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# Line 1  Line 1 
1    #
2    # Copyright (c) 2003-2006 University of Chicago and Fellowship
3    # for Interpretations of Genomes. All Rights Reserved.
4    #
5    # This file is part of the SEED Toolkit.
6    #
7    # The SEED Toolkit is free software. You can redistribute
8    # it and/or modify it under the terms of the SEED Toolkit
9    # Public License.
10    #
11    # You should have received a copy of the SEED Toolkit Public License
12    # along with this program; if not write to the University of Chicago
13    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14    # Genomes at veronika@thefig.info or download a copy from
15    # http://www.theseed.org/LICENSE.TXT.
16    #
17    
18  package Tracer;  package Tracer;
19    
20      require Exporter;      require Exporter;
21      @ISA = ('Exporter');      @ISA = ('Exporter');
22      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir 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 $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);
1189      # Process according to the destination.      # Process according to the destination.
1190      if ($Destination eq "TEXT") {      if ($Destination eq "TEXT") {
1191          # Write the message to the standard output.          # Write the message to the standard output.
# Line 730  Line 1264 
1264              if (!$package) {              if (!$package) {
1265                  $category = "main";                  $category = "main";
1266              } else {              } else {
1267                  $category = $package;                  my @cats = split /::/, $package;
1268                    $category = $cats[$#cats];
1269              }              }
1270          }          }
1271          # Save the category name.          # Save the category name.
# Line 738  Line 1273 
1273          # Convert it to lower case before we hash it.          # Convert it to lower case before we hash it.
1274          $category = lc $category;          $category = lc $category;
1275          # Use the category and tracelevel to compute the result.          # Use the category and tracelevel to compute the result.
1276            if (ref $traceLevel) {
1277                Confess("Bad trace level.");
1278            } elsif (ref $TraceLevel) {
1279                Confess("Bad trace config.");
1280            }
1281          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));          $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
1282      }      }
1283      # Return the computed result.      # Return the computed result.
# Line 755  Line 1295 
1295    
1296  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>
1297    
1298  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,
1299  B<errors> and B<logFile>. If @words has the following format  B<errors> and B<logFile>. If @words has the following format
1300    
1301  C<< -logFile=error.log apple orange rutabaga >>  C<< -logFile=error.log apple orange rutabaga >>
# Line 769  Line 1309 
1309  C<< apple orange rutabaga >>  C<< apple orange rutabaga >>
1310    
1311  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
1312  support for quote characters.  support for quote characters. Options can be specified with single or double hyphens.
1313    
1314  =over 4  =over 4
1315    
# Line 794  Line 1334 
1334      my ($optionTable, @inputList) = @_;      my ($optionTable, @inputList) = @_;
1335      # Process any options in the input list.      # Process any options in the input list.
1336      my %overrides = ();      my %overrides = ();
1337      while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {      while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1338          # Get the current option.          # Get the current option.
1339          my $arg = shift @inputList;          my $arg = shift @inputList;
1340          # Pull out the option name.          # Pull out the option name.
1341          $arg =~ /^-([^=]*)/g;          $arg =~ /^--?([^=]*)/g;
1342          my $name = $1;          my $name = $1;
1343          # Check for an option value.          # Check for an option value.
1344          if ($arg =~ /\G=(.*)$/g) {          if ($arg =~ /\G=(.*)$/g) {
# Line 824  Line 1364 
1364    
1365  C<< my $codedString = Tracer::Escape($realString); >>  C<< my $codedString = Tracer::Escape($realString); >>
1366    
1367  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
1368  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
1369  doubled. The effect is to exactly reverse the effect of L</UnEscape>.  result is to reverse the effect of L</UnEscape>.
1370    
1371  =over 4  =over 4
1372    
# Line 850  Line 1390 
1390      # Loop through the parameter string, looking for sequences to escape.      # Loop through the parameter string, looking for sequences to escape.
1391      while (length $realString > 0) {      while (length $realString > 0) {
1392          # Look for the first sequence to escape.          # Look for the first sequence to escape.
1393          if ($realString =~ /^(.*?)([ \n\t\\])/) {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1394              # 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
1395              # 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.
1396              $retVal .= $1;              $retVal .= $1;
1397              # Strip the processed section off the real string.              # Strip the processed section off the real string.
1398              $realString = substr $realString, (length $2) + (length $1);              $realString = substr $realString, (length $2) + (length $1);
1399              # Encode the escape sequence.              # Get the matched character.
1400              my $char = $2;              my $char = $2;
1401              $char =~ tr/ \t\n/btn/;              # If we have a CR, we are done.
1402                if ($char ne "\r") {
1403                    # It's not a CR, so encode the escape sequence.
1404                    $char =~ tr/\t\n/tn/;
1405              $retVal .= "\\" . $char;              $retVal .= "\\" . $char;
1406                }
1407          } else {          } else {
1408              # 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
1409              # transferred unmodified.              # transferred unmodified.
# Line 875  Line 1419 
1419    
1420  C<< my $realString = Tracer::UnEscape($codedString); >>  C<< my $realString = Tracer::UnEscape($codedString); >>
1421    
1422  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
1423  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
1424    be deleted.
1425    
1426  =over 4  =over 4
1427    
# Line 896  Line 1441 
1441  sub UnEscape {  sub UnEscape {
1442      # Get the parameter.      # Get the parameter.
1443      my ($codedString) = @_;      my ($codedString) = @_;
     Tracer("Coded string is \"$codedString\".") if T(4);  
1444      # Initialize the return variable.      # Initialize the return variable.
1445      my $retVal = "";      my $retVal = "";
1446      # Only proceed if the incoming string is nonempty.      # Only proceed if the incoming string is nonempty.
1447      if (defined $codedString) {      if (defined $codedString) {
1448          # 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
1449          # translating because it causes problems with the escaped slash. ("\\b" becomes          # translating because it causes problems with the escaped slash. ("\\t" becomes
1450          # "\ " no matter what we do.)          # "\<tab>" no matter what we do.)
1451          while (length $codedString > 0) {          while (length $codedString > 0) {
1452              # Look for the first escape sequence.              # Look for the first escape sequence.
1453              if ($codedString =~ /^(.*?)\\(\\|b|n|t)/) {              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
1454                  # 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
1455                  # 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.
1456                  $retVal .= $1;                  $retVal .= $1;
1457                  $codedString = substr $codedString, (2 + length $1);                  $codedString = substr $codedString, (2 + length $1);
1458                  # Decode the escape sequence.                  # Get the escape value.
1459                  my $char = $2;                  my $char = $2;
1460                  $char =~ tr/\\btn/\\ \t\n/;                  # If we have a "\r", we are done.
1461                    if ($char ne 'r') {
1462                        # Here it's not an 'r', so we convert it.
1463                        $char =~ tr/\\tn/\\\t\n/;
1464                  $retVal .= $char;                  $retVal .= $char;
1465                    }
1466              } else {              } else {
1467                  # 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
1468                  # transferred unmodified.                  # transferred unmodified.
# Line 1020  Line 1568 
1568      return @inputList;      return @inputList;
1569  }  }
1570    
1571    =head3 Percent
1572    
1573    C<< my $percent = Tracer::Percent($number, $base); >>
1574    
1575    Returns the percent of the base represented by the given number. If the base
1576    is zero, returns zero.
1577    
1578    =over 4
1579    
1580    =item number
1581    
1582    Percent numerator.
1583    
1584    =item base
1585    
1586    Percent base.
1587    
1588    =item RETURN
1589    
1590    Returns the percentage of the base represented by the numerator.
1591    
1592    =back
1593    
1594    =cut
1595    
1596    sub Percent {
1597        # Get the parameters.
1598        my ($number, $base) = @_;
1599        # Declare the return variable.
1600        my $retVal = 0;
1601        # Compute the percent.
1602        if ($base != 0) {
1603            $retVal = $number * 100 / $base;
1604        }
1605        # Return the result.
1606        return $retVal;
1607    }
1608    
1609  =head3 GetFile  =head3 GetFile
1610    
1611  C<< my @fileContents = Tracer::GetFile($fileName); >>  C<< my @fileContents = Tracer::GetFile($fileName); >>
1612    
1613  Return the entire contents of a file.      or
1614    
1615    C<< my $fileContents = Tracer::GetFile($fileName); >>
1616    
1617    Return the entire contents of a file. In list context, line-ends are removed and
1618    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1619    
1620  =over 4  =over 4
1621    
# Line 1035  Line 1626 
1626  =item RETURN  =item RETURN
1627    
1628  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.
1629  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
1630    the file, an empty list will be returned.
1631    
1632  =back  =back
1633    
# Line 1047  Line 1639 
1639      # Declare the return variable.      # Declare the return variable.
1640      my @retVal = ();      my @retVal = ();
1641      # Open the file for input.      # Open the file for input.
1642      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 {  
1643          # Read the whole file into the return variable, stripping off any terminator          # Read the whole file into the return variable, stripping off any terminator
1644          # characters.          # characters.
1645          my $lineCount = 0;          my $lineCount = 0;
1646          while (my $line = <INPUTFILE>) {      while (my $line = <$handle>) {
1647              $lineCount++;              $lineCount++;
1648              $line = Strip($line);              $line = Strip($line);
1649              push @retVal, $line;              push @retVal, $line;
1650          }          }
1651          # Close it.          # Close it.
1652          close INPUTFILE;      close $handle;
1653          my $actualLines = @retVal;          my $actualLines = @retVal;
1654      }      Trace("$actualLines lines read from file $fileName.") if T(File => 2);
1655      # Return the file's contents in the desired format.      # Return the file's contents in the desired format.
1656      if (wantarray) {      if (wantarray) {
1657          return @retVal;          return @retVal;
# Line 1072  Line 1660 
1660      }      }
1661  }  }
1662    
1663    =head3 PutFile
1664    
1665    C<< Tracer::PutFile($fileName, \@lines); >>
1666    
1667    Write out a file from a list of lines of text.
1668    
1669    =over 4
1670    
1671    =item fileName
1672    
1673    Name of the output file.
1674    
1675    =item lines
1676    
1677    Reference to a list of text lines. The lines will be written to the file in order, with trailing
1678    new-line characters. Alternatively, may be a string, in which case the string will be written without
1679    modification.
1680    
1681    =back
1682    
1683    =cut
1684    
1685    sub PutFile {
1686        # Get the parameters.
1687        my ($fileName, $lines) = @_;
1688        # Open the output file.
1689        my $handle = Open(undef, ">$fileName");
1690        # Count the lines written.
1691        if (ref $lines ne 'ARRAY') {
1692            # Here we have a scalar, so we write it raw.
1693            print $handle $lines;
1694            Trace("Scalar put to file $fileName.") if T(File => 3);
1695        } else {
1696            # Write the lines one at a time.
1697            my $count = 0;
1698            for my $line (@{$lines}) {
1699                print $handle "$line\n";
1700                $count++;
1701            }
1702            Trace("$count lines put to file $fileName.") if T(File => 3);
1703        }
1704        # Close the output file.
1705        close $handle;
1706    }
1707    
1708  =head3 QTrace  =head3 QTrace
1709    
1710  C<< my $data = QTrace($format); >>  C<< my $data = QTrace($format); >>
# Line 1140  Line 1773 
1773  sub Confess {  sub Confess {
1774      # Get the parameters.      # Get the parameters.
1775      my ($message) = @_;      my ($message) = @_;
1776        if (! defined($FIG_Config::no_tool_hdr)) {
1777            # Here we have a tool header. Display its length so that the user can adjust the line numbers.
1778            my @lines = GetFile("$FIG_Config::common_runtime/tool_hdr");
1779            Trace("Tool header has " . scalar(@lines) . " lines.");
1780        }
1781      # Trace the call stack.      # Trace the call stack.
1782      Cluck($message);      Cluck($message);
1783      # Abort the program.      # Abort the program.
# Line 1151  Line 1789 
1789  C<< Assert($condition1, $condition2, ... $conditionN); >>  C<< Assert($condition1, $condition2, ... $conditionN); >>
1790    
1791  Return TRUE if all the conditions are true. This method can be used in conjunction with  Return TRUE if all the conditions are true. This method can be used in conjunction with
1792  the OR operator and the L</Confess> method, B<Assert> can function as a debugging assert.  the OR operator and the L</Confess> method as a debugging assert.
1793  So, for example  So, for example
1794    
1795  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
# Line 1272  Line 1910 
1910    
1911  =head3 AddToListMap  =head3 AddToListMap
1912    
1913  C<< Tracer::AddToListMap(\%hash, $key, $value); >>  C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>
1914    
1915  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list  Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list
1916  is created for the key. Otherwise, the new value is pushed onto the list.  is created for the key. Otherwise, the new value is pushed onto the list.
# Line 1287  Line 1925 
1925    
1926  Key for which the value is to be added.  Key for which the value is to be added.
1927    
1928  =item value  =item value1, value2, ... valueN
1929    
1930  Value to add to the key's value list.  List of values to add to the key's value list.
1931    
1932  =back  =back
1933    
# Line 1297  Line 1935 
1935    
1936  sub AddToListMap {  sub AddToListMap {
1937      # Get the parameters.      # Get the parameters.
1938      my ($hash, $key, $value) = @_;      my ($hash, $key, @values) = @_;
1939      # Process according to whether or not the key already has a value.      # Process according to whether or not the key already has a value.
1940      if (! exists $hash->{$key}) {      if (! exists $hash->{$key}) {
1941          $hash->{$key} = [$value];          $hash->{$key} = [@values];
1942      } else {      } else {
1943          push @{$hash->{$key}}, $value;          push @{$hash->{$key}}, @values;
1944      }      }
1945  }  }
1946    
# Line 1310  Line 1948 
1948    
1949  C<< if (Tracer::DebugMode) { ...code... } >>  C<< if (Tracer::DebugMode) { ...code... } >>
1950    
1951  Return TRUE if debug mode has been turned on, else output an error  Return TRUE if debug mode has been turned on, else abort.
 page and return FALSE.  
1952    
1953  Certain CGI scripts are too dangerous to exist in the production  Certain CGI scripts are too dangerous to exist in the production
1954  environment. This method provides a simple way to prevent them  environment. This method provides a simple way to prevent them
1955  from working unless they are explicitly turned on by creating a password  from working unless they are explicitly turned on by creating a password
1956  cookie via the B<SetPassword> script.  If debugging mode  cookie via the B<SetPassword> script.  If debugging mode
1957  is not turned on, an error web page will be output directing the  is not turned on, an error will occur.
 user to enter in the correct password.  
1958    
1959  =cut  =cut
1960    
# Line 1331  Line 1967 
1967      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {      if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1968          $retVal = 1;          $retVal = 1;
1969      } else {      } else {
1970          # Here debug mode is off, so we generate an error page.          # Here debug mode is off, so we generate an error.
1971          my $pageString = PageBuilder::Build("<Html/ErrorPage.html", {}, "Html");          Confess("Cannot use this facility without logging in.");
         print $pageString;  
1972      }      }
1973      # Return the determination indicator.      # Return the determination indicator.
1974      return $retVal;      return $retVal;
# Line 1364  Line 1999 
1999  sub Strip {  sub Strip {
2000      # Get a copy of the parameter string.      # Get a copy of the parameter string.
2001      my ($string) = @_;      my ($string) = @_;
2002      my $retVal = $string;      my $retVal = (defined $string ? $string : "");
2003      # Strip the line terminator characters.      # Strip the line terminator characters.
2004      $retVal =~ s/(\r|\n)+$//g;      $retVal =~ s/(\r|\n)+$//g;
2005      # Return the result.      # Return the result.
# Line 1432  Line 2067 
2067      return $retVal;      return $retVal;
2068  }  }
2069    
2070    =head3 EOF
2071    
2072    This is a constant that is lexically greater than any useful string.
2073    
2074    =cut
2075    
2076    sub EOF {
2077        return "\xFF\xFF\xFF\xFF\xFF";
2078    }
2079    
2080  =head3 TICK  =head3 TICK
2081    
2082  C<< my @results = TICK($commandString); >>  C<< my @results = TICK($commandString); >>
# Line 1473  Line 2118 
2118      return `$commandString`;      return `$commandString`;
2119  }  }
2120    
2121    =head3 ScriptSetup
2122    
2123    C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>
2124    
2125    Perform standard tracing and debugging setup for scripts. The value returned is
2126    the CGI object followed by a pre-built variable hash. At the end of the script,
2127    the client should call L</ScriptFinish> to output the web page.
2128    
2129    This method calls L</ETracing> to configure tracing, which allows the tracing
2130    to be configured via the emergency tracing form on the debugging control panel.
2131    Tracing will then be turned on automatically for all programs that use the L</ETracing>
2132    method, which includes every program that uses this method or L</StandardSetup>.
2133    
2134    =over 4
2135    
2136    =item noTrace (optional)
2137    
2138    If specified, tracing will be suppressed. This is useful if the script wants to set up
2139    tracing manually.
2140    
2141    =item RETURN
2142    
2143    Returns a two-element list consisting of a CGI query object and a variable hash for
2144    the output page.
2145    
2146    =back
2147    
2148    =cut
2149    
2150    sub ScriptSetup {
2151        # Get the parameters.
2152        my ($noTrace) = @_;
2153        # Get the CGI query object.
2154        my $cgi = CGI->new();
2155        # Set up tracing if it's not suppressed.
2156        ETracing($cgi) unless $noTrace;
2157        # Create the variable hash.
2158        my $varHash = { results => '' };
2159        # Return the query object and variable hash.
2160        return ($cgi, $varHash);
2161    }
2162    
2163    =head3 ETracing
2164    
2165    C<< ETracing($parameter); >>
2166    
2167    Set up emergency tracing. Emergency tracing is tracing that is turned
2168    on automatically for any program that calls this method. The emergency
2169    tracing parameters are stored in a a file identified by a tracing key.
2170    If this method is called with a CGI object, then the tracing key is
2171    taken from a cookie. If it is called with no parameters, then the tracing
2172    key is taken from an environment variable. If it is called with a string,
2173    the tracing key is that string.
2174    
2175    =over 4
2176    
2177    =item parameter
2178    
2179    A parameter from which the tracing key is computed. If it is a scalar,
2180    that scalar is used as the tracing key. If it is a CGI object, the
2181    tracing key is taken from the C<IP> cookie. If it is omitted, the
2182    tracing key is taken from the C<TRACING> environment variable. If it
2183    is a CGI object and emergency tracing is not on, the C<Trace> and
2184    C<TF> parameters will be used to determine the type of tracing.
2185    
2186    =back
2187    
2188    =cut
2189    
2190    sub ETracing {
2191        # Get the parameter.
2192        my ($parameter) = @_;
2193        # Check for CGI mode.
2194        my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
2195        # Default to no tracing except errors.
2196        my ($tracing, $dest) = ("0", "WARN");
2197        # Check for emergency tracing.
2198        my $tkey = EmergencyKey($parameter);
2199        my $emergencyFile = EmergencyFileName($tkey);
2200        if (-e $emergencyFile) {
2201            # We have the file. Read in the data.
2202            my @tracing = GetFile($emergencyFile);
2203            # Pull off the time limit.
2204            my $expire = shift @tracing;
2205            # Convert it to seconds.
2206            $expire *= 3600;
2207            # Check the file data.
2208            my $stat = stat($emergencyFile);
2209            my ($now) = gettimeofday;
2210            if ($now - $stat->mtime > $expire) {
2211                # Delete the expired file.
2212                unlink $emergencyFile;
2213            } else {
2214                # Emergency tracing is on. Pull off the destination and
2215                # the trace level;
2216                $dest = shift @tracing;
2217                my $level = shift @tracing;
2218                # Convert the destination to a real tracing destination.
2219                # temp directory.
2220                $dest = EmergencyTracingDest($tkey, $dest);
2221                # Insure Tracer is specified.
2222                my %moduleHash = map { $_ => 1 } @tracing;
2223                $moduleHash{Tracer} = 1;
2224                # Set the trace parameter.
2225                $tracing = join(" ", $level, sort keys %moduleHash);
2226            }
2227        } elsif (defined $cgi) {
2228            # There's no emergency tracing, but we have a CGI object, so check
2229            # for tracing from the form parameters.
2230            if ($cgi->param('Trace')) {
2231                # Here the user has requested tracing via a form.
2232                $dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
2233                $tracing = $cgi->param('Trace') . " Tracer";
2234            }
2235        }
2236        # Setup the tracing we've determined from all the stuff above.
2237        TSetup($tracing, $dest);
2238        # If we're a web script, trace the parameter and environment data.
2239        if (defined $cgi) {
2240            TraceParms($cgi);
2241        }
2242    }
2243    
2244    =head3 EmergencyFileName
2245    
2246    C<< my $fileName = Tracer::EmergencyFileName($tkey); >>
2247    
2248    Return the emergency tracing file name. This is the file that specifies
2249    the tracing information.
2250    
2251    =over 4
2252    
2253    =item tkey
2254    
2255    Tracing key for the current program.
2256    
2257    =item RETURN
2258    
2259    Returns the name of the file to contain the emergency tracing information.
2260    
2261    =back
2262    
2263    =cut
2264    
2265    sub EmergencyFileName {
2266        # Get the parameters.
2267        my ($tkey) = @_;
2268        # Compute the emergency tracing file name.
2269        return "$FIG_Config::temp/Emergency$tkey.txt";
2270    }
2271    
2272    =head3 EmergencyFileTarget
2273    
2274    C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>
2275    
2276    Return the emergency tracing target file name. This is the file that receives
2277    the tracing output for file-based tracing.
2278    
2279    =over 4
2280    
2281    =item tkey
2282    
2283    Tracing key for the current program.
2284    
2285    =item RETURN
2286    
2287    Returns the name of the file to contain the trace output.
2288    
2289    =back
2290    
2291    =cut
2292    
2293    sub EmergencyFileTarget {
2294        # Get the parameters.
2295        my ($tkey) = @_;
2296        # Compute the emergency tracing file name.
2297        return "$FIG_Config::temp/trace$tkey.log";
2298    }
2299    
2300    =head3 EmergencyTracingDest
2301    
2302    C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>
2303    
2304    This method converts an emergency tracing destination to a real
2305    tracing destination. The main difference is that if the
2306    destination is C<FILE> or C<APPEND>, we convert it to file
2307    output. If the destination is C<DUAL>, we convert it to file
2308    and standard output.
2309    
2310    =over 4
2311    
2312    =item tkey
2313    
2314    Tracing key for this environment.
2315    
2316    =item myDest
2317    
2318    Destination from the emergency tracing file.
2319    
2320    =item RETURN
2321    
2322    Returns a destination that can be passed into L</TSetup>.
2323    
2324    =back
2325    
2326    =cut
2327    
2328    sub EmergencyTracingDest {
2329        # Get the parameters.
2330        my ($tkey, $myDest) = @_;
2331        # Declare the return variable.
2332        my $retVal = $myDest;
2333        # Process according to the destination value.
2334        if ($myDest eq 'FILE') {
2335            $retVal = ">" . EmergencyFileTarget($tkey);
2336        } elsif ($myDest eq 'APPEND') {
2337            $retVal = ">>" . EmergencyFileTarget($tkey);
2338        } elsif ($myDest eq 'DUAL') {
2339            $retVal = "+>" . EmergencyFileTarget($tkey);
2340        }
2341        # Return the result.
2342        return $retVal;
2343    }
2344    
2345    =head3 Emergency
2346    
2347    C<< Emergency($key, $hours, $dest, $level, @modules); >>
2348    
2349    Turn on emergency tracing. This method is normally invoked over the web from
2350    a debugging console, but it can also be called by the C<trace.pl> script.
2351    The caller specifies the duration of the emergency in hours, the desired tracing
2352    destination, the trace level, and a list of the trace modules to activate.
2353    For the length of the duration, when a program in an environment with the
2354    specified tracing key active invokes a Sprout CGI script, tracing will be
2355    turned on automatically. See L</TSetup> for more about tracing setup and
2356    L</ETracing> for more about emergency tracing.
2357    
2358    =over 4
2359    
2360    =item tkey
2361    
2362    The tracing key. This is used to identify the control file and the trace file.
2363    
2364    =item hours
2365    
2366    Number of hours to keep emergency tracing alive.
2367    
2368    =item dest
2369    
2370    Tracing destination. If no path information is specified for a file
2371    destination, it is put in the FIG temporary directory.
2372    
2373    =item level
2374    
2375    Tracing level. A higher level means more trace messages.
2376    
2377    =item modules
2378    
2379    A list of the tracing modules to activate.
2380    
2381    =back
2382    
2383    =cut
2384    
2385    sub Emergency {
2386        # Get the parameters.
2387        my ($tkey, $hours, $dest, $level, @modules) = @_;
2388        # Create the emergency file.
2389        my $specFile = EmergencyFileName($tkey);
2390        my $outHandle = Open(undef, ">$specFile");
2391        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
2392    }
2393    
2394    =head3 EmergencyKey
2395    
2396    C<< my $tkey = EmergencyKey($parameter); >>
2397    
2398    Return the Key to be used for emergency tracing. This could be an IP address,
2399     a session ID, or a user name, depending on the environment.
2400    
2401    =over 4
2402    
2403    =item parameter
2404    
2405    Parameter defining the method for finding the tracing key. If it is a scalar,
2406    then it is presumed to be the tracing key itself. If it is a CGI object, then
2407    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
2408    taken from the C<TRACING> environment variable.
2409    
2410    =item RETURN
2411    
2412    Returns the key to be used for labels in emergency tracing.
2413    
2414    =back
2415    
2416    =cut
2417    
2418    sub EmergencyKey {
2419        # Get the parameters.
2420        my ($parameter) = @_;
2421        # Declare the return variable.
2422        my $retVal;
2423        # Determine the parameter type.
2424        if (! defined $parameter) {
2425            # Here we're supposed to check the environment.
2426            $retVal = $ENV{TRACING};
2427        } else {
2428            my $ptype = ref $parameter;
2429            if ($ptype eq 'CGI') {
2430                # Here we were invoked from a web page. Look for a cookie.
2431                $retVal = $parameter->cookie('IP');
2432            } elsif (! $ptype) {
2433                # Here the key was passed in.
2434                $retVal = $parameter;
2435            }
2436        }
2437        # If no luck finding a key, use the PID.
2438        if (! defined $retVal) {
2439            $retVal = $$;
2440        }
2441        # Return the result.
2442        return $retVal;
2443    }
2444    
2445    
2446    =head3 TraceParms
2447    
2448    C<< Tracer::TraceParms($cgi); >>
2449    
2450    Trace the CGI parameters at trace level CGI => 3 and the environment variables
2451    at level CGI => 4.
2452    
2453    =over 4
2454    
2455    =item cgi
2456    
2457    CGI query object containing the parameters to trace.
2458    
2459    =back
2460    
2461    =cut
2462    
2463    sub TraceParms {
2464        # Get the parameters.
2465        my ($cgi) = @_;
2466        if (T(CGI => 3)) {
2467            # Here we want to trace the parameter data.
2468            my @names = $cgi->param;
2469            for my $parmName (sort @names) {
2470                # Note we skip the Trace parameters, which are for our use only.
2471                if ($parmName ne 'Trace' && $parmName ne 'TF') {
2472                    my @values = $cgi->param($parmName);
2473                    Trace("CGI: $parmName = " . join(", ", @values));
2474                }
2475            }
2476            # Display the request method.
2477            my $method = $cgi->request_method();
2478            Trace("Method: $method");
2479        }
2480        if (T(CGI => 4)) {
2481            # Here we want the environment data too.
2482            for my $envName (sort keys %ENV) {
2483                Trace("ENV: $envName = $ENV{$envName}");
2484            }
2485        }
2486    }
2487    
2488    =head3 ScriptFinish
2489    
2490    C<< ScriptFinish($webData, $varHash); >>
2491    
2492    Output a web page at the end of a script. Either the string to be output or the
2493    name of a template file can be specified. If the second parameter is omitted,
2494    it is assumed we have a string to be output; otherwise, it is assumed we have the
2495    name of a template file. The template should have the variable C<DebugData>
2496    specified in any form that invokes a standard script. If debugging mode is turned
2497    on, a form field will be put in that allows the user to enter tracing data.
2498    Trace messages will be placed immediately before the terminal C<BODY> tag in
2499    the output, formatted as a list.
2500    
2501    A typical standard script would loook like the following.
2502    
2503        BEGIN {
2504            # Print the HTML header.
2505            print "CONTENT-TYPE: text/html\n\n";
2506        }
2507        use Tracer;
2508        use CGI;
2509        use FIG;
2510        # ... more uses ...
2511    
2512        my ($cgi, $varHash) = ScriptSetup();
2513        eval {
2514            # ... get data from $cgi, put it in $varHash ...
2515        };
2516        if ($@) {
2517            Trace("Script Error: $@") if T(0);
2518        }
2519        ScriptFinish("Html/MyTemplate.html", $varHash);
2520    
2521    The idea here is that even if the script fails, you'll see trace messages and
2522    useful output.
2523    
2524    =over 4
2525    
2526    =item webData
2527    
2528    A string containing either the full web page to be written to the output or the
2529    name of a template file from which the page is to be constructed. If the name
2530    of a template file is specified, then the second parameter must be present;
2531    otherwise, it must be absent.
2532    
2533    =item varHash (optional)
2534    
2535    If specified, then a reference to a hash mapping variable names for a template
2536    to their values. The template file will be read into memory, and variable markers
2537    will be replaced by data in this hash reference.
2538    
2539    =back
2540    
2541    =cut
2542    
2543    sub ScriptFinish {
2544        # Get the parameters.
2545        my ($webData, $varHash) = @_;
2546        # Check for a template file situation.
2547        my $outputString;
2548        if (defined $varHash) {
2549            # Here we have a template file. We need to determine the template type.
2550            my $template;
2551            if ($FIG_Config::template_url && $webData =~ /\.php$/) {
2552                $template = "$FIG_Config::template_url/$webData";
2553            } else {
2554                $template = "<<$webData";
2555            }
2556            $outputString = PageBuilder::Build($template, $varHash, "Html");
2557        } else {
2558            # Here the user gave us a raw string.
2559            $outputString = $webData;
2560        }
2561        # Check for trace messages.
2562        if ($Destination ne "NONE" && $TraceLevel > 0) {
2563            # We have trace messages, so we want to put them at the end of the body. This
2564            # is either at the end of the whole string or at the beginning of the BODY
2565            # end-tag.
2566            my $pos = length $outputString;
2567            if ($outputString =~ m#</body>#gi) {
2568                $pos = (pos $outputString) - 7;
2569            }
2570            # If the trace messages were queued, we unroll them. Otherwise, we display the
2571            # destination.
2572            my $traceHtml;
2573            if ($Destination eq "QUEUE") {
2574                $traceHtml = QTrace('Html');
2575            } elsif ($Destination =~ /^>>(.+)$/) {
2576                # Here the tracing output it to a file. We code it as a hyperlink so the user
2577                # can copy the file name into the clipboard easily.
2578                my $actualDest = $1;
2579                $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
2580            } else {
2581                # Here we have one of the special destinations.
2582                $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
2583            }
2584            substr $outputString, $pos, 0, $traceHtml;
2585        }
2586        # Write the output string.
2587        print $outputString;
2588    }
2589    
2590    =head3 Insure
2591    
2592    C<< Insure($dirName); >>
2593    
2594    Insure a directory is present.
2595    
2596    =over 4
2597    
2598    =item dirName
2599    
2600    Name of the directory to check. If it does not exist, it will be created.
2601    
2602    =back
2603    
2604    =cut
2605    
2606    sub Insure {
2607        my ($dirName) = @_;
2608        if (! -d $dirName) {
2609            Trace("Creating $dirName directory.") if T(File => 2);
2610            eval { mkpath $dirName; };
2611            if ($@) {
2612                Confess("Error creating $dirName: $@");
2613            }
2614        }
2615    }
2616    
2617    =head3 ChDir
2618    
2619    C<< ChDir($dirName); >>
2620    
2621    Change to the specified directory.
2622    
2623    =over 4
2624    
2625    =item dirName
2626    
2627    Name of the directory to which we want to change.
2628    
2629    =back
2630    
2631    =cut
2632    
2633    sub ChDir {
2634        my ($dirName) = @_;
2635        if (! -d $dirName) {
2636            Confess("Cannot change to directory $dirName: no such directory.");
2637        } else {
2638            Trace("Changing to directory $dirName.") if T(File => 4);
2639            my $okFlag = chdir $dirName;
2640            if (! $okFlag) {
2641                Confess("Error switching to directory $dirName.");
2642            }
2643        }
2644    }
2645    
2646    =head3 SendSMS
2647    
2648    C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>
2649    
2650    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
2651    user name, password, and API ID for the relevant account in the hash reference variable
2652    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
2653    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
2654    is C<2561022>, then the FIG_Config file must contain
2655    
2656        $phone =  { user => 'BruceTheHumanPet',
2657                    password => 'silly',
2658                    api_id => '2561022' };
2659    
2660    The original purpose of this method was to insure Bruce would be notified immediately when the
2661    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
2662    when you call this method.
2663    
2664    The message ID will be returned if successful, and C<undef> if an error occurs.
2665    
2666    =over 4
2667    
2668    =item phoneNumber
2669    
2670    Phone number to receive the message, in international format. A United States phone number
2671    would be prefixed by "1". A British phone number would be prefixed by "44".
2672    
2673    =item msg
2674    
2675    Message to send to the specified phone.
2676    
2677    =item RETURN
2678    
2679    Returns the message ID if successful, and C<undef> if the message could not be sent.
2680    
2681    =back
2682    
2683    =cut
2684    
2685    sub SendSMS {
2686        # Get the parameters.
2687        my ($phoneNumber, $msg) = @_;
2688        # Declare the return variable. If we do not change it, C<undef> will be returned.
2689        my $retVal;
2690        # Only proceed if we have phone support.
2691        if (! defined $FIG_Config::phone) {
2692            Trace("Phone support not present in FIG_Config.") if T(1);
2693        } else {
2694            # Get the phone data.
2695            my $parms = $FIG_Config::phone;
2696            # Get the Clickatell URL.
2697            my $url = "http://api.clickatell.com/http/";
2698            # Create the user agent.
2699            my $ua = LWP::UserAgent->new;
2700            # Request a Clickatell session.
2701            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
2702                                         password => $parms->{password},
2703                                         api_id => $parms->{api_id},
2704                                         to => $phoneNumber,
2705                                         text => $msg});
2706            # Check for an error.
2707            if (! $resp->is_success) {
2708                Trace("Alert failed.") if T(1);
2709            } else {
2710                # Get the message ID.
2711                my $rstring = $resp->content;
2712                if ($rstring =~ /^ID:\s+(.*)$/) {
2713                    $retVal = $1;
2714                } else {
2715                    Trace("Phone attempt failed with $rstring") if T(1);
2716                }
2717            }
2718        }
2719        # Return the result.
2720        return $retVal;
2721    }
2722    
2723    =head3 CommaFormat
2724    
2725    C<< my $formatted = Tracer::CommaFormat($number); >>
2726    
2727    Insert commas into a number.
2728    
2729    =over 4
2730    
2731    =item number
2732    
2733    A sequence of digits.
2734    
2735    =item RETURN
2736    
2737    Returns the same digits with commas strategically inserted.
2738    
2739    =back
2740    
2741    =cut
2742    
2743    sub CommaFormat {
2744        # Get the parameters.
2745        my ($number) = @_;
2746        # Pad the length up to a multiple of three.
2747        my $padded = "$number";
2748        $padded = " " . $padded while length($padded) % 3 != 0;
2749        # This is a fancy PERL trick. The parentheses in the SPLIT pattern
2750        # cause the delimiters to be included in the output stream. The
2751        # GREP removes the empty strings in between the delimiters.
2752        my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
2753        # Clean out the spaces.
2754        $retVal =~ s/ //g;
2755        # Return the result.
2756        return $retVal;
2757    }
2758    =head3 SetPermissions
2759    
2760    C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>
2761    
2762    Set the permissions for a directory and all the files and folders inside it.
2763    In addition, the group ownership will be changed to the specified value.
2764    
2765    This method is more vulnerable than most to permission and compatability
2766    problems, so it does internal error recovery.
2767    
2768    =over 4
2769    
2770    =item dirName
2771    
2772    Name of the directory to process.
2773    
2774    =item group
2775    
2776    Name of the group to be assigned.
2777    
2778    =item mask
2779    
2780    Permission mask. Bits that are C<1> in this mask will be ORed into the
2781    permission bits of any file or directory that does not already have them
2782    set to 1.
2783    
2784    =item otherMasks
2785    
2786    Map of search patterns to permission masks. If a directory name matches
2787    one of the patterns, that directory and all its members and subdirectories
2788    will be assigned the new pattern. For example, the following would
2789    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2790    
2791        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2792    
2793    The list is ordered, so the following would use 0777 for C<tmp1> and
2794    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2795    
2796        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2797                                                       '^tmp' => 0666);
2798    
2799    Note that the pattern matches are all case-insensitive, and only directory
2800    names are matched, not file names.
2801    
2802    =back
2803    
2804    =cut
2805    
2806    sub SetPermissions {
2807        # Get the parameters.
2808        my ($dirName, $group, $mask, @otherMasks) = @_;
2809        # Set up for error recovery.
2810        eval {
2811            # Switch to the specified directory.
2812            ChDir($dirName);
2813            # Get the group ID.
2814            my $gid = getgrnam($group);
2815            # Get the mask for tracing.
2816            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2817            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2818            my $fixCount = 0;
2819            my $lookCount = 0;
2820            # @dirs will be a stack of directories to be processed.
2821            my @dirs = (getcwd());
2822            while (scalar(@dirs) > 0) {
2823                # Get the current directory.
2824                my $dir = pop @dirs;
2825                # Check for a match to one of the specified directory names. To do
2826                # that, we need to pull the individual part of the name off of the
2827                # whole path.
2828                my $simpleName = $dir;
2829                if ($dir =~ m!/([^/]+)$!) {
2830                    $simpleName = $1;
2831                }
2832                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2833                # Search for a match.
2834                my $match = 0;
2835                my $i;
2836                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2837                    my $pattern = $otherMasks[$i];
2838                    if ($simpleName =~ /$pattern/i) {
2839                        $match = 1;
2840                    }
2841                }
2842                # Check for a match. Note we use $i-1 because the loop added 2
2843                # before terminating due to the match.
2844                if ($match && $otherMasks[$i-1] != $mask) {
2845                    # This directory matches one of the incoming patterns, and it's
2846                    # a different mask, so we process it recursively with that mask.
2847                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2848                } else {
2849                    # Here we can process normally. Get all of the non-hidden members.
2850                    my @submems = OpenDir($dir, 1);
2851                    for my $submem (@submems) {
2852                        # Get the full name.
2853                        my $thisMem = "$dir/$submem";
2854                        Trace("Checking member $thisMem.") if T(4);
2855                        $lookCount++;
2856                        if ($lookCount % 1000 == 0) {
2857                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2858                        }
2859                        # Fix the group.
2860                        chown -1, $gid, $thisMem;
2861                        # Insure this member is not a symlink.
2862                        if (! -l $thisMem) {
2863                            # Get its info.
2864                            my $fileInfo = stat $thisMem;
2865                            # Only proceed if we got the info. Otherwise, it's a hard link
2866                            # and we want to skip it anyway.
2867                            if ($fileInfo) {
2868                                my $fileMode = $fileInfo->mode;
2869                                if (($fileMode & $mask) != $mask) {
2870                                    # Fix this member.
2871                                    $fileMode |= $mask;
2872                                    chmod $fileMode, $thisMem;
2873                                    $fixCount++;
2874                                }
2875                                # If it's a subdirectory, stack it.
2876                                if (-d $thisMem) {
2877                                    push @dirs, $thisMem;
2878                                }
2879                            }
2880                        }
2881                    }
2882                }
2883            }
2884            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2885        };
2886        # Check for an error.
2887        if ($@) {
2888            Confess("SetPermissions error: $@");
2889        }
2890    }
2891    
2892    =head3 CompareLists
2893    
2894    C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>
2895    
2896    Compare two lists of tuples, and return a hash analyzing the differences. The lists
2897    are presumed to be sorted alphabetically by the value in the $keyIndex column.
2898    The return value contains a list of items that are only in the new list
2899    (inserted) and only in the old list (deleted).
2900    
2901    =over 4
2902    
2903    =item newList
2904    
2905    Reference to a list of new tuples.
2906    
2907    =item oldList
2908    
2909    Reference to a list of old tuples.
2910    
2911    =item keyIndex (optional)
2912    
2913    Index into each tuple of its key field. The default is 0.
2914    
2915    =item RETURN
2916    
2917    Returns a 2-tuple consisting of a reference to the list of items that are only in the new
2918    list (inserted) followed by a reference to the list of items that are only in the old
2919    list (deleted).
2920    
2921    =back
2922    
2923    =cut
2924    
2925    sub CompareLists {
2926        # Get the parameters.
2927        my ($newList, $oldList, $keyIndex) = @_;
2928        if (! defined $keyIndex) {
2929            $keyIndex = 0;
2930        }
2931        # Declare the return variables.
2932        my ($inserted, $deleted) = ([], []);
2933        # Loop through the two lists simultaneously.
2934        my ($newI, $oldI) = (0, 0);
2935        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
2936        while ($newI < $newN || $oldI < $oldN) {
2937            # Get the current object in each list. Note that if one
2938            # of the lists is past the end, we'll get undef.
2939            my $newItem = $newList->[$newI];
2940            my $oldItem = $oldList->[$oldI];
2941            if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
2942                # The old item is not in the new list, so mark it deleted.
2943                push @{$deleted}, $oldItem;
2944                $oldI++;
2945            } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
2946                # The new item is not in the old list, so mark it inserted.
2947                push @{$inserted}, $newItem;
2948                $newI++;
2949            } else {
2950                # The item is in both lists, so push forward.
2951                $oldI++;
2952                $newI++;
2953            }
2954        }
2955        # Return the result.
2956        return ($inserted, $deleted);
2957    }
2958    
2959    =head3 GetLine
2960    
2961    C<< my @data = Tracer::GetLine($handle); >>
2962    
2963    Read a line of data from a tab-delimited file.
2964    
2965    =over 4
2966    
2967    =item handle
2968    
2969    Open file handle from which to read.
2970    
2971    =item RETURN
2972    
2973    Returns a list of the fields in the record read. The fields are presumed to be
2974    tab-delimited. If we are at the end of the file, then an empty list will be
2975    returned. If an empty line is read, a single list item consisting of a null
2976    string will be returned.
2977    
2978    =back
2979    
2980    =cut
2981    
2982    sub GetLine {
2983        # Get the parameters.
2984        my ($handle) = @_;
2985        # Declare the return variable.
2986        my @retVal = ();
2987        Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2988        # Read from the file.
2989        my $line = <$handle>;
2990        # Only proceed if we found something.
2991        if (defined $line) {
2992            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2993            # upload control and have a nonstandard EOL combination.
2994            $line =~ s/(\r|\n)+$//;
2995            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2996            if (T(File => 4)) {
2997                my $escapedLine = $line;
2998                $escapedLine =~ s/\n/\\n/g;
2999                $escapedLine =~ s/\r/\\r/g;
3000                $escapedLine =~ s/\t/\\t/g;
3001                Trace("Line read: -->$escapedLine<--");
3002            }
3003            # If the line is empty, return a single empty string; otherwise, parse
3004            # it into fields.
3005            if ($line eq "") {
3006                push @retVal, "";
3007            } else {
3008                push @retVal, split /\t/,$line;
3009            }
3010        } else {
3011            # Trace the reason the read failed.
3012            Trace("End of file: $!") if T(File => 3);
3013        }
3014        # Return the result.
3015        return @retVal;
3016    }
3017    
3018    =head3 PutLine
3019    
3020    C<< Tracer::PutLine($handle, \@fields, $eol); >>
3021    
3022    Write a line of data to a tab-delimited file. The specified field values will be
3023    output in tab-separated form, with a trailing new-line.
3024    
3025    =over 4
3026    
3027    =item handle
3028    
3029    Output file handle.
3030    
3031    =item fields
3032    
3033    List of field values.
3034    
3035    =item eol (optional)
3036    
3037    End-of-line character (default is "\n").
3038    
3039    =back
3040    
3041    =cut
3042    
3043    sub PutLine {
3044        # Get the parameters.
3045        my ($handle, $fields, $eol) = @_;
3046        # Write the data.
3047        print $handle join("\t", @{$fields}) . ($eol || "\n");
3048    }
3049    
3050    =head3 GenerateURL
3051    
3052    C<< my $queryUrl = Tracer::GenerateURL($page, %parameters); >>
3053    
3054    Generate a GET-style URL for the specified page with the specified parameter
3055    names and values. The values will be URL-escaped automatically. So, for
3056    example
3057    
3058        Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3059    
3060    would return
3061    
3062        form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3063    
3064    =over 4
3065    
3066    =item page
3067    
3068    Page URL.
3069    
3070    =item parameters
3071    
3072    Hash mapping parameter names to parameter values.
3073    
3074    =item RETURN
3075    
3076    Returns a GET-style URL that goes to the specified page and passes in the
3077    specified parameters and values.
3078    
3079    =back
3080    
3081    =cut
3082    
3083    sub GenerateURL {
3084        # Get the parameters.
3085        my ($page, %parameters) = @_;
3086        # Prime the return variable with the page URL.
3087        my $retVal = $page;
3088        # Loop through the parameters, creating parameter elements in a list.
3089        my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3090        # If the list is nonempty, tack it on.
3091        if (@parmList) {
3092            $retVal .= "?" . join(";", @parmList);
3093        }
3094        # Return the result.
3095        return $retVal;
3096    }
3097    
3098    =head3 ApplyURL
3099    
3100    C<< Tracer::ApplyURL($table, $target, $url); >>
3101    
3102    Run through a two-dimensional table (or more accurately, a list of lists), converting the
3103    I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3104    URL column will be deleted by this process and the target column will be HTML-escaped.
3105    
3106    This provides a simple way to process the results of a database query into something
3107    displayable by combining a URL with text.
3108    
3109    =over 4
3110    
3111    =item table
3112    
3113    Reference to a list of lists. The elements in the containing list will be updated by
3114    this method.
3115    
3116    =item target
3117    
3118    The index of the column to be converted into HTML.
3119    
3120    =item url
3121    
3122    The index of the column containing the URL. Note that the URL must have a recognizable
3123    C<http:> at the beginning.
3124    
3125    =back
3126    
3127    =cut
3128    
3129    sub ApplyURL {
3130        # Get the parameters.
3131        my ($table, $target, $url) = @_;
3132        # Loop through the table.
3133        for my $row (@{$table}) {
3134            # Apply the URL to the target cell.
3135            $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3136            # Delete the URL from the row.
3137            delete $row->[$url];
3138        }
3139    }
3140    
3141    =head3 CombineURL
3142    
3143    C<< my $combinedHtml = Tracer::CombineURL($text, $url); >>
3144    
3145    This method will convert the specified text into HTML hyperlinked to the specified
3146    URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3147    is defined and begins with an C<http:> header.
3148    
3149    =over 4
3150    
3151    =item text
3152    
3153    Text to return. This will be HTML-escaped automatically.
3154    
3155    =item url
3156    
3157    A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3158    will be returned without any hyperlinking.
3159    
3160    =item RETURN
3161    
3162    Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3163    doesn't look right, the HTML-escaped text will be returned without any further
3164    modification.
3165    
3166    =back
3167    
3168    =cut
3169    
3170    sub CombineURL {
3171        # Get the parameters.
3172        my ($text, $url) = @_;
3173        # Declare the return variable.
3174        my $retVal = CGI::escapeHTML($text);
3175        # Verify the URL.
3176        if (defined($url) && $url =~ m!http://!i) {
3177            # It's good, so we apply it to the text.
3178            $retVal = "<a href=\"$url\">$retVal</a>";
3179        }
3180        # Return the result.
3181        return $retVal;
3182    }
3183    
3184    
3185  1;  1;

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