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revision 1.43, Mon Apr 24 21:05:17 2006 UTC revision 1.52, Wed Jun 14 01:12:42 2006 UTC
# Line 19  Line 19 
19    
20      require Exporter;      require Exporter;
21      @ISA = ('Exporter');      @ISA = ('Exporter');
22      @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup ScriptSetup ScriptFinish Insure);      @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 Cwd;
28      use FIG_Config;      use FIG_Config;
29      use PageBuilder;      use PageBuilder;
30      use Digest::MD5;      use Digest::MD5;
31      use File::Basename;      use File::Basename;
32      use File::Path;      use File::Path;
33        use File::stat;
34    
35  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
36    
# Line 344  Line 346 
346          -start    start with this genome          -start    start with this genome
347          -tblFiles output TBL files containing the corrected IDs          -tblFiles output TBL files containing the corrected IDs
348    
349    The caller has the option of modifying the tracing scheme by placing a value
350    for C<trace> in the incoming options hash. The default value can be overridden,
351    or the tracing to the standard output can be turned off by suffixing a minus
352    sign to the trace level. So, for example,
353    
354        { trace => [0, "tracing level (default 0)"],
355           ...
356    
357    would set the default trace level to 0 instead of 2, while
358    
359        { trace => ["2-", "tracing level (default 2)"],
360           ...
361    
362    would leave the default at 2, but trace only to the log file, not to the
363    standard output.
364    
365  The parameters to this method are as follows.  The parameters to this method are as follows.
366    
367  =over 4  =over 4
# Line 361  Line 379 
379  by specifying the options as command-line switches prefixed by a hyphen.  by specifying the options as command-line switches prefixed by a hyphen.
380  Tracing-related options may be added to this hash. If the C<-h> option is  Tracing-related options may be added to this hash. If the C<-h> option is
381  specified on the command line, the option descriptions will be used to  specified on the command line, the option descriptions will be used to
382  explain the options.  explain the options. To turn off tracing to the standard output, add a
383    minus sign to the value for C<trace> (see above).
384    
385  =item parmHelp  =item parmHelp
386    
387  A string that vaguely describes the positional parameters. This is used  A string that vaguely describes the positional parameters. This is used
388  if the user specifies the C<-h> option.  if the user specifies the C<-h> option.
389    
390  =item ARGV  =item argv
391    
392  List of command line parameters, including the option switches, which must  List of command line parameters, including the option switches, which must
393  precede the positional parameters and be prefixed by a hyphen.  precede the positional parameters and be prefixed by a hyphen.
# Line 426  Line 445 
445      }      }
446      # Add the default categories.      # Add the default categories.
447      push @cats, "Tracer", "FIG";      push @cats, "Tracer", "FIG";
448      # Next, we create the category string by prefixing the trace level      # Next, we create the category string by joining the categories.
449      # and joining the categories.      my $cats = join(" ", @cats);
450      my $cats = join(" ", $parseOptions{trace}, @cats);      # Check to determine whether or not the caller wants to turn off tracing
451      # Verify that we can open a file in the temporary directory.      # to the standard output.
452      my $traceMode = "TEXT";      my $traceLevel = $retOptions->{trace};
453        my $textOKFlag = 1;
454        if ($traceLevel =~ /^(.)-/) {
455            $traceLevel = $1;
456            $textOKFlag = 0;
457        }
458        # Now we set up the trace mode.
459        my $traceMode;
460        # Verify that we can open a file in the FIG temporary directory.
461      my $traceFileName = "$FIG_Config::temp/trace$suffix.log";      my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
462      if (open TESTTRACE, ">$traceFileName") {      if (open TESTTRACE, ">$traceFileName") {
463          $traceMode = "+>$traceFileName";          # Here we can trace to a file.
464            $traceMode = ">$traceFileName";
465            if ($textOKFlag) {
466                # Echo to standard output if the text-OK flag is set.
467                $traceMode = "+$traceMode";
468            }
469            # Close the test file.
470          close TESTTRACE;          close TESTTRACE;
471        } else {
472            # Here we can't trace to a file. We trace to the standard output if it's
473            # okay, and the error log otherwise.
474            if ($textOKFlag) {
475                $traceMode = "TEXT";
476            } else {
477                $traceMode = "WARN";
478            }
479      }      }
480      # Now set up the tracing.      # Now set up the tracing.
481      TSetup($cats, $traceMode);      TSetup("$traceLevel $cats", $traceMode);
482      # Check for the "h" option. If it is specified, dump the command-line      # Check for the "h" option. If it is specified, dump the command-line
483      # options and exit the program.      # options and exit the program.
484      if ($retOptions->{h}) {      if ($retOptions->{h}) {
# Line 1969  Line 2010 
2010      }      }
2011  }  }
2012    
2013    =head3 SetPermissions
2014    
2015    C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>
2016    
2017    Set the permissions for a directory and all the files and folders inside it.
2018    In addition, the group ownership will be changed to the specified value.
2019    
2020    This method is more vulnerable than most to permission and compatability
2021    problems, so it does internal error recovery.
2022    
2023    =over 4
2024    
2025    =item dirName
2026    
2027    Name of the directory to process.
2028    
2029    =item group
2030    
2031    Name of the group to be assigned.
2032    
2033    =item mask
2034    
2035    Permission mask. Bits that are C<1> in this mask will be ORed into the
2036    permission bits of any file or directory that does not already have them
2037    set to 1.
2038    
2039    =item otherMasks
2040    
2041    Map of search patterns to permission masks. If a directory name matches
2042    one of the patterns, that directory and all its members and subdirectories
2043    will be assigned the new pattern. For example, the following would
2044    assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2045    
2046        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2047    
2048    The list is ordered, so the following would use 0777 for C<tmp1> and
2049    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2050    
2051        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2052                                                       '^tmp' => 0666);
2053    
2054    Note that the pattern matches are all case-insensitive, and only directory
2055    names are matched, not file names.
2056    
2057    =back
2058    
2059    =cut
2060    
2061    sub SetPermissions {
2062        # Get the parameters.
2063        my ($dirName, $group, $mask, @otherMasks) = @_;
2064        # Set up for error recovery.
2065        eval {
2066            # Switch to the specified directory.
2067            ChDir($dirName);
2068            # Get the group ID.
2069            my $gid = getgrnam($group);
2070            # Get the mask for tracing.
2071            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2072            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(2);
2073            my $fixCount = 0;
2074            my $lookCount = 0;
2075            # @dirs will be a stack of directories to be processed.
2076            my @dirs = (getcwd());
2077            while (scalar(@dirs) > 0) {
2078                # Get the current directory.
2079                my $dir = pop @dirs;
2080                # Check for a match to one of the specified directory names. To do
2081                # that, we need to pull the individual part of the name off of the
2082                # whole path.
2083                my $simpleName = $dir;
2084                if ($dir =~ m!/(.+)$!) {
2085                    $simpleName = $1;
2086                }
2087                # Search for a match.
2088                my $match = 0;
2089                my $i;
2090                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2091                    my $pattern = $otherMasks[$i];
2092                    if ($simpleName =~ /$pattern/i) {
2093                        $match = 1;
2094                    }
2095                }
2096                # Check for a match. Note we use $i-1 because the loop added 2
2097                # before terminating due to the match.
2098                if ($match && $otherMasks[$i-1] != $mask) {
2099                    # This directory matches one of the incoming patterns, and it's
2100                    # a different mask, so we process it recursively with that mask.
2101                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2102                } else {
2103                    # Here we can process normally. Get all of the non-hidden members.
2104                    my @submems = OpenDir($dir, 1);
2105                    for my $submem (@submems) {
2106                        # Get the full name.
2107                        my $thisMem = "$dir/$submem";
2108                        Trace("Checking member $thisMem.") if T(4);
2109                        $lookCount++;
2110                        if ($lookCount % 1000 == 0) {
2111                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(3);
2112                        }
2113                        # Fix the group.
2114                        chown -1, $gid, $thisMem;
2115                        # Insure this member is not a symlink.
2116                        if (! -l $thisMem) {
2117                            # Get its info.
2118                            my $fileInfo = stat $thisMem;
2119                            # Only proceed if we got the info. Otherwise, it's a hard link
2120                            # and we want to skip it anyway.
2121                            if ($fileInfo) {
2122                                my $fileMode = $fileInfo->mode;
2123                                if (($fileMode & $mask) == 0) {
2124                                    # Fix this member.
2125                                    $fileMode |= $mask;
2126                                    chmod $fileMode, $thisMem;
2127                                    $fixCount++;
2128                                }
2129                                # If it's a subdirectory, stack it.
2130                                if (-d $thisMem) {
2131                                    push @dirs, $thisMem;
2132                                }
2133                            }
2134                        }
2135                    }
2136                }
2137            }
2138            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(2);
2139        };
2140        # Check for an error.
2141        if ($@) {
2142            Confess("SetPermissions error: $@");
2143        }
2144    }
2145    
2146  1;  1;

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