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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);      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup ScriptSetup ScriptFinish Insure ChDir);
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 FIG_Config;          use FIG_Config;
28      use PageBuilder;      use PageBuilder;
29        use Digest::MD5;
30        use File::Basename;
31        use File::Path;
32    
33  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
34    
# Line 20  Line 40 
40  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace
41  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 this package's trace level and whose category is activated will
42  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
43  is less likely to be seen. A higher trace level passed to B<Setup> means more trace messages will  is less likely to be seen. A higher trace level passed to B<TSetup> means more trace messages will
44  appear. To generate a trace message, use the following syntax.  appear. To generate a trace message, use the following syntax.
45    
46  C<< Trace($message) if T(errors => 4); >>  C<< Trace($message) if T(errors => 4); >>
# Line 38  Line 58 
58    
59  C<< Trace($message) if T(2); >>  C<< Trace($message) if T(2); >>
60    
61  To set up tracing, you call the C</Setup> method. The method takes as input a trace level, a list  To set up tracing, you call the L</TSetup> method. The method takes as input a trace level, a list
62  of category names, and a set of options. The trace level and list of category names are  of category names, and a set of options. The trace level and list of category names are
63  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
64    
65  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>
66    
67  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
68  specifies that messages should be output as HTML paragraphs. The parameters are formatted  specifies that messages should be output as HTML paragraphs.
69  to make it easier to input tracing configuration on a web form.  
70    To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
71    level 3 and writes the output to the standard error output. This sort of thing might be
72    useful in a CGI environment.
73    
74    C<< TSetup('3 *', 'WARN'); >>
75    
76  In addition to HTML and file output for trace messages, you can specify that the trace messages  In addition to HTML and file output for trace messages, you can specify that the trace messages
77  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
# Line 61  Line 86 
86  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
87  being used out in the field.  being used out in the field.
88    
89    There is no hard and fast rule on how to use trace levels. The following is therefore only
90    a suggestion.
91    
92    =over 4
93    
94    =item Error 0
95    
96    Message indicates an error that may lead to incorrect results or that has stopped the
97    application entirely.
98    
99    =item Warning 1
100    
101    Message indicates something that is unexpected but that probably did not interfere
102    with program execution.
103    
104    =item Notice 2
105    
106    Message indicates the beginning or end of a major task.
107    
108    =item Information 3
109    
110    Message indicates a subtask. In the FIG system, a subtask generally relates to a single
111    genome. This would be a big loop that is not expected to execute more than 500 times or so.
112    
113    =item Detail 4
114    
115    Message indicates a low-level loop iteration.
116    
117    =back
118    
119  =cut  =cut
120    
121  # Declare the configuration variables.  # Declare the configuration variables.
122    
123  my $Destination = "NONE";       # Description of where to send the trace output.  my $Destination = "NONE";       # Description of where to send the trace output.
124    my $TeeFlag = 0;            # TRUE if output is going to a file and to the
125                                # standard output
126  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
127                                                          # hash of active category names                                                          # hash of active category names
128  my $TraceLevel = 0;                     # trace level; a higher trace level produces more  my $TraceLevel = 0;                     # trace level; a higher trace level produces more
129                                                          # messages                                                          # messages
130  my @Queue = ();                         # queued list of trace messages.  my @Queue = ();                         # queued list of trace messages.
131  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
132    my $SetupCount = 0;         # number of times TSetup called
133    my $AllTrace = 0;           # TRUE if we are tracing all categories.
134    
135  =head2 Public Methods  =head2 Public Methods
136    
# Line 93  Line 152 
152    
153  The destination for the trace output. To send the trace output to a file, specify the file  The destination for the trace output. To send the trace output to a file, specify the file
154  name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended  name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
155  to the file. Otherwise the file is cleared before tracing begins. In addition to sending  to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
156  the trace messages to a file, you can specify a special destination. C<HTML> will cause  symbol with a C<+> to echo output to a file AND to the standard output. In addition to
157  tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>  sending the trace messages to a file, you can specify a special destination. C<HTML> will
158    cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
159  will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace  will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
160  messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace  messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
161  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
# Line 113  Line 173 
173          my @categoryData = split /\s+/, $categoryList;          my @categoryData = split /\s+/, $categoryList;
174          # Extract the trace level.          # Extract the trace level.
175          $TraceLevel = shift @categoryData;          $TraceLevel = shift @categoryData;
176          # Build the category hash.      # Presume category-based tracing until we learn otherwise.
177        $AllTrace = 0;
178        # Build the category hash. Note that if we find a "*", we turn on non-category
179        # tracing. We must also clear away any pre-existing data.
180        %Categories = ( main => 1 );
181          for my $category (@categoryData) {          for my $category (@categoryData) {
182                  $Categories{$category} = 1;          if ($category eq '*') {
183                $AllTrace = 1;
184            } else {
185                $Categories{lc $category} = 1;
186            }
187          }          }
188          # Now we need to process the destination information. The most important special          # Now we need to process the destination information. The most important special
189          # case is the single ">", which requires we clear the file first. After doing      # cases are the single ">", which requires we clear the file first, and the
190          # so, we tack on another ">" sign so that future trace messages are appended.      # "+" prefix which indicates a double echo.
191        if ($target =~ m/^\+?>>?/) {
192            if ($target =~ m/^\+/) {
193                $TeeFlag = 1;
194                $target = substr($target, 1);
195            }
196          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
197                  open TRACEFILE, $target;                  open TRACEFILE, $target;
198                  print TRACEFILE Now() . " Tracing initialized.\n";                  print TRACEFILE Now() . " Tracing initialized.\n";
199                  close TRACEFILE;                  close TRACEFILE;
200                  $Destination = ">$target";                  $Destination = ">$target";
201          } else {          } else {
202                $Destination = $target;
203            }
204        } else {
205                  $Destination = uc($target);                  $Destination = uc($target);
206          }          }
207        # Increment the setup counter.
208        $SetupCount++;
209    }
210    
211    =head3 StandardSetup
212    
213    C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>
214    
215    This method performs standard command-line parsing and tracing setup. The return
216    values are a hash of the command-line options and a list of the positional
217    parameters. Tracing is automatically set up and the command-line options are
218    validated.
219    
220    This is a complex method that does a lot of grunt work. The parameters can
221    be more easily understood, however, once they are examined individually.
222    
223    The I<categories> parameter is the most obtuse. It is a reference to a list of
224    special-purpose tracing categories. Most tracing categories are PERL package
225    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
226    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
227    
228        ["Sprout", "SproutLoad", "ERDB"]
229    
230    This would cause trace messages in the specified three packages to appear in
231    the output. There are threer special tracing categories that are automatically
232    handled by this method. In other words, if you used L</TSetup> you would need
233    to include these categories manually, but if you use this method they are turned
234    on automatically.
235    
236    =over 4
237    
238    =item FIG
239    
240    Turns on trace messages inside the B<FIG> package.
241    
242    =item SQL
243    
244    Traces SQL commands and activity.
245    
246    =item Tracer
247    
248    Traces error messages and call stacks.
249    
250    =back
251    
252    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
253    The trace level is specified using the C<-trace> command-line option. For example,
254    the following command line for C<TransactFeatures> turns on SQL tracing and runs
255    all tracing at level 3.
256    
257        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
258    
259    Standard tracing is output to the standard output and echoed to the file
260    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
261    process ID. You can also specify the C<user> parameter to put a user ID
262    instead of a process ID in the trace file name. So, for example
263    
264    The default trace level is 2. To get all messages, specify a trace level of 4.
265    For a genome-by-genome update, use 3.
266    
267        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
268    
269    would send the trace output to C<traceBruce.log> in the temporary directory.
270    
271    The I<options> parameter is a reference to a hash containing the command-line
272    options, their default values, and an explanation of what they mean. Command-line
273    options may be in the form of switches or keywords. In the case of a switch, the
274    option value is 1 if it is specified and 0 if it is not specified. In the case
275    of a keyword, the value is separated from the option name by an equal sign. You
276    can see this last in the command-line example above.
277    
278    You can specify a different default trace level by setting C<$options->{trace}>
279    prior to calling this method.
280    
281    An example at this point would help. Consider, for example, the command-line utility
282    C<TransactFeatures>. It accepts a list of positional parameters plus the options
283    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
284    the following code.
285    
286        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
287                            { safe => [0, "use database transactions"],
288                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
289                              start => [' ', "start with this genome"],
290                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
291                            "command transactionDirectory IDfile",
292                          @ARGV);
293    
294    
295    The call to C<ParseCommand> specifies the default values for the options and
296    stores the actual options in a hash that is returned as C<$options>. The
297    positional parameters are returned in C<@parameters>.
298    
299    The following is a sample command line for C<TransactFeatures>.
300    
301        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
302    
303    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
304    parameters, and would find themselves in I<@parameters> after executing the
305    above code fragment. The tracing would be set to level 2, and the categories
306    would be C<FIG>, C<Tracer>, and <DocUtils>. C<FIG> and C<Tracer> are standard,
307    and C<DocUtils> was included because it came in within the first parameter
308    to this method. The I<$options> hash would be
309    
310        { trace => 2, sql => 0, safe => 0,
311          noAlias => 1, start => ' ', tblFiles => 0 }
312    
313    Use of C<StandardSetup> in this way provides a simple way of performing
314    standard tracing setup and command-line parsing. Note that the caller is
315    not even aware of the command-line switches C<-trace> and C<-sql>, which
316    are used by this method to control the tracing. If additional tracing features
317    need to be added in the future, they can be processed by this method without
318    upsetting the command-line utilities.
319    
320    If the C<background> option is specified on the command line, then the
321    standard and error outputs will be directed to files in the temporary
322    directory, using the same suffix as the trace file. So, if the command
323    line specified
324    
325        -user=Bruce -background
326    
327    then the trace output would go to C<traceBruce.log>, the standard output to
328    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
329    simplify starting a command in the background.
330    
331    Finally, if the special option C<-h> is specified, the option names will
332    be traced at level 0 and the program will exit without processing.
333    This provides a limited help capability. For example, if the user enters
334    
335        TransactFeatures -h
336    
337    he would see the following output.
338    
339        TransactFeatures [options] command transactionDirectory IDfile
340            -trace    tracing level (default 2)
341            -sql      trace SQL commands
342            -safe     use database transactions
343            -noAlias  do not expect aliases in CHANGE transactions
344            -start    start with this genome
345            -tblFiles output TBL files containing the corrected IDs
346    
347    The caller has the option of modifying the tracing scheme by placing a value
348    for C<trace> in the incoming options hash. The default value can be overridden,
349    or the tracing to the standard output can be turned off by suffixing a minus
350    sign to the trace level. So, for example,
351    
352        { trace => [0, "tracing level (default 0)"],
353           ...
354    
355    would set the default trace level to 0 instead of 2, while
356    
357        { trace => ["2-", "tracing level (default 2)"],
358           ...
359    
360    would leave the default at 2, but trace only to the log file, not to the
361    standard output.
362    
363    The parameters to this method are as follows.
364    
365    =over 4
366    
367    =item categories
368    
369    Reference to a list of tracing category names. These should be names of
370    packages whose internal workings will need to be debugged to get the
371    command working.
372    
373    =item options
374    
375    Reference to a hash containing the legal options for the current command mapped
376    to their default values and descriptions. The user can override the defaults
377    by specifying the options as command-line switches prefixed by a hyphen.
378    Tracing-related options may be added to this hash. If the C<-h> option is
379    specified on the command line, the option descriptions will be used to
380    explain the options. To turn off tracing to the standard output, add a
381    minus sign to the value for C<trace> (see above).
382    
383    =item parmHelp
384    
385    A string that vaguely describes the positional parameters. This is used
386    if the user specifies the C<-h> option.
387    
388    =item argv
389    
390    List of command line parameters, including the option switches, which must
391    precede the positional parameters and be prefixed by a hyphen.
392    
393    =item RETURN
394    
395    Returns a list. The first element of the list is the reference to a hash that
396    maps the command-line option switches to their values. These will either be the
397    default values or overrides specified on the command line. The remaining
398    elements of the list are the position parameters, in order.
399    
400    =back
401    
402    =cut
403    
404    sub StandardSetup {
405        # Get the parameters.
406        my ($categories, $options, $parmHelp, @argv) = @_;
407        # Add the tracing options.
408        if (! exists $options->{trace}) {
409            $options->{trace} = [2, "tracing level"];
410        }
411        $options->{sql} = [0, "turn on SQL tracing"];
412        $options->{h} = [0, "display command-line options"];
413        $options->{user} = [$$, "trace log file name suffix"];
414        $options->{background} = [0, "spool standard and error output"];
415        # Create a parsing hash from the options hash. The parsing hash
416        # contains the default values rather than the default value
417        # and the description. While we're at it, we'll memorize the
418        # length of the longest option name.
419        my $longestName = 0;
420        my %parseOptions = ();
421        for my $key (keys %{$options}) {
422            if (length $key > $longestName) {
423                $longestName = length $key;
424            }
425            $parseOptions{$key} = $options->{$key}->[0];
426        }
427        # Parse the command line.
428        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
429        # Get the logfile suffix.
430        my $suffix = $retOptions->{user};
431        # Check for background mode.
432        if ($retOptions->{background}) {
433            my $outFileName = "$FIG_Config::temp/out$suffix.log";
434            my $errFileName = "$FIG_Config::temp/err$suffix.log";
435            open STDOUT, ">$outFileName";
436            open STDERR, ">$errFileName";
437        }
438        # Now we want to set up tracing. First, we need to know if SQL is to
439        # be traced.
440        my @cats = @{$categories};
441        if ($retOptions->{sql}) {
442            push @cats, "SQL";
443        }
444        # Add the default categories.
445        push @cats, "Tracer", "FIG";
446        # Next, we create the category string by joining the categories.
447        my $cats = join(" ", @cats);
448        # Check to determine whether or not the caller wants to turn off tracing
449        # to the standard output.
450        my $traceLevel = $retOptions->{trace};
451        my $textOKFlag = 1;
452        if ($traceLevel =~ /^(.)-/) {
453            $traceLevel = $1;
454            $textOKFlag = 0;
455        }
456        # Now we set up the trace mode.
457        my $traceMode;
458        # Verify that we can open a file in the FIG temporary directory.
459        my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
460        if (open TESTTRACE, ">$traceFileName") {
461            # Here we can trace to a file.
462            $traceMode = ">$traceFileName";
463            if ($textOKFlag) {
464                # Echo to standard output if the text-OK flag is set.
465                $traceMode = "+$traceMode";
466            }
467            # Close the test file.
468            close TESTTRACE;
469        } else {
470            # Here we can't trace to a file. We trace to the standard output if it's
471            # okay, and the error log otherwise.
472            if ($textOKFlag) {
473                $traceMode = "TEXT";
474            } else {
475                $traceMode = "WARN";
476            }
477        }
478        # Now set up the tracing.
479        TSetup("$traceLevel $cats", $traceMode);
480        # Check for the "h" option. If it is specified, dump the command-line
481        # options and exit the program.
482        if ($retOptions->{h}) {
483            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
484            Trace("$1 [options] $parmHelp") if T(0);
485            for my $key (sort keys %{$options}) {
486                my $name = Pad($key, $longestName, 0, ' ');
487                my $desc = $options->{$key}->[1];
488                if ($options->{$key}->[0]) {
489                    $desc .= " (default " . $options->{$key}->[0] . ")";
490                }
491                Trace("  $name $desc") if T(0);
492            }
493            exit(0);
494        }
495        # Return the parsed parameters.
496        return ($retOptions, @retParameters);
497    }
498    
499    =head3 Setups
500    
501    C<< my $count = Tracer::Setups(); >>
502    
503    Return the number of times L</TSetup> has been called.
504    
505    This method allows for the creation of conditional tracing setups where, for example, we
506    may want to set up tracing if nobody else has done it before us.
507    
508    =cut
509    
510    sub Setups {
511        return $SetupCount;
512    }
513    
514    =head3 Open
515    
516    C<< my $handle = Open($fileHandle, $fileSpec, $message); >>
517    
518    Open a file.
519    
520    The I<$fileSpec> is essentially the second argument of the PERL C<open>
521    function. The mode is specified using Unix-like shell information. So, for
522    example,
523    
524        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
525    
526    would open for output appended to the specified file, and
527    
528        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
529    
530    would open a pipe that sorts the records written and removes duplicates. Note
531    the use of file handle syntax in the Open call. To use anonymous file handles,
532    code as follows.
533    
534        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
535    
536    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
537    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
538    failed open will throw an exception and the third parameter will be used to construct
539    an error message. If the parameter is omitted, a standard message is constructed
540    using the file spec.
541    
542        Could not open "/usr/spool/news/twitlog"
543    
544    Note that the mode characters are automatically cleaned from the file name.
545    The actual error message from the file system will be captured and appended to the
546    message in any case.
547    
548        Could not open "/usr/spool/news/twitlog": file not found.
549    
550    In some versions of PERL the only error message we get is a number, which
551    corresponds to the C++ C<errno> value.
552    
553        Could not open "/usr/spool/news/twitlog": 6.
554    
555    =over 4
556    
557    =item fileHandle
558    
559    File handle. If this parameter is C<undef>, a file handle will be generated
560    and returned as the value of this method.
561    
562    =item fileSpec
563    
564    File name and mode, as per the PERL C<open> function.
565    
566    =item message (optional)
567    
568    Error message to use if the open fails. If omitted, a standard error message
569    will be generated. In either case, the error information from the file system
570    is appended to the message. To specify a conditional open that does not throw
571    an error if it fails, use C<0>.
572    
573    =item RETURN
574    
575    Returns the name of the file handle assigned to the file, or C<undef> if the
576    open failed.
577    
578    =back
579    
580    =cut
581    
582    sub Open {
583        # Get the parameters.
584        my ($fileHandle, $fileSpec, $message) = @_;
585        # Attempt to open the file.
586        my $rv = open $fileHandle, $fileSpec;
587        # If the open failed, generate an error message.
588        if (! $rv) {
589            # Save the system error message.
590            my $sysMessage = $!;
591            # See if we need a default message.
592            if (!$message) {
593                # Clean any obvious mode characters and leading spaces from the
594                # filename.
595                my ($fileName) = FindNamePart($fileSpec);
596                $message = "Could not open \"$fileName\"";
597            }
598            # Terminate with an error using the supplied message and the
599            # error message from the file system.
600            Confess("$message: $!");
601        }
602        # Return the file handle.
603        return $fileHandle;
604    }
605    
606    =head3 FindNamePart
607    
608    C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>
609    
610    Extract the portion of a file specification that contains the file name.
611    
612    A file specification is the string passed to an C<open> call. It specifies the file
613    mode and name. In a truly complex situation, it can specify a pipe sequence. This
614    method assumes that the file name is whatever follows the first angle bracket
615    sequence.  So, for example, in the following strings the file name is
616    C</usr/fig/myfile.txt>.
617    
618        >>/usr/fig/myfile.txt
619        </usr/fig/myfile.txt
620        | sort -u > /usr/fig/myfile.txt
621    
622    If the method cannot find a file name using its normal methods, it will return the
623    whole incoming string.
624    
625    =over 4
626    
627    =item fileSpec
628    
629    File specification string from which the file name is to be extracted.
630    
631    =item RETURN
632    
633    Returns a three-element list. The first element contains the file name portion of
634    the specified string, or the whole string if a file name cannot be found via normal
635    methods. The second element contains the start position of the file name portion and
636    the third element contains the length.
637    
638    =back
639    
640    =cut
641    #: Return Type $;
642    sub FindNamePart {
643        # Get the parameters.
644        my ($fileSpec) = @_;
645        # Default to the whole input string.
646        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
647        # Parse out the file name if we can.
648        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
649            $retVal = $2;
650            $len = length $retVal;
651            $pos = (length $fileSpec) - (length $3) - $len;
652        }
653        # Return the result.
654        return ($retVal, $pos, $len);
655    }
656    
657    =head3 OpenDir
658    
659    C<< my @files = OpenDir($dirName, $filtered, $flag); >>
660    
661    Open a directory and return all the file names. This function essentially performs
662    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
663    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
664    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
665    filtered out of the return list. If the directory does not open and I<$flag> is not
666    set, an exception is thrown. So, for example,
667    
668        my @files = OpenDir("/Volumes/fig/contigs", 1);
669    
670    is effectively the same as
671    
672        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
673        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
674    
675    Similarly, the following code
676    
677        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
678    
679    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
680    automatically returns an empty list if the directory fails to open.
681    
682    =over 4
683    
684    =item dirName
685    
686    Name of the directory to open.
687    
688    =item filtered
689    
690    TRUE if files whose names begin with a period (C<.>) should be automatically removed
691    from the list, else FALSE.
692    
693    =item flag
694    
695    TRUE if a failure to open is okay, else FALSE
696    
697    =back
698    
699    =cut
700    #: Return Type @;
701    sub OpenDir {
702        # Get the parameters.
703        my ($dirName, $filtered, $flag) = @_;
704        # Declare the return variable.
705        my @retVal = ();
706        # Open the directory.
707        if (opendir(my $dirHandle, $dirName)) {
708            # The directory opened successfully. Get the appropriate list according to the
709            # strictures of the filter parameter.
710            if ($filtered) {
711                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
712            } else {
713                @retVal = readdir $dirHandle;
714            }
715        } elsif (! $flag) {
716            # Here the directory would not open and it's considered an error.
717            Confess("Could not open directory $dirName.");
718        }
719        # Return the result.
720        return @retVal;
721  }  }
722    
723  =head3 SetLevel  =head3 SetLevel
# Line 394  Line 984 
984         warn $message;         warn $message;
985          } elsif ($Destination =~ m/^>>/) {          } elsif ($Destination =~ m/^>>/) {
986                  # Write the trace message to an output file.                  # Write the trace message to an output file.
987                  open TRACING, $Destination;          (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
988                  print TRACING "$formatted\n";                  print TRACING "$formatted\n";
989                  close TRACING;                  close TRACING;
990            # If the Tee flag is on, echo it to the standard output.
991            if ($TeeFlag) {
992                print "$formatted\n";
993            }
994          }          }
995  }  }
996    
# Line 439  Line 1033 
1033                  my ($category, $traceLevel) = @_;                  my ($category, $traceLevel) = @_;
1034                  if (!defined $traceLevel) {                  if (!defined $traceLevel) {
1035                          # Here we have no category, so we need to get the calling package.                          # Here we have no category, so we need to get the calling package.
1036                # The calling package is normally the first parameter. If it is
1037                # omitted, the first parameter will be the tracelevel. So, the
1038                # first thing we do is shift the so-called category into the
1039                # $traceLevel variable where it belongs.
1040                          $traceLevel = $category;                          $traceLevel = $category;
1041                          my ($package, $fileName, $line) = caller;                          my ($package, $fileName, $line) = caller;
1042              # If there is no calling package, we default to "main".              # If there is no calling package, we default to "main".
# Line 450  Line 1048 
1048                  }                  }
1049          # Save the category name.          # Save the category name.
1050          $LastCategory = $category;          $LastCategory = $category;
1051            # Convert it to lower case before we hash it.
1052            $category = lc $category;
1053                  # Use the category and tracelevel to compute the result.                  # Use the category and tracelevel to compute the result.
1054                  $retVal = ($traceLevel <= $TraceLevel && exists $Categories{$category});          if (ref $traceLevel) {
1055                Confess("Bad trace level.");
1056            } elsif (ref $TraceLevel) {
1057                Confess("Bad trace config.");
1058            }
1059            $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
1060      }      }
1061          # Return the computed result.          # Return the computed result.
1062      return $retVal;      return $retVal;
# Line 537  Line 1142 
1142    
1143  C<< my $codedString = Tracer::Escape($realString); >>  C<< my $codedString = Tracer::Escape($realString); >>
1144    
1145  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
1146  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
1147  doubled. The effect is to exactly reverse the effect of L</UnEscape>.  result is to reverse the effect of L</UnEscape>.
1148    
1149  =over 4  =over 4
1150    
# Line 563  Line 1168 
1168          # Loop through the parameter string, looking for sequences to escape.          # Loop through the parameter string, looking for sequences to escape.
1169          while (length $realString > 0) {          while (length $realString > 0) {
1170                  # Look for the first sequence to escape.                  # Look for the first sequence to escape.
1171                  if ($realString =~ /^(.*?)([ \n\t\\])/) {          if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1172                          # 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
1173                          # 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.
1174                          $retVal .= $1;                          $retVal .= $1;
1175                          $realString = substr $realString, (length $2 + length $1);              # Strip the processed section off the real string.
1176                          # Encode the escape sequence.              $realString = substr $realString, (length $2) + (length $1);
1177                # Get the matched character.
1178                          my $char = $2;                          my $char = $2;
1179                          $char =~ tr/ \t\n/btn/;              # If we have a CR, we are done.
1180                if ($char ne "\r") {
1181                    # It's not a CR, so encode the escape sequence.
1182                    $char =~ tr/\t\n/tn/;
1183                          $retVal .= "\\" . $char;                          $retVal .= "\\" . $char;
1184                }
1185                  } else {                  } else {
1186                          # 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
1187                          # transferred unmodified.                          # transferred unmodified.
# Line 587  Line 1197 
1197    
1198  C<< my $realString = Tracer::UnEscape($codedString); >>  C<< my $realString = Tracer::UnEscape($codedString); >>
1199    
1200  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
1201  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
1202    be deleted.
1203    
1204  =over 4  =over 4
1205    
# Line 613  Line 1224 
1224          # Only proceed if the incoming string is nonempty.          # Only proceed if the incoming string is nonempty.
1225          if (defined $codedString) {          if (defined $codedString) {
1226                  # 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
1227                  # translating because it causes problems with the escaped slash. ("\\b" becomes          # translating because it causes problems with the escaped slash. ("\\t" becomes
1228                  # "\ " no matter what we do.)          # "\<tab>" no matter what we do.)
1229                  while (length $codedString > 0) {                  while (length $codedString > 0) {
1230                          # Look for the first escape sequence.                          # Look for the first escape sequence.
1231                          if ($codedString =~ /^(.*?)\\(\\|b|n|t)/) {              if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
1232                                  # 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
1233                                  # 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.
1234                                  $retVal .= $1;                                  $retVal .= $1;
1235                                  $codedString = substr $codedString, (2 + length $1);                                  $codedString = substr $codedString, (2 + length $1);
1236                                  # Decode the escape sequence.                  # Get the escape value.
1237                                  my $char = $2;                                  my $char = $2;
1238                                  $char =~ tr/\\btn/\\ \t\n/;                  # If we have a "\r", we are done.
1239                    if ($char ne 'r') {
1240                        # Here it's not an 'r', so we convert it.
1241                        $char =~ tr/\\tn/\\\t\n/;
1242                                  $retVal .= $char;                                  $retVal .= $char;
1243                    }
1244                          } else {                          } else {
1245                                  # Here there are no more escape sequences. The rest of the string is                                  # Here there are no more escape sequences. The rest of the string is
1246                                  # transferred unmodified.                                  # transferred unmodified.
# Line 735  Line 1350 
1350    
1351  C<< my @fileContents = Tracer::GetFile($fileName); >>  C<< my @fileContents = Tracer::GetFile($fileName); >>
1352    
1353  Return the entire contents of a file.      or
1354    
1355    C<< my $fileContents = Tracer::GetFile($fileName); >>
1356    
1357    Return the entire contents of a file. In list context, line-ends are removed and
1358    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1359    
1360  =over 4  =over 4
1361    
# Line 746  Line 1366 
1366  =item RETURN  =item RETURN
1367    
1368  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.
1369  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
1370    the file, an empty list will be returned.
1371    
1372  =back  =back
1373    
# Line 761  Line 1382 
1382          my $ok = open INPUTFILE, "<$fileName";          my $ok = open INPUTFILE, "<$fileName";
1383          if (!$ok) {          if (!$ok) {
1384                  # If we had an error, trace it. We will automatically return a null value.                  # If we had an error, trace it. We will automatically return a null value.
1385                  Trace("Could not open \"$fileName\" for input.") if T(0);          Trace("Could not open \"$fileName\" for input: $!") if T(0);
1386          } else {          } else {
1387                  # Read the whole file into the return variable, stripping off any terminator                  # Read the whole file into the return variable, stripping off any terminator
1388          # characters.          # characters.
# Line 774  Line 1395 
1395                  # Close it.                  # Close it.
1396                  close INPUTFILE;                  close INPUTFILE;
1397          my $actualLines = @retVal;          my $actualLines = @retVal;
         Trace("$lineCount lines read from $fileName. $actualLines processed.") if T(3);  
1398          }          }
1399          # Return the file's contents in the desired format.          # Return the file's contents in the desired format.
1400      if (wantarray) {      if (wantarray) {
# Line 805  Line 1425 
1425          my ($format) = @_;          my ($format) = @_;
1426          # Create the return variable.          # Create the return variable.
1427          my $retVal = "";          my $retVal = "";
1428        # Only proceed if there is an actual queue.
1429        if (@Queue) {
1430          # Process according to the format.          # Process according to the format.
1431          if ($format =~ m/^HTML$/i) {          if ($format =~ m/^HTML$/i) {
1432                  # Convert the queue into an HTML list.                  # Convert the queue into an HTML list.
# Line 820  Line 1442 
1442          }          }
1443          # Clear the queue.          # Clear the queue.
1444          @Queue = ();          @Queue = ();
1445        }
1446          # Return the formatted list.          # Return the formatted list.
1447          return $retVal;          return $retVal;
1448  }  }
# Line 828  Line 1451 
1451    
1452  C<< Confess($message); >>  C<< Confess($message); >>
1453    
1454  Trace the call stack and abort the program with the specified message. The stack  Trace the call stack and abort the program with the specified message. When used with
 trace will only appear if the trace level for this package is 1 or more. When used with  
1455  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.  the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
1456  So, for example  So, for example
1457    
# Line 851  Line 1473 
1473          # Get the parameters.          # Get the parameters.
1474          my ($message) = @_;          my ($message) = @_;
1475          # Trace the call stack.          # Trace the call stack.
1476          Cluck($message) if T(1);      Cluck($message);
1477          # Abort the program.          # Abort the program.
1478          croak(">>> $message");          croak(">>> $message");
1479  }  }
# Line 861  Line 1483 
1483  C<< Assert($condition1, $condition2, ... $conditionN); >>  C<< Assert($condition1, $condition2, ... $conditionN); >>
1484    
1485  Return TRUE if all the conditions are true. This method can be used in conjunction with  Return TRUE if all the conditions are true. This method can be used in conjunction with
1486  the OR operator and the L</Confess> method, B<Assert> can function as a debugging assert.  the OR operator and the L</Confess> method as a debugging assert.
1487  So, for example  So, for example
1488    
1489  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>  C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
# Line 1020  Line 1642 
1642    
1643  C<< if (Tracer::DebugMode) { ...code... } >>  C<< if (Tracer::DebugMode) { ...code... } >>
1644    
1645  Return TRUE if debug mode has been turned on in FIG_Config, else output  Return TRUE if debug mode has been turned on, else output an error
1646  an error page and return FALSE.  page and return FALSE.
1647    
1648  Certain CGI scripts are too dangerous to exist in the production  Certain CGI scripts are too dangerous to exist in the production
1649  environment. This method provides a simple way to prevent them  environment. This method provides a simple way to prevent them
1650  from working unless they are explicitly turned on in the configuration  from working unless they are explicitly turned on by creating a password
1651  file by setting C<$FIG_Config::debug_mode> to 1. If debugging mode  cookie via the B<SetPassword> script.  If debugging mode
1652  is not turned on, an error web page will be output.  is not turned on, an error web page will be output directing the
1653    user to enter in the correct password.
1654    
1655  =cut  =cut
1656    
1657  sub DebugMode {  sub DebugMode {
1658          # Declare the return variable.          # Declare the return variable.
1659          my $retVal;      my $retVal = 0;
1660          # Check the debug configuration.          # Check the debug configuration.
1661          if ($FIG_Config::debug_mode) {      my $password = CGI::cookie("DebugMode");
1662        my $encrypted = Digest::MD5::md5_hex($password);
1663        if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1664                  $retVal = 1;                  $retVal = 1;
1665          } else {          } else {
1666                  # Here debug mode is off, so we generate an error page.                  # Here debug mode is off, so we generate an error page.
# Line 1071  Line 1696 
1696  sub Strip {  sub Strip {
1697          # Get a copy of the parameter string.          # Get a copy of the parameter string.
1698          my ($string) = @_;          my ($string) = @_;
1699          my $retVal = $string;      my $retVal = (defined $string ? $string : "");
1700      # Strip the line terminator characters.      # Strip the line terminator characters.
1701      $retVal =~ s/(\r|\n)+$//g;      $retVal =~ s/(\r|\n)+$//g;
1702          # Return the result.          # Return the result.
# Line 1102  Line 1727 
1727    
1728  =item padChar (optional)  =item padChar (optional)
1729    
1730    Character to use for padding. The default is a space.
1731    
1732  =item RETURN  =item RETURN
1733    
1734  Returns a copy of the original string with the spaces added to the specified end so  Returns a copy of the original string with the pad character added to the
1735  that it achieves the desired length.  specified end so that it achieves the desired length.
1736    
1737  =back  =back
1738    
# Line 1137  Line 1764 
1764          return $retVal;          return $retVal;
1765  }  }
1766    
1767    =head3 EOF
1768    
1769    This is a constant that is lexically greater than any useful string.
1770    
1771    =cut
1772    
1773    sub EOF {
1774        return "\xFF\xFF\xFF\xFF\xFF";
1775    }
1776    
1777    =head3 TICK
1778    
1779    C<< my @results = TICK($commandString); >>
1780    
1781    Perform a back-tick operation on a command. If this is a Windows environment, any leading
1782    dot-slash (C<./> will be removed. So, for example, if you were doing
1783    
1784        `./protein.cgi`
1785    
1786    from inside a CGI script, it would work fine in Unix, but would issue an error message
1787    in Windows complaining that C<'.'> is not a valid command. If instead you code
1788    
1789        TICK("./protein.cgi")
1790    
1791    it will work correctly in both environments.
1792    
1793    =over 4
1794    
1795    =item commandString
1796    
1797    The command string to pass to the system.
1798    
1799    =item RETURN
1800    
1801    Returns the standard output from the specified command, as a list.
1802    
1803    =back
1804    
1805    =cut
1806    #: Return Type @;
1807    sub TICK {
1808        # Get the parameters.
1809        my ($commandString) = @_;
1810        # Chop off the dot-slash if this is Windows.
1811        if ($FIG_Config::win_mode) {
1812            $commandString =~ s!^\./!!;
1813        }
1814        # Activate the command and return the result.
1815        return `$commandString`;
1816    }
1817    
1818    =head3 ScriptSetup
1819    
1820    C<< my ($query, $varHash) = ScriptSetup(); >>
1821    
1822    Perform standard tracing and debugging setup for scripts. The value returned is
1823    the CGI object followed by a pre-built variable hash.
1824    
1825    The C<Trace> query parameter is used to determine whether or not tracing is active and
1826    which trace modules (other than C<Tracer> and C<FIG>) should be turned on. Specifying
1827    the C<CGI> trace module will trace parameter and environment information. Parameters are
1828    traced at level 3 and environment variables at level 4. At the end of the script, the
1829    client should call L</ScriptFinish> to output the web page.
1830    
1831    =cut
1832    
1833    sub ScriptSetup {
1834        # Get the CGI query object.
1835        my $query = CGI->new();
1836        # Check for tracing. Set it up if the user asked for it.
1837        if ($query->param('Trace')) {
1838            # Set up tracing to be queued for display at the bottom of the web page.
1839            TSetup($query->param('Trace') . " FIG Tracer", "QUEUE");
1840            # Trace the parameter and environment data.
1841            if (T(CGI => 3)) {
1842                # Here we want to trace the parameter data.
1843                my @names = $query->param;
1844                for my $parmName (sort @names) {
1845                    # Note we skip "Trace", which is for our use only.
1846                    if ($parmName ne 'Trace') {
1847                        my @values = $query->param($parmName);
1848                        Trace("CGI: $parmName = " . join(", ", @values));
1849                    }
1850                }
1851            }
1852            if (T(CGI => 4)) {
1853                # Here we want the environment data too.
1854                for my $envName (sort keys %ENV) {
1855                    Trace("ENV: $envName = $ENV{$envName}");
1856                }
1857            }
1858        } else {
1859            # Here tracing is to be turned off. All we allow is errors traced into the
1860            # error log.
1861            TSetup("0", "WARN");
1862        }
1863        # Create the variable hash.
1864        my $varHash = { DebugData => '' };
1865        # If we're in DEBUG mode, set up the debug mode data for forms.
1866        if (Tracer::DebugMode) {
1867            $varHash->{DebugData} = GetFile("Html/DebugFragment.html");
1868        }
1869        # Return the query object and variable hash.
1870        return ($query, $varHash);
1871    }
1872    
1873    =head3 ScriptFinish
1874    
1875    C<< ScriptFinish($webData, $varHash); >>
1876    
1877    Output a web page at the end of a script. Either the string to be output or the
1878    name of a template file can be specified. If the second parameter is omitted,
1879    it is assumed we have a string to be output; otherwise, it is assumed we have the
1880    name of a template file. The template should have the variable C<DebugData>
1881    specified in any form that invokes a standard script. If debugging mode is turned
1882    on, a form field will be put in that allows the user to enter tracing data.
1883    Trace messages will be placed immediately before the terminal C<BODY> tag in
1884    the output, formatted as a list.
1885    
1886    A typical standard script would loook like the following.
1887    
1888        BEGIN {
1889            # Print the HTML header.
1890            print "CONTENT-TYPE: text/html\n\n";
1891        }
1892        use Tracer;
1893        use CGI;
1894        use FIG;
1895        # ... more uses ...
1896    
1897        my ($query, $varHash) = ScriptSetup();
1898        eval {
1899            # ... get data from $query, put it in $varHash ...
1900        };
1901        if ($@) {
1902            Trace("Script Error: $@") if T(0);
1903        }
1904        ScriptFinish("Html/MyTemplate.html", $varHash);
1905    
1906    The idea here is that even if the script fails, you'll see trace messages and
1907    useful output.
1908    
1909    =over 4
1910    
1911    =item webData
1912    
1913    A string containing either the full web page to be written to the output or the
1914    name of a template file from which the page is to be constructed. If the name
1915    of a template file is specified, then the second parameter must be present;
1916    otherwise, it must be absent.
1917    
1918    =item varHash (optional)
1919    
1920    If specified, then a reference to a hash mapping variable names for a template
1921    to their values. The template file will be read into memory, and variable markers
1922    will be replaced by data in this hash reference.
1923    
1924    =back
1925    
1926    =cut
1927    
1928    sub ScriptFinish {
1929        # Get the parameters.
1930        my ($webData, $varHash) = @_;
1931        # Check for a template file situation.
1932        my $outputString;
1933        if (defined $varHash) {
1934            # Here we have a template file. We need to apply the variables to the template.
1935            $outputString = PageBuilder::Build("<$webData", $varHash, "Html");
1936        } else {
1937            # Here the user gave us a raw string.
1938            $outputString = $webData;
1939        }
1940        # Check for trace messages.
1941        if ($Destination eq "QUEUE") {
1942            # We have trace messages, so we want to put them at the end of the body. This
1943            # is either at the end of the whole string or at the beginning of the BODY
1944            # end-tag.
1945            my $pos = length $outputString;
1946            if ($outputString =~ m#</body>#gi) {
1947                $pos = (pos $outputString) - 7;
1948            }
1949            substr $outputString, $pos, 0, QTrace('Html');
1950        }
1951        # Write the output string.
1952        print $outputString;
1953    }
1954    
1955    =head3 Insure
1956    
1957    C<< Insure($dirName); >>
1958    
1959    Insure a directory is present.
1960    
1961    =over 4
1962    
1963    =item dirName
1964    
1965    Name of the directory to check. If it does not exist, it will be created.
1966    
1967    =back
1968    
1969    =cut
1970    
1971    sub Insure {
1972        my ($dirName) = @_;
1973        if (! -d $dirName) {
1974            Trace("Creating $dirName directory.") if T(2);
1975            eval { mkpath $dirName; };
1976            if ($@) {
1977                Confess("Error creating $dirName: $@");
1978            }
1979        }
1980    }
1981    
1982    =head3 ChDir
1983    
1984    C<< ChDir($dirName); >>
1985    
1986    Change to the specified directory.
1987    
1988    =over 4
1989    
1990    =item dirName
1991    
1992    Name of the directory to which we want to change.
1993    
1994    =back
1995    
1996    =cut
1997    
1998    sub ChDir {
1999        my ($dirName) = @_;
2000        if (! -d $dirName) {
2001            Confess("Cannot change to directory $dirName: no such directory.");
2002        } else {
2003            Trace("Changing to directory $dirName.") if T(4);
2004            my $okFlag = chdir $dirName;
2005            if (! $okFlag) {
2006                Confess("Error switching to directory $dirName.");
2007            }
2008        }
2009    }
2010    
2011  1;  1;

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