruce.log> in the temporary directory.
430    
431    The I<options> parameter is a reference to a hash containing the command-line
432    options, their default values, and an explanation of what they mean. Command-line
433    options may be in the form of switches or keywords. In the case of a switch, the
434    option value is 1 if it is specified and 0 if it is not specified. In the case
435    of a keyword, the value is separated from the option name by an equal sign. You
436    can see this last in the command-line example above.
437    
438    You can specify a different default trace level by setting C<$options->{trace}>
439    prior to calling this method.
440    
441    An example at this point would help. Consider, for example, the command-line utility
442    C<TransactFeatures>. It accepts a list of positional parameters plus the options
443    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
444    the following code.
445    
446        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
447                            { safe => [0, "use database transactions"],
448                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
449                              start => [' ', "start with this genome"],
450                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
451                            "<command> <transactionDirectory> <IDfile>",
452                          @ARGV);
453    
454    
455    The call to C<ParseCommand> specifies the default values for the options and
456    stores the actual options in a hash that is returned as C<$options>. The
457    positional parameters are returned in C<@parameters>.
458    
459    The following is a sample command line for C<TransactFeatures>.
460    
461        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
462    
463    Single and double hyphens are equivalent. So, you could also code the
464    above command as
465    
466        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
467    
468    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
469    parameters, and would find themselves in I<@parameters> after executing the
470    above code fragment. The tracing would be set to level 2, and the categories
471    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
472    and C<DocUtils> was included because it came in within the first parameter
473    to this method. The I<$options> hash would be
474    
475        { trace => 2, sql => 0, safe => 0,
476          noAlias => 1, start => ' ', tblFiles => 0 }
477    
478    Use of C<StandardSetup> in this way provides a simple way of performing
479    standard tracing setup and command-line parsing. Note that the caller is
480    not even aware of the command-line switches C<-trace> and C<-sql>, which
481    are used by this method to control the tracing. If additional tracing features
482    need to be added in the future, they can be processed by this method without
483    upsetting the command-line utilities.
484    
485    If the C<background> option is specified on the command line, then the
486    standard and error outputs will be directed to files in the temporary
487    directory, using the same suffix as the trace file. So, if the command
488    line specified
489    
490        -user=Bruce -background
491    
492    then the trace output would go to C<traceBruce.log>, the standard output to
493    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
494    simplify starting a command in the background.
495    
496    The user name is also used as the tracing key for L</Emergency Tracing>.
497    Specifying a value of C<E> for the trace level causes emergency tracing to
498    be used instead of custom tracing. If the user name is not specified,
499    the tracing key is taken from the C<Tracing> environment variable. If there
500    is no value for that variable, the tracing key will be computed from the PID.
501    
502    Finally, if the special option C<-help> is specified, the option
503    names will be traced at level 0 and the program will exit without processing.
504    This provides a limited help capability. For example, if the user enters
505    
506        TransactFeatures -help
507    
508    he would see the following output.
509    
510        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
511            -trace    tracing level (default E)
512            -sql      trace SQL commands
513            -safe     use database transactions
514            -noAlias  do not expect aliases in CHANGE transactions
515            -start    start with this genome
516            -tblFiles output TBL files containing the corrected IDs
517    
518    The caller has the option of modifying the tracing scheme by placing a value
519    for C<trace> in the incoming options hash. The default value can be overridden,
520    or the tracing to the standard output can be turned off by suffixing a minus
521    sign to the trace level. So, for example,
522    
523        { trace => [0, "tracing level (default 0)"],
524           ...
525    
526    would set the default trace level to 0 instead of E, while
527    
528        { trace => ["2-", "tracing level (default 2)"],
529           ...
530    
531    would set the default to 2, but trace only to the log file, not to the
532    standard output.
533    
534    The parameters to this method are as follows.
535    
536    =over 4
537    
538    =item categories
539    
540    Reference to a list of tracing category names. These should be names of
541    packages whose internal workings will need to be debugged to get the
542    command working.
543    
544    =item options
545    
546    Reference to a hash containing the legal options for the current command mapped
547    to their default values and descriptions. The user can override the defaults
548    by specifying the options as command-line switches prefixed by a hyphen.
549    Tracing-related options may be added to this hash. If the C<-h> option is
550    specified on the command line, the option descriptions will be used to
551    explain the options. To turn off tracing to the standard output, add a
552    minus sign to the value for C<trace> (see above).
553    
554    =item parmHelp
555    
556    A string that vaguely describes the positional parameters. This is used
557    if the user specifies the C<-h> option.
558    
559    =item argv
560    
561    List of command line parameters, including the option switches, which must
562    precede the positional parameters and be prefixed by a hyphen.
563    
564    =item RETURN
565    
566    Returns a list. The first element of the list is the reference to a hash that
567    maps the command-line option switches to their values. These will either be the
568    default values or overrides specified on the command line. The remaining
569    elements of the list are the position parameters, in order.
570    
571    =back
572    
573    =cut
574    
575    sub StandardSetup {
576        # Get the parameters.
577        my ($categories, $options, $parmHelp, @argv) = @_;
578        # Get the default tracing key.
579        my $tkey = EmergencyKey();
580        # Add the tracing options.
581        if (! exists $options->{trace}) {
582            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
583        }
584        $options->{sql} = [0, "turn on SQL tracing"];
585        $options->{help} = [0, "display command-line options"];
586        $options->{user} = [$tkey, "tracing key"];
587        $options->{background} = [0, "spool standard and error output"];
588        # Create a parsing hash from the options hash. The parsing hash
589        # contains the default values rather than the default value
590        # and the description. While we're at it, we'll memorize the
591        # length of the longest option name.
592        my $longestName = 0;
593        my %parseOptions = ();
594        for my $key (keys %{$options}) {
595            if (length $key > $longestName) {
596                $longestName = length $key;
597            }
598            $parseOptions{$key} = $options->{$key}->[0];
599        }
600        # Parse the command line.
601        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
602        # Get the logfile suffix.
603        my $suffix = $retOptions->{user};
604        # Check for background mode.
605        if ($retOptions->{background}) {
606            my $outFileName = "$FIG_Config::temp/out$suffix.log";
607            my $errFileName = "$FIG_Config::temp/err$suffix.log";
608            open STDOUT, ">$outFileName";
609            open STDERR, ">$errFileName";
610        }
611        # Now we want to set up tracing. First, we need to know if the user
612        # wants emergency tracing.
613        if ($retOptions->{trace} eq 'E') {
614            ETracing($retOptions->{user});
615        } else {
616            # Here the tracing is controlled from the command line.
617            my @cats = @{$categories};
618            if ($retOptions->{sql}) {
619                push @cats, "SQL";
620            }
621            # Add the default categories.
622            push @cats, "Tracer";
623            # Next, we create the category string by joining the categories.
624            my $cats = join(" ", @cats);
625            # Check to determine whether or not the caller wants to turn off tracing
626            # to the standard output.
627            my $traceLevel = $retOptions->{trace};
628            my $textOKFlag = 1;
629            if ($traceLevel =~ /^(.)-/) {
630                $traceLevel = $1;
631                $textOKFlag = 0;
632            }
633            # Now we set up the trace mode.
634            my $traceMode;
635            # Verify that we can open a file in the FIG temporary directory.
636            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
637            if (open TESTTRACE, ">$traceFileName") {
638                # Here we can trace to a file.
639                $traceMode = ">$traceFileName";
640                if ($textOKFlag) {
641                    # Echo to standard output if the text-OK flag is set.
642                    $traceMode = "+$traceMode";
643                }
644                # Close the test file.
645                close TESTTRACE;
646            } else {
647                # Here we can't trace to a file. We trace to the standard output if it's
648                # okay, and the error log otherwise.
649                if ($textOKFlag) {
650                    $traceMode = "TEXT";
651                } else {
652                    $traceMode = "WARN";
653                }
654            }
655            # Now set up the tracing.
656            TSetup("$traceLevel $cats", $traceMode);
657        }
658        # Check for the "h" option. If it is specified, dump the command-line
659        # options and exit the program.
660        if ($retOptions->{help}) {
661            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
662            print "$1 [options] $parmHelp\n";
663            for my $key (sort keys %{$options}) {
664                my $name = Pad($key, $longestName, 0, ' ');
665                my $desc = $options->{$key}->[1];
666                if ($options->{$key}->[0]) {
667                    $desc .= " (default " . $options->{$key}->[0] . ")";
668                }
669                print "  $name $desc\n";
670            }
671            exit(0);
672        }
673        # Trace the options, if applicable.
674        if (T(3)) {
675            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
676            Trace("Selected options: " . join(", ", sort @parms) . ".");
677        }
678        # Return the parsed parameters.
679        return ($retOptions, @retParameters);
680    }
681    
682  =head3 Setups  =head3 Setups
683    
684  C<< my $count = Tracer::Setups(); >>  C<< my $count = Tracer::Setups(); >>
# Line 348  Line 839 
839    
840  =head3 OpenDir  =head3 OpenDir
841    
842  C<< my @files = OpenDir($dirName, $filtered); >>  C<< my @files = OpenDir($dirName, $filtered, $flag); >>
843    
844  Open a directory and return all the file names. This function essentially performs  Open a directory and return all the file names. This function essentially performs
845  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is  the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
846  set to TRUE, all filenames beginning with a period (C<.>) will be filtered out of  set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
847  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
848  for example,  filtered out of the return list. If the directory does not open and I<$flag> is not
849    set, an exception is thrown. So, for example,
850    
851      my @files = OpenDir("/Volumes/fig/contigs", 1);      my @files = OpenDir("/Volumes/fig/contigs", 1);
852    
853  is effectively the same as  is effectively the same as
854    
855      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");      opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
856      my @files = grep { $_ !~ /^\./ } readdir(TMP);      my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
857    
858  Similarly, the following code  Similarly, the following code
859    
860      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs");      my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
861    
862  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and  Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
863  automatically throws an error if the directory fails to open.  automatically returns an empty list if the directory fails to open.
864    
865  =over 4  =over 4
866    
# Line 381  Line 873 
873  TRUE if files whose names begin with a period (C<.>) should be automatically removed  TRUE if files whose names begin with a period (C<.>) should be automatically removed
874  from the list, else FALSE.  from the list, else FALSE.
875    
876    =item flag
877    
878    TRUE if a failure to open is okay, else FALSE
879    
880  =back  =back
881    
882  =cut  =cut
883  #: Return Type @;  #: Return Type @;
884  sub OpenDir {  sub OpenDir {
885      # Get the parameters.      # Get the parameters.
886      my ($dirName, $filtered) = @_;      my ($dirName, $filtered, $flag) = @_;
887      # Declare the return variable.      # Declare the return variable.
888      my @retVal;      my @retVal = ();
889      # Open the directory.      # Open the directory.
890      if (opendir(my $dirHandle, $dirName)) {      if (opendir(my $dirHandle, $dirName)) {
891          # The directory opened successfully. Get the appropriate list according to the          # The directory opened successfully. Get the appropriate list according to the
892          # strictures of the filter parameter.          # strictures of the filter parameter.
893          if ($filtered) {          if ($filtered) {
894              @retVal = grep { $_ !~ /^\./ } readdir $dirHandle;              @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
895          } else {          } else {
896              @retVal = readdir $dirHandle;              @retVal = readdir $dirHandle;
897          }          }
898      } else {      } elsif (! $flag) {
899          # Here the directory would not open.          # Here the directory would not open and it's considered an error.
900          Confess("Could not open directory $dirName.");          Confess("Could not open directory $dirName.");
901      }      }
902      # Return the result.      # Return the result.
# Line 449  Line 945 
945      return $value;      return $value;
946  }  }
947    
948    =head3 ParseTraceDate
949    
950    C<< my $time = Tracer::ParseTraceDate($dateString); >>
951    
952    Convert a date from the trace file into a PERL timestamp.
953    
954    =over 4
955    
956    =item dateString
957    
958    The date string from the trace file. The format of the string is determined by the
959    L</Now> method.
960    
961    =item RETURN
962    
963    Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
964    the time string is invalid.
965    
966    =back
967    
968    =cut
969    
970    sub ParseTraceDate {
971        # Get the parameters.
972        my ($dateString) = @_;
973        # Declare the return variable.
974        my $retVal;
975        # Parse the date.
976        if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {
977            # Create a time object. Note we need to convert the day, month,
978            # and year to a different base. Years count from 1900, and
979            # the internal month value is relocated to January = 0.
980            $retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);
981        }
982        # Return the result.
983        return $retVal;
984    }
985    
986  =head3 LogErrors  =head3 LogErrors
987    
988  C<< Tracer::LogErrors($fileName); >>  C<< Tracer::LogErrors($fileName); >>
# Line 651  Line 1185 
1185      # Get the timestamp.      # Get the timestamp.
1186      my $timeStamp = Now();      my $timeStamp = Now();
1187      # 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.
1188      my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);      my $prefix = "[$timeStamp] <$LastCategory>: ";
1189        my $formatted = $prefix . Strip($message);
1190      # Process according to the destination.      # Process according to the destination.
1191      if ($Destination eq "TEXT") {      if ($Destination eq "TEXT") {
1192          # Write the message to the standard output.          # Write the message to the standard output.
# Line 665  Line 1200 
1200      } elsif ($Destination eq "HTML") {      } elsif ($Destination eq "HTML") {
1201          # Convert the message to HTML and write it to the standard output.          # Convert the message to HTML and write it to the standard output.
1202          my $escapedMessage = CGI::escapeHTML($message);          my $escapedMessage = CGI::escapeHTML($message);
1203          print "<p>$formatted</p>\n";          print "<p>$timeStamp $LastCategory: $escapedMessage</p>\n";
1204      } elsif ($Destination eq "WARN") {      } elsif ($Destination eq "WARN") {
1205         # Emit the message as a warning.         # Emit the message as a warning.
1206         warn $message;         warn $message;
# Line 730  Line 1265 
1265              if (!$package) {              if (!$package) {
1266                  $category = "main";                  $category = "main";
1267              } else {              } else {
1268                  $category = $package;                  my @cats = split /::/, $package;
1269                    $category = $cats[$#cats];
1270              }              }
1271          }          }
1272          # Save the category name.          # Save the category name.
# Line 738  Line 1274 
1274          # Convert it to lower case before we hash it.          # Convert it to lower case before we hash it.
1275          $category = lc $category;          $category = lc $category;
1276          # Use the category and tracelevel to compute the result.          # Use the category and tracelevel to compute the result.
1277            if (ref $traceLevel) {
1278                Confess("Bad trace level.");
1279            } elsif (ref $TraceLevel) {
1280                Confess("Bad trace config.");
1281            }
1282          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
1283      }      }
1284      # Return the computed result.      # Return the computed result.
# Line 755  Line 1296 
1296    
1297  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>
1298    
1299  In this case, the list @words will be treated as a command line. There are two options available,  In this case, the list @words will be treated as a command line and there are two options available,
1300  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
1301    
1302  C<< -logFile=error.log apple orange rutabaga >>  C<< -logFile=error.log apple orange rutabaga >>
# Line 769  Line 1310 
1310  C<< apple orange rutabaga >>  C<< apple orange rutabaga >>
1311    
1312  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1313  support for quote characters.  support for quote characters. Options can be specified with single or double hyphens.
1314    
1315  =over 4  =over 4
1316    
# Line 794  Line 1335 
1335      my ($optionTable, @inputList) = @_;      my ($optionTable, @inputList) = @_;
1336      # Process any options in the input list.      # Process any options in the input list.
1337      my %overrides = ();      my %overrides = ();
1338      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1339          # Get the current option.          # Get the current option.
1340          my $arg = shift @inputList;          my $arg = shift @inputList;
1341          # Pull out the option name.          # Pull out the option name.
1342          $arg =~ /^-([^=]*)/g;          $arg =~ /^--?([^=]*)/g;
1343          my $name = $1;          my $name = $1;
1344          # Check for an option value.          # Check for an option value.
1345          if ($arg =~ /\G=(.*)$/g) {          if ($arg =~ /\G=(.*)$/g) {
# Line 824  Line 1365 
1365    
1366  C<< my $codedString = Tracer::Escape($realString); >>  C<< my $codedString = Tracer::Escape($realString); >>
1367    
1368  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
1369  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
1370  doubled. The effect is to exactly reverse the effect of L</UnEscape>.  result is to reverse the effect of L</UnEscape>.
1371    
1372  =over 4  =over 4
1373    
# Line 850  Line 1391 
1391      # Loop through the parameter string, looking for sequences to escape.      # Loop through the parameter string, looking for sequences to escape.
1392      while (length $realString > 0) {      while (length $realString > 0) {
1393          # Look for the first sequence to escape.          # Look for the first sequence to escape.
1394          if ($realString =~ /^(.*?)([ \n\t\\])/) {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1395              # 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
1396              # 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.
1397              $retVal .= $1;              $retVal .= $1;
1398              # Strip the processed section off the real string.              # Strip the processed section off the real string.
1399              $realString = substr $realString, (length $2) + (length $1);              $realString = substr $realString, (length $2) + (length $1);
1400              # Encode the escape sequence.              # Get the matched character.
1401              my $char = $2;              my $char = $2;
1402              $char =~ tr/ \t\n/btn/;              # If we have a CR, we are done.
1403                if ($char ne "\r") {
1404                    # It's not a CR, so encode the escape sequence.
1405                    $char =~ tr/\t\n/tn/;
1406              $retVal .= "\\" . $char;              $retVal .= "\\" . $char;
1407                }
1408          } else {          } else {
1409              # 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
1410              # transferred unmodified.              # transferred unmodified.
# Line 875  Line 1420 
1420    
1421  C<< my $realString = Tracer::UnEscape($codedString); >>  C<< my $realString = Tracer::UnEscape($codedString); >>
1422    
1423  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
1424  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
1425    be deleted.
1426    
1427  =over 4  =over 4
1428    
# Line 896  Line 1442 
1442  sub UnEscape {  sub UnEscape {
1443      # Get the parameter.      # Get the parameter.
1444      my ($codedString) = @_;      my ($codedString) = @_;
     Tracer("Coded string is \"$codedString\".") if T(4);  
1445      # Initialize the return variable.      # Initialize the return variable.
1446      my $retVal = "";      my $retVal = "";
1447      # Only proceed if the incoming string is nonempty.      # Only proceed if the incoming string is nonempty.
1448      if (defined $codedString) {      if (defined $codedString) {
1449          # 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
1450          # translating because it causes problems with the escaped slash. ("\\b" becomes          # translating because it causes problems with the escaped slash. ("\\t" becomes
1451          # "\ " no matter what we do.)          # "\<tab>" no matter what we do.)
1452          while (length $codedString > 0) {          while (length $codedString > 0) {
1453              # Look for the first escape sequence.              # Look for the first escape sequence.
1454              if ($codedString =~ /^(.*?)\\(\\|b|n|t)/) {              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
1455                  # 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
1456                  # 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.
1457                  $retVal .= $1;                  $retVal .= $1;
1458                  $codedString = substr $codedString, (2 + length $1);                  $codedString = substr $codedString, (2 + length $1);
1459                  # Decode the escape sequence.                  # Get the escape value.
1460                  my $char = $2;                  my $char = $2;
1461                  $char =~ tr/\\btn/\\ \t\n/;                  # If we have a "\r", we are done.
1462                    if ($char ne 'r') {
1463                        # Here it's not an 'r', so we convert it.
1464                        $char =~ tr/\\tn/\\\t\n/;
1465                  $retVal .= $char;                  $retVal .= $char;
1466                    }
1467              } else {              } else {
1468                  # 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
1469                  # transferred unmodified.                  # transferred unmodified.
# Line 1020  Line 1569 
1569      return @inputList;      return @inputList;
1570  }  }
1571    
1572    =head3 Percent
1573    
1574    C<< my $percent = Tracer::Percent($number, $base); >>
1575    
1576    Returns the percent of the base represented by the given number. If the base
1577    is zero, returns zero.
1578    
1579    =over 4
1580    
1581    =item number
1582    
1583    Percent numerator.
1584    
1585    =item base
1586    
1587    Percent base.
1588    
1589    =item RETURN
1590    
1591    Returns the percentage of the base represented by the numerator.
1592    
1593    =back
1594    
1595    =cut
1596    
1597    sub Percent {
1598        # Get the parameters.
1599        my ($number, $base) = @_;
1600        # Declare the return variable.
1601        my $retVal = 0;
1602        # Compute the percent.
1603        if ($base != 0) {
1604            $retVal = $number * 100 / $base;
1605        }
1606        # Return the result.
1607        return $retVal;
1608    }
1609    
1610  =head3 GetFile  =head3 GetFile
1611    
1612  C<< my @fileContents = Tracer::GetFile($fileName); >>  C<< my @fileContents = Tracer::GetFile($fileName); >>
1613    
1614  Return the entire contents of a file.      or
1615    
1616    C<< my $fileContents = Tracer::GetFile($fileName); >>
1617    
1618    Return the entire contents of a file. In list context, line-ends are removed and
1619    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1620    
1621  =over 4  =over 4
1622    
# Line 1035  Line 1627 
1627  =item RETURN  =item RETURN
1628    
1629  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.
1630  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
1631    the file, an empty list will be returned.
1632    
1633  =back  =back
1634    
# Line 1047  Line 1640 
1640      # Declare the return variable.      # Declare the return variable.
1641      my @retVal = ();      my @retVal = ();
1642      # Open the file for input.      # Open the file for input.
1643      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 {  
1644          # Read the whole file into the return variable, stripping off any terminator          # Read the whole file into the return variable, stripping off any terminator
1645          # characters.          # characters.
1646          my $lineCount = 0;          my $lineCount = 0;
1647          while (my $line = <INPUTFILE>) {      while (my $line = <$handle>) {
1648              $lineCount++;              $lineCount++;
1649              $line = Strip($line);              $line = Strip($line);
1650              push @retVal, $line;              push @retVal, $line;
1651          }          }
1652          # Close it.          # Close it.
1653          close INPUTFILE;      close $handle;
1654          my $actualLines = @retVal;          my $actualLines = @retVal;
1655      }      Trace("$actualLines lines read from file $fileName.") if T(File => 2);
1656      # Return the file's contents in the desired format.      # Return the file's contents in the desired format.
1657      if (wantarray) {      if (wantarray) {
1658          return @retVal;          return @retVal;
# Line 1072  Line 1661 
1661      }      }
1662  }  }
1663    
1664    =head3 PutFile
1665    
1666    C<< Tracer::PutFile($fileName, \@lines); >>
1667    
1668    Write out a file from a list of lines of text.
1669    
1670    =over 4
1671    
1672    =item fileName
1673    
1674    Name of the output file.
1675    
1676    =item lines
1677    
1678    Reference to a list of text lines. The lines will be written to the file in order, with trailing
1679    new-line characters. Alternatively, may be a string, in which case the string will be written without
1680    modification.
1681    
1682    =back
1683    
1684    =cut
1685    
1686    sub PutFile {
1687        # Get the parameters.
1688        my ($fileName, $lines) = @_;
1689        # Open the output file.
1690        my $handle = Open(undef, ">$fileName");
1691        # Count the lines written.
1692        if (ref $lines ne 'ARRAY') {
1693            # Here we have a scalar, so we write it raw.
1694            print $handle $lines;
1695            Trace("Scalar put to file $fileName.") if T(File => 3);
1696        } else {
1697            # Write the lines one at a time.
1698            my $count = 0;
1699            for my $line (@{$lines}) {
1700                print $handle "$line\n";
1701                $count++;
1702            }
1703            Trace("$count lines put to file $fileName.") if T(File => 3);
1704        }
1705        # Close the output file.
1706        close $handle;
1707    }
1708    
1709  =head3 QTrace  =head3 QTrace
1710    
1711  C<< my $data = QTrace($format); >>  C<< my $data = QTrace($format); >>
# Line 1140  Line 1774 
1774  sub Confess {  sub Confess {
1775      # Get the parameters.      # Get the parameters.
1776      my ($message) = @_;      my ($message) = @_;
1777        if (! defined($FIG_Config::no_tool_hdr)) {
1778            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
1779            my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
1780            # Only proceed if the tool header file is actually present.
1781            if (-f $toolHeaderFile) {
1782                my @lines = GetFile($toolHeaderFile);
1783                Trace("Tool header has " . scalar(@lines) . " lines.");
1784            }
1785        }
1786      # Trace the call stack.      # Trace the call stack.
1787      Cluck($message);      Cluck($message);
1788      # Abort the program.      # Abort the program.
# Line 1151  Line 1794 
1794  C<< Assert($condition1, $condition2, ... $conditionN); >>  C<< Assert($condition1, $condition2, ... $conditionN); >>
1795    
1796  Return TRUE if all the conditions are true. This method can be used in conjunction with  Return TRUE if all the conditions are true. This method can be used in conjunction with
1797  the OR operator and the L</Confess> method, B<Assert> can function as a debugging assert.  the OR operator and the L</Confess> method as a debugging assert.
1798  So, for example  So, for example
1799    
1800  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
# Line 1272  Line 1915 
1915    
1916  =head3 AddToListMap  =head3 AddToListMap
1917    
1918  C<< Tracer::AddToListMap(\%hash, $key, $value); >>  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>
1919    
1920  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list
1921  is created for the key. Otherwise, the new value is pushed onto the list.  is created for the key. Otherwise, the new value is pushed onto the list.
# Line 1287  Line 1930 
1930    
1931  Key for which the value is to be added.  Key for which the value is to be added.
1932    
1933  =item value  =item value1, value2, ... valueN
1934    
1935  Value to add to the key's value list.  List of values to add to the key's value list.
1936    
1937  =back  =back
1938    
# Line 1297  Line 1940 
1940    
1941  sub AddToListMap {  sub AddToListMap {
1942      # Get the parameters.      # Get the parameters.
1943      my ($hash, $key, $value) = @_;      my ($hash, $key, @values) = @_;
1944      # Process according to whether or not the key already has a value.      # Process according to whether or not the key already has a value.
1945      if (! exists $hash->{$key}) {      if (! exists $hash->{$key}) {
1946          $hash->{$key} = [$value];          $hash->{$key} = [@values];
1947      } else {      } else {
1948          push @{$hash->{$key}}, $value;          push @{$hash->{$key}}, @values;
1949      }      }
1950  }  }
1951    
# Line 1310  Line 1953 
1953    
1954  C<< if (Tracer::DebugMode) { ...code... } >>  C<< if (Tracer::DebugMode) { ...code... } >>
1955    
1956  Return TRUE if debug mode has been turned on, else output an error  Return TRUE if debug mode has been turned on, else abort.
 page and return FALSE.  
1957    
1958  Certain CGI scripts are too dangerous to exist in the production  Certain CGI scripts are too dangerous to exist in the production
1959  environment. This method provides a simple way to prevent them  environment. This method provides a simple way to prevent them
1960  from working unless they are explicitly turned on by creating a password  from working unless they are explicitly turned on by creating a password
1961  cookie via the B<SetPassword> script.  If debugging mode  cookie via the B<SetPassword> script.  If debugging mode
1962  is not turned on, an error web page will be output directing the  is not turned on, an error will occur.
 user to enter in the correct password.  
1963    
1964  =cut  =cut
1965    
# Line 1331  Line 1972 
1972      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1973          $retVal = 1;          $retVal = 1;
1974      } else {      } else {
1975          # Here debug mode is off, so we generate an error page.          # Here debug mode is off, so we generate an error.
1976          my $pageString = PageBuilder::Build("<Html/ErrorPage.html", {}, "Html");          Confess("Cannot use this facility without logging in.");
         print $pageString;  
1977      }      }
1978      # Return the determination indicator.      # Return the determination indicator.
1979      return $retVal;      return $retVal;
# Line 1364  Line 2004 
2004  sub Strip {  sub Strip {
2005      # Get a copy of the parameter string.      # Get a copy of the parameter string.
2006      my ($string) = @_;      my ($string) = @_;
2007      my $retVal = $string;      my $retVal = (defined $string ? $string : "");
2008      # Strip the line terminator characters.      # Strip the line terminator characters.
2009      $retVal =~ s/(\r|\n)+$//g;      $retVal =~ s/(\r|\n)+$//g;
2010      # Return the result.      # Return the result.
# Line 1432  Line 2072 
2072      return $retVal;      return $retVal;
2073  }  }
2074    
2075    =head3 EOF
2076    
2077    This is a constant that is lexically greater than any useful string.
2078    
2079    =cut
2080    
2081    sub EOF {
2082        return "\xFF\xFF\xFF\xFF\xFF";
2083    }
2084    
2085  =head3 TICK  =head3 TICK
2086    
2087  C<< my @results = TICK($commandString); >>  C<< my @results = TICK($commandString); >>
# Line 1473  Line 2123 
2123      return `$commandString`;      return `$commandString`;
2124  }  }
2125    
2126    =head3 ScriptSetup
2127    
2128    C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>
2129    
2130    Perform standard tracing and debugging setup for scripts. The value returned is
2131    the CGI object followed by a pre-built variable hash. At the end of the script,
2132    the client should call L</ScriptFinish> to output the web page.
2133    
2134    This method calls L</ETracing> to configure tracing, which allows the tracing
2135    to be configured via the emergency tracing form on the debugging control panel.
2136    Tracing will then be turned on automatically for all programs that use the L</ETracing>
2137    method, which includes every program that uses this method or L</StandardSetup>.
2138    
2139    =over 4
2140    
2141    =item noTrace (optional)
2142    
2143    If specified, tracing will be suppressed. This is useful if the script wants to set up
2144    tracing manually.
2145    
2146    =item RETURN
2147    
2148    Returns a two-element list consisting of a CGI query object and a variable hash for
2149    the output page.
2150    
2151    =back
2152    
2153    =cut
2154    
2155    sub ScriptSetup {
2156        # Get the parameters.
2157        my ($noTrace) = @_;
2158        # Get the CGI query object.
2159        my $cgi = CGI->new();
2160        # Set up tracing if it's not suppressed.
2161        ETracing($cgi) unless $noTrace;
2162        # Create the variable hash.
2163        my $varHash = { results => '' };
2164        # Return the query object and variable hash.
2165        return ($cgi, $varHash);
2166    }
2167    
2168    =head3 ETracing
2169    
2170    C<< ETracing($parameter); >>
2171    
2172    Set up emergency tracing. Emergency tracing is tracing that is turned
2173    on automatically for any program that calls this method. The emergency
2174    tracing parameters are stored in a a file identified by a tracing key.
2175    If this method is called with a CGI object, then the tracing key is
2176    taken from a cookie. If it is called with no parameters, then the tracing
2177    key is taken from an environment variable. If it is called with a string,
2178    the tracing key is that string.
2179    
2180    =over 4
2181    
2182    =item parameter
2183    
2184    A parameter from which the tracing key is computed. If it is a scalar,
2185    that scalar is used as the tracing key. If it is a CGI object, the
2186    tracing key is taken from the C<IP> cookie. If it is omitted, the
2187    tracing key is taken from the C<TRACING> environment variable. If it
2188    is a CGI object and emergency tracing is not on, the C<Trace> and
2189    C<TF> parameters will be used to determine the type of tracing.
2190    
2191    =back
2192    
2193    =cut
2194    
2195    sub ETracing {
2196        # Get the parameter.
2197        my ($parameter) = @_;
2198        # Check for CGI mode.
2199        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
2200        # Default to no tracing except errors.
2201        my ($tracing, $dest) = ("0", "WARN");
2202        # Check for emergency tracing.
2203        my $tkey = EmergencyKey($parameter);
2204        my $emergencyFile = EmergencyFileName($tkey);
2205        if (-e $emergencyFile) {
2206            # We have the file. Read in the data.
2207            my @tracing = GetFile($emergencyFile);
2208            # Pull off the time limit.
2209            my $expire = shift @tracing;
2210            # Convert it to seconds.
2211            $expire *= 3600;
2212            # Check the file data.
2213            my $stat = stat($emergencyFile);
2214            my ($now) = gettimeofday;
2215            if ($now - $stat->mtime > $expire) {
2216                # Delete the expired file.
2217                unlink $emergencyFile;
2218            } else {
2219                # Emergency tracing is on. Pull off the destination and
2220                # the trace level;
2221                $dest = shift @tracing;
2222                my $level = shift @tracing;
2223                # Convert the destination to a real tracing destination.
2224                # temp directory.
2225                $dest = EmergencyTracingDest($tkey, $dest);
2226                # Insure Tracer is specified.
2227                my %moduleHash = map { $_ => 1 } @tracing;
2228                $moduleHash{Tracer} = 1;
2229                # Set the trace parameter.
2230                $tracing = join(" ", $level, sort keys %moduleHash);
2231            }
2232        } elsif (defined $cgi) {
2233            # There's no emergency tracing, but we have a CGI object, so check
2234            # for tracing from the form parameters.
2235            if ($cgi->param('Trace')) {
2236                # Here the user has requested tracing via a form.
2237                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
2238                $tracing = $cgi->param('Trace') . " Tracer";
2239            }
2240        }
2241        # Setup the tracing we've determined from all the stuff above.
2242        TSetup($tracing, $dest);
2243        # If we're a web script, trace the parameter and environment data.
2244        if (defined $cgi) {
2245            TraceParms($cgi);
2246        }
2247    }
2248    
2249    =head3 EmergencyFileName
2250    
2251    C<< my $fileName = Tracer::EmergencyFileName($tkey); >>
2252    
2253    Return the emergency tracing file name. This is the file that specifies
2254    the tracing information.
2255    
2256    =over 4
2257    
2258    =item tkey
2259    
2260    Tracing key for the current program.
2261    
2262    =item RETURN
2263    
2264    Returns the name of the file to contain the emergency tracing information.
2265    
2266    =back
2267    
2268    =cut
2269    
2270    sub EmergencyFileName {
2271        # Get the parameters.
2272        my ($tkey) = @_;
2273        # Compute the emergency tracing file name.
2274        return "$FIG_Config::temp/Emergency$tkey.txt";
2275    }
2276    
2277    =head3 EmergencyFileTarget
2278    
2279    C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>
2280    
2281    Return the emergency tracing target file name. This is the file that receives
2282    the tracing output for file-based tracing.
2283    
2284    =over 4
2285    
2286    =item tkey
2287    
2288    Tracing key for the current program.
2289    
2290    =item RETURN
2291    
2292    Returns the name of the file to contain the trace output.
2293    
2294    =back
2295    
2296    =cut
2297    
2298    sub EmergencyFileTarget {
2299        # Get the parameters.
2300        my ($tkey) = @_;
2301        # Compute the emergency tracing file name.
2302        return "$FIG_Config::temp/trace$tkey.log";
2303    }
2304    
2305    =head3 EmergencyTracingDest
2306    
2307    C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>
2308    
2309    This method converts an emergency tracing destination to a real
2310    tracing destination. The main difference is that if the
2311    destination is C<FILE> or C<APPEND>, we convert it to file
2312    output. If the destination is C<DUAL>, we convert it to file
2313    and standard output.
2314    
2315    =over 4
2316    
2317    =item tkey
2318    
2319    Tracing key for this environment.
2320    
2321    =item myDest
2322    
2323    Destination from the emergency tracing file.
2324    
2325    =item RETURN
2326    
2327    Returns a destination that can be passed into L</TSetup>.
2328    
2329    =back
2330    
2331    =cut
2332    
2333    sub EmergencyTracingDest {
2334        # Get the parameters.
2335        my ($tkey, $myDest) = @_;
2336        # Declare the return variable.
2337        my $retVal = $myDest;
2338        # Process according to the destination value.
2339        if ($myDest eq 'FILE') {
2340            $retVal = ">" . EmergencyFileTarget($tkey);
2341        } elsif ($myDest eq 'APPEND') {
2342            $retVal = ">>" . EmergencyFileTarget($tkey);
2343        } elsif ($myDest eq 'DUAL') {
2344            $retVal = "+>" . EmergencyFileTarget($tkey);
2345        }
2346        # Return the result.
2347        return $retVal;
2348    }
2349    
2350    =head3 Emergency
2351    
2352    C<< Emergency($key, $hours, $dest, $level, @modules); >>
2353    
2354    Turn on emergency tracing. This method is normally invoked over the web from
2355    a debugging console, but it can also be called by the C<trace.pl> script.
2356    The caller specifies the duration of the emergency in hours, the desired tracing
2357    destination, the trace level, and a list of the trace modules to activate.
2358    For the length of the duration, when a program in an environment with the
2359    specified tracing key active invokes a Sprout CGI script, tracing will be
2360    turned on automatically. See L</TSetup> for more about tracing setup and
2361    L</ETracing> for more about emergency tracing.
2362    
2363    =over 4
2364    
2365    =item tkey
2366    
2367    The tracing key. This is used to identify the control file and the trace file.
2368    
2369    =item hours
2370    
2371    Number of hours to keep emergency tracing alive.
2372    
2373    =item dest
2374    
2375    Tracing destination. If no path information is specified for a file
2376    destination, it is put in the FIG temporary directory.
2377    
2378    =item level
2379    
2380    Tracing level. A higher level means more trace messages.
2381    
2382    =item modules
2383    
2384    A list of the tracing modules to activate.
2385    
2386    =back
2387    
2388    =cut
2389    
2390    sub Emergency {
2391        # Get the parameters.
2392        my ($tkey, $hours, $dest, $level, @modules) = @_;
2393        # Create the emergency file.
2394        my $specFile = EmergencyFileName($tkey);
2395        my $outHandle = Open(undef, ">$specFile");
2396        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
2397    }
2398    
2399    =head3 EmergencyKey
2400    
2401    C<< my $tkey = EmergencyKey($parameter); >>
2402    
2403    Return the Key to be used for emergency tracing. This could be an IP address,
2404     a session ID, or a user name, depending on the environment.
2405    
2406    =over 4
2407    
2408    =item parameter
2409    
2410    Parameter defining the method for finding the tracing key. If it is a scalar,
2411    then it is presumed to be the tracing key itself. If it is a CGI object, then
2412    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
2413    taken from the C<TRACING> environment variable.
2414    
2415    =item RETURN
2416    
2417    Returns the key to be used for labels in emergency tracing.
2418    
2419    =back
2420    
2421    =cut
2422    
2423    sub EmergencyKey {
2424        # Get the parameters.
2425        my ($parameter) = @_;
2426        # Declare the return variable.
2427        my $retVal;
2428        # Determine the parameter type.
2429        if (! defined $parameter) {
2430            # Here we're supposed to check the environment.
2431            $retVal = $ENV{TRACING};
2432        } else {
2433            my $ptype = ref $parameter;
2434            if ($ptype eq 'CGI') {
2435                # Here we were invoked from a web page. Look for a cookie.
2436                $retVal = $parameter->cookie('IP');
2437            } elsif (! $ptype) {
2438                # Here the key was passed in.
2439                $retVal = $parameter;
2440            }
2441        }
2442        # If no luck finding a key, use the PID.
2443        if (! defined $retVal) {
2444            $retVal = $$;
2445        }
2446        # Return the result.
2447        return $retVal;
2448    }
2449    
2450    
2451    =head3 TraceParms
2452    
2453    C<< Tracer::TraceParms($cgi); >>
2454    
2455    Trace the CGI parameters at trace level CGI => 3 and the environment variables
2456    at level CGI => 4.
2457    
2458    =over 4
2459    
2460    =item cgi
2461    
2462    CGI query object containing the parameters to trace.
2463    
2464    =back
2465    
2466    =cut
2467    
2468    sub TraceParms {
2469        # Get the parameters.
2470        my ($cgi) = @_;
2471        if (T(CGI => 3)) {
2472            # Here we want to trace the parameter data.
2473            my @names = $cgi->param;
2474            for my $parmName (sort @names) {
2475                # Note we skip the Trace parameters, which are for our use only.
2476                if ($parmName ne 'Trace' && $parmName ne 'TF') {
2477                    my @values = $cgi->param($parmName);
2478                    Trace("CGI: $parmName = " . join(", ", @values));
2479                }
2480            }
2481            # Display the request method.
2482            my $method = $cgi->request_method();
2483            Trace("Method: $method");
2484        }
2485        if (T(CGI => 4)) {
2486            # Here we want the environment data too.
2487            for my $envName (sort keys %ENV) {
2488                Trace("ENV: $envName = $ENV{$envName}");
2489            }
2490        }
2491    }
2492    
2493    =head3 ScriptFinish
2494    
2495    C<< ScriptFinish($webData, $varHash); >>
2496    
2497    Output a web page at the end of a script. Either the string to be output or the
2498    name of a template file can be specified. If the second parameter is omitted,
2499    it is assumed we have a string to be output; otherwise, it is assumed we have the
2500    name of a template file. The template should have the variable C<DebugData>
2501    specified in any form that invokes a standard script. If debugging mode is turned
2502    on, a form field will be put in that allows the user to enter tracing data.
2503    Trace messages will be placed immediately before the terminal C<BODY> tag in
2504    the output, formatted as a list.
2505    
2506    A typical standard script would loook like the following.
2507    
2508        BEGIN {
2509            # Print the HTML header.
2510            print "CONTENT-TYPE: text/html\n\n";
2511        }
2512        use Tracer;
2513        use CGI;
2514        use FIG;
2515        # ... more uses ...
2516    
2517        my ($cgi, $varHash) = ScriptSetup();
2518        eval {
2519            # ... get data from $cgi, put it in $varHash ...
2520        };
2521        if ($@) {
2522            Trace("Script Error: $@") if T(0);
2523        }
2524        ScriptFinish("Html/MyTemplate.html", $varHash);
2525    
2526    The idea here is that even if the script fails, you'll see trace messages and
2527    useful output.
2528    
2529    =over 4
2530    
2531    =item webData
2532    
2533    A string containing either the full web page to be written to the output or the
2534    name of a template file from which the page is to be constructed. If the name
2535    of a template file is specified, then the second parameter must be present;
2536    otherwise, it must be absent.
2537    
2538    =item varHash (optional)
2539    
2540    If specified, then a reference to a hash mapping variable names for a template
2541    to their values. The template file will be read into memory, and variable markers
2542    will be replaced by data in this hash reference.
2543    
2544    =back
2545    
2546    =cut
2547    
2548    sub ScriptFinish {
2549        # Get the parameters.
2550        my ($webData, $varHash) = @_;
2551        # Check for a template file situation.
2552        my $outputString;
2553        if (defined $varHash) {
2554            # Here we have a template file. We need to determine the template type.
2555            my $template;
2556            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
2557                $template = "$FIG_Config::template_url/$webData";
2558            } else {
2559                $template = "<<$webData";
2560            }
2561            $outputString = PageBuilder::Build($template, $varHash, "Html");
2562        } else {
2563            # Here the user gave us a raw string.
2564            $outputString = $webData;
2565        }
2566        # Check for trace messages.
2567        if ($Destination ne "NONE" && $TraceLevel > 0) {
2568            # We have trace messages, so we want to put them at the end of the body. This
2569            # is either at the end of the whole string or at the beginning of the BODY
2570            # end-tag.
2571            my $pos = length $outputString;
2572            if ($outputString =~ m#</body>#gi) {
2573                $pos = (pos $outputString) - 7;
2574            }
2575            # If the trace messages were queued, we unroll them. Otherwise, we display the
2576            # destination.
2577            my $traceHtml;
2578            if ($Destination eq "QUEUE") {
2579                $traceHtml = QTrace('Html');
2580            } elsif ($Destination =~ /^>>(.+)$/) {
2581                # Here the tracing output it to a file. We code it as a hyperlink so the user
2582                # can copy the file name into the clipboard easily.
2583                my $actualDest = $1;
2584                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
2585            } else {
2586                # Here we have one of the special destinations.
2587                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
2588            }
2589            substr $outputString, $pos, 0, $traceHtml;
2590        }
2591        # Write the output string.
2592        print $outputString;
2593    }
2594    
2595    =head3 Insure
2596    
2597    C<< Insure($dirName); >>
2598    
2599    Insure a directory is present.
2600    
2601    =over 4
2602    
2603    =item dirName
2604    
2605    Name of the directory to check. If it does not exist, it will be created.
2606    
2607    =back
2608    
2609    =cut
2610    
2611    sub Insure {
2612        my ($dirName) = @_;
2613        if (! -d $dirName) {
2614            Trace("Creating $dirName directory.") if T(File => 2);
2615            eval { mkpath $dirName; };
2616            if ($@) {
2617                Confess("Error creating $dirName: $@");
2618            }
2619        }
2620    }
2621    
2622    =head3 ChDir
2623    
2624    C<< ChDir($dirName); >>
2625    
2626    Change to the specified directory.
2627    
2628    =over 4
2629    
2630    =item dirName
2631    
2632    Name of the directory to which we want to change.
2633    
2634    =back
2635    
2636    =cut
2637    
2638    sub ChDir {
2639        my ($dirName) = @_;
2640        if (! -d $dirName) {
2641            Confess("Cannot change to directory $dirName: no such directory.");
2642        } else {
2643            Trace("Changing to directory $dirName.") if T(File => 4);
2644            my $okFlag = chdir $dirName;
2645            if (! $okFlag) {
2646                Confess("Error switching to directory $dirName.");
2647            }
2648        }
2649    }
2650    
2651    =head3 SendSMS
2652    
2653    C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>
2654    
2655    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
2656    user name, password, and API ID for the relevant account in the hash reference variable
2657    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
2658    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
2659    is C<2561022>, then the FIG_Config file must contain
2660    
2661        $phone =  { user => 'BruceTheHumanPet',
2662                    password => 'silly',
2663                    api_id => '2561022' };
2664    
2665    The original purpose of this method was to insure Bruce would be notified immediately when the
2666    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
2667    when you call this method.
2668    
2669    The message ID will be returned if successful, and C<undef> if an error occurs.
2670    
2671    =over 4
2672    
2673    =item phoneNumber
2674    
2675    Phone number to receive the message, in international format. A United States phone number
2676    would be prefixed by "1". A British phone number would be prefixed by "44".
2677    
2678    =item msg
2679    
2680    Message to send to the specified phone.
2681    
2682    =item RETURN
2683    
2684    Returns the message ID if successful, and C<undef> if the message could not be sent.
2685    
2686    =back
2687    
2688    =cut
2689    
2690    sub SendSMS {
2691        # Get the parameters.
2692        my ($phoneNumber, $msg) = @_;
2693        # Declare the return variable. If we do not change it, C<undef> will be returned.
2694        my $retVal;
2695        # Only proceed if we have phone support.
2696        if (! defined $FIG_Config::phone) {
2697            Trace("Phone support not present in FIG_Config.") if T(1);
2698        } else {
2699            # Get the phone data.
2700            my $parms = $FIG_Config::phone;
2701            # Get the Clickatell URL.
2702            my $url = "http://api.clickatell.com/http/";
2703            # Create the user agent.
2704            my $ua = LWP::UserAgent->new;
2705            # Request a Clickatell session.
2706            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
2707                                         password => $parms->{password},
2708                                         api_id => $parms->{api_id},
2709                                         to => $phoneNumber,
2710                                         text => $msg});
2711            # Check for an error.
2712            if (! $resp->is_success) {
2713                Trace("Alert failed.") if T(1);
2714            } else {
2715                # Get the message ID.
2716                my $rstring = $resp->content;
2717                if ($rstring =~ /^ID:\s+(.*)$/) {
2718                    $retVal = $1;
2719                } else {
2720                    Trace("Phone attempt failed with $rstring") if T(1);
2721                }
2722            }
2723        }
2724        # Return the result.
2725        return $retVal;
2726    }
2727    
2728    =head3 CommaFormat
2729    
2730    C<< my $formatted = Tracer::CommaFormat($number); >>
2731    
2732    Insert commas into a number.
2733    
2734    =over 4
2735    
2736    =item number
2737    
2738    A sequence of digits.
2739    
2740    =item RETURN
2741    
2742    Returns the same digits with commas strategically inserted.
2743    
2744    =back
2745    
2746    =cut
2747    
2748    sub CommaFormat {
2749        # Get the parameters.
2750        my ($number) = @_;
2751        # Pad the length up to a multiple of three.
2752        my $padded = "$number";
2753        $padded = " " . $padded while length($padded) % 3 != 0;
2754        # This is a fancy PERL trick. The parentheses in the SPLIT pattern
2755        # cause the delimiters to be included in the output stream. The
2756        # GREP removes the empty strings in between the delimiters.
2757        my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
2758        # Clean out the spaces.
2759        $retVal =~ s/ //g;
2760        # Return the result.
2761        return $retVal;
2762    }
2763    =head3 SetPermissions
2764    
2765    C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>
2766    
2767    Set the permissions for a directory and all the files and folders inside it.
2768    In addition, the group ownership will be changed to the specified value.
2769    
2770    This method is more vulnerable than most to permission and compatability
2771    problems, so it does internal error recovery.
2772    
2773    =over 4
2774    
2775    =item dirName
2776    
2777    Name of the directory to process.
2778    
2779    =item group
2780    
2781    Name of the group to be assigned.
2782    
2783    =item mask
2784    
2785    Permission mask. Bits that are C<1> in this mask will be ORed into the
2786    permission bits of any file or directory that does not already have them
2787    set to 1.
2788    
2789    =item otherMasks
2790    
2791    Map of search patterns to permission masks. If a directory name matches
2792    one of the patterns, that directory and all its members and subdirectories
2793    will be assigned the new pattern. For example, the following would
2794    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2795    
2796        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2797    
2798    The list is ordered, so the following would use 0777 for C<tmp1> and
2799    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2800    
2801        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2802                                                       '^tmp' => 0666);
2803    
2804    Note that the pattern matches are all case-insensitive, and only directory
2805    names are matched, not file names.
2806    
2807    =back
2808    
2809    =cut
2810    
2811    sub SetPermissions {
2812        # Get the parameters.
2813        my ($dirName, $group, $mask, @otherMasks) = @_;
2814        # Set up for error recovery.
2815        eval {
2816            # Switch to the specified directory.
2817            ChDir($dirName);
2818            # Get the group ID.
2819            my $gid = getgrnam($group);
2820            # Get the mask for tracing.
2821            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2822            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2823            my $fixCount = 0;
2824            my $lookCount = 0;
2825            # @dirs will be a stack of directories to be processed.
2826            my @dirs = (getcwd());
2827            while (scalar(@dirs) > 0) {
2828                # Get the current directory.
2829                my $dir = pop @dirs;
2830                # Check for a match to one of the specified directory names. To do
2831                # that, we need to pull the individual part of the name off of the
2832                # whole path.
2833                my $simpleName = $dir;
2834                if ($dir =~ m!/([^/]+)$!) {
2835                    $simpleName = $1;
2836                }
2837                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2838                # Search for a match.
2839                my $match = 0;
2840                my $i;
2841                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2842                    my $pattern = $otherMasks[$i];
2843                    if ($simpleName =~ /$pattern/i) {
2844                        $match = 1;
2845                    }
2846                }
2847                # Check for a match. Note we use $i-1 because the loop added 2
2848                # before terminating due to the match.
2849                if ($match && $otherMasks[$i-1] != $mask) {
2850                    # This directory matches one of the incoming patterns, and it's
2851                    # a different mask, so we process it recursively with that mask.
2852                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2853                } else {
2854                    # Here we can process normally. Get all of the non-hidden members.
2855                    my @submems = OpenDir($dir, 1);
2856                    for my $submem (@submems) {
2857                        # Get the full name.
2858                        my $thisMem = "$dir/$submem";
2859                        Trace("Checking member $thisMem.") if T(4);
2860                        $lookCount++;
2861                        if ($lookCount % 1000 == 0) {
2862                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2863                        }
2864                        # Fix the group.
2865                        chown -1, $gid, $thisMem;
2866                        # Insure this member is not a symlink.
2867                        if (! -l $thisMem) {
2868                            # Get its info.
2869                            my $fileInfo = stat $thisMem;
2870                            # Only proceed if we got the info. Otherwise, it's a hard link
2871                            # and we want to skip it anyway.
2872                            if ($fileInfo) {
2873                                my $fileMode = $fileInfo->mode;
2874                                if (($fileMode & $mask) != $mask) {
2875                                    # Fix this member.
2876                                    $fileMode |= $mask;
2877                                    chmod $fileMode, $thisMem;
2878                                    $fixCount++;
2879                                }
2880                                # If it's a subdirectory, stack it.
2881                                if (-d $thisMem) {
2882                                    push @dirs, $thisMem;
2883                                }
2884                            }
2885                        }
2886                    }
2887                }
2888            }
2889            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2890        };
2891        # Check for an error.
2892        if ($@) {
2893            Confess("SetPermissions error: $@");
2894        }
2895    }
2896    
2897    =head3 CompareLists
2898    
2899    C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>
2900    
2901    Compare two lists of tuples, and return a hash analyzing the differences. The lists
2902    are presumed to be sorted alphabetically by the value in the $keyIndex column.
2903    The return value contains a list of items that are only in the new list
2904    (inserted) and only in the old list (deleted).
2905    
2906    =over 4
2907    
2908    =item newList
2909    
2910    Reference to a list of new tuples.
2911    
2912    =item oldList
2913    
2914    Reference to a list of old tuples.
2915    
2916    =item keyIndex (optional)
2917    
2918    Index into each tuple of its key field. The default is 0.
2919    
2920    =item RETURN
2921    
2922    Returns a 2-tuple consisting of a reference to the list of items that are only in the new
2923    list (inserted) followed by a reference to the list of items that are only in the old
2924    list (deleted).
2925    
2926    =back
2927    
2928    =cut
2929    
2930    sub CompareLists {
2931        # Get the parameters.
2932        my ($newList, $oldList, $keyIndex) = @_;
2933        if (! defined $keyIndex) {
2934            $keyIndex = 0;
2935        }
2936        # Declare the return variables.
2937        my ($inserted, $deleted) = ([], []);
2938        # Loop through the two lists simultaneously.
2939        my ($newI, $oldI) = (0, 0);
2940        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
2941        while ($newI < $newN || $oldI < $oldN) {
2942            # Get the current object in each list. Note that if one
2943            # of the lists is past the end, we'll get undef.
2944            my $newItem = $newList->[$newI];
2945            my $oldItem = $oldList->[$oldI];
2946            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
2947                # The old item is not in the new list, so mark it deleted.
2948                push @{$deleted}, $oldItem;
2949                $oldI++;
2950            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
2951                # The new item is not in the old list, so mark it inserted.
2952                push @{$inserted}, $newItem;
2953                $newI++;
2954            } else {
2955                # The item is in both lists, so push forward.
2956                $oldI++;
2957                $newI++;
2958            }
2959        }
2960        # Return the result.
2961        return ($inserted, $deleted);
2962    }
2963    
2964    =head3 GetLine
2965    
2966    C<< my @data = Tracer::GetLine($handle); >>
2967    
2968    Read a line of data from a tab-delimited file.
2969    
2970    =over 4
2971    
2972    =item handle
2973    
2974    Open file handle from which to read.
2975    
2976    =item RETURN
2977    
2978    Returns a list of the fields in the record read. The fields are presumed to be
2979    tab-delimited. If we are at the end of the file, then an empty list will be
2980    returned. If an empty line is read, a single list item consisting of a null
2981    string will be returned.
2982    
2983    =back
2984    
2985    =cut
2986    
2987    sub GetLine {
2988        # Get the parameters.
2989        my ($handle) = @_;
2990        # Declare the return variable.
2991        my @retVal = ();
2992        Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2993        # Read from the file.
2994        my $line = <$handle>;
2995        # Only proceed if we found something.
2996        if (defined $line) {
2997            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2998            # upload control and have a nonstandard EOL combination.
2999            $line =~ s/(\r|\n)+$//;
3000            # Here we do some fancy tracing to help in debugging complicated EOL marks.
3001            if (T(File => 4)) {
3002                my $escapedLine = $line;
3003                $escapedLine =~ s/\n/\\n/g;
3004                $escapedLine =~ s/\r/\\r/g;
3005                $escapedLine =~ s/\t/\\t/g;
3006                Trace("Line read: -->$escapedLine<--");
3007            }
3008            # If the line is empty, return a single empty string; otherwise, parse
3009            # it into fields.
3010            if ($line eq "") {
3011                push @retVal, "";
3012            } else {
3013                push @retVal, split /\t/,$line;
3014            }
3015        } else {
3016            # Trace the reason the read failed.
3017            Trace("End of file: $!") if T(File => 3);
3018        }
3019        # Return the result.
3020        return @retVal;
3021    }
3022    
3023    =head3 PutLine
3024    
3025    C<< Tracer::PutLine($handle, \@fields, $eol); >>
3026    
3027    Write a line of data to a tab-delimited file. The specified field values will be
3028    output in tab-separated form, with a trailing new-line.
3029    
3030    =over 4
3031    
3032    =item handle
3033    
3034    Output file handle.
3035    
3036    =item fields
3037    
3038    List of field values.
3039    
3040    =item eol (optional)
3041    
3042    End-of-line character (default is "\n").
3043    
3044    =back
3045    
3046    =cut
3047    
3048    sub PutLine {
3049        # Get the parameters.
3050        my ($handle, $fields, $eol) = @_;
3051        # Write the data.
3052        print $handle join("\t", @{$fields}) . ($eol || "\n");
3053    }
3054    
3055    =head3 GenerateURL
3056    
3057    C<< my $queryUrl = Tracer::GenerateURL($page, %parameters); >>
3058    
3059    Generate a GET-style URL for the specified page with the specified parameter
3060    names and values. The values will be URL-escaped automatically. So, for
3061    example
3062    
3063        Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3064    
3065    would return
3066    
3067        form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3068    
3069    =over 4
3070    
3071    =item page
3072    
3073    Page URL.
3074    
3075    =item parameters
3076    
3077    Hash mapping parameter names to parameter values.
3078    
3079    =item RETURN
3080    
3081    Returns a GET-style URL that goes to the specified page and passes in the
3082    specified parameters and values.
3083    
3084    =back
3085    
3086    =cut
3087    
3088    sub GenerateURL {
3089        # Get the parameters.
3090        my ($page, %parameters) = @_;
3091        # Prime the return variable with the page URL.
3092        my $retVal = $page;
3093        # Loop through the parameters, creating parameter elements in a list.
3094        my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3095        # If the list is nonempty, tack it on.
3096        if (@parmList) {
3097            $retVal .= "?" . join(";", @parmList);
3098        }
3099        # Return the result.
3100        return $retVal;
3101    }
3102    
3103    =head3 ApplyURL
3104    
3105    C<< Tracer::ApplyURL($table, $target, $url); >>
3106    
3107    Run through a two-dimensional table (or more accurately, a list of lists), converting the
3108    I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3109    URL column will be deleted by this process and the target column will be HTML-escaped.
3110    
3111    This provides a simple way to process the results of a database query into something
3112    displayable by combining a URL with text.
3113    
3114    =over 4
3115    
3116    =item table
3117    
3118    Reference to a list of lists. The elements in the containing list will be updated by
3119    this method.
3120    
3121    =item target
3122    
3123    The index of the column to be converted into HTML.
3124    
3125    =item url
3126    
3127    The index of the column containing the URL. Note that the URL must have a recognizable
3128    C<http:> at the beginning.
3129    
3130    =back
3131    
3132    =cut
3133    
3134    sub ApplyURL {
3135        # Get the parameters.
3136        my ($table, $target, $url) = @_;
3137        # Loop through the table.
3138        for my $row (@{$table}) {
3139            # Apply the URL to the target cell.
3140            $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3141            # Delete the URL from the row.
3142            delete $row->[$url];
3143        }
3144    }
3145    
3146    =head3 CombineURL
3147    
3148    C<< my $combinedHtml = Tracer::CombineURL($text, $url); >>
3149    
3150    This method will convert the specified text into HTML hyperlinked to the specified
3151    URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3152    is defined and begins with an C<http:> header.
3153    
3154    =over 4
3155    
3156    =item text
3157    
3158    Text to return. This will be HTML-escaped automatically.
3159    
3160    =item url
3161    
3162    A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3163    will be returned without any hyperlinking.
3164    
3165    =item RETURN
3166    
3167    Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3168    doesn't look right, the HTML-escaped text will be returned without any further
3169    modification.
3170    
3171    =back
3172    
3173    =cut
3174    
3175    sub CombineURL {
3176        # Get the parameters.
3177        my ($text, $url) = @_;
3178        # Declare the return variable.
3179        my $retVal = CGI::escapeHTML($text);
3180        # Verify the URL.
3181        if (defined($url) && $url =~ m!http://!i) {
3182            # It's good, so we apply it to the text.
3183            $retVal = "<a href=\"$url\">$retVal</a>";
3184        }
3185        # Return the result.
3186        return $retVal;
3187    }
3188    
3189    
3190  1;  1;

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