src/utils/qa/getJoinerKeyErrors.pl 1.5

Index: src/utils/qa/getJoinerKeyErrors.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/getJoinerKeyErrors.pl,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 1000000 -r1.4 -r1.5
--- src/utils/qa/getJoinerKeyErrors.pl	27 Aug 2008 23:04:53 -0000	1.4
+++ src/utils/qa/getJoinerKeyErrors.pl	21 May 2010 23:52:35 -0000	1.5
@@ -1,135 +1,135 @@
 #!/usr/local/bin/perl5
 
 # Program : getJoinerKeyErrors.pl
 # Purpose : parses output of joinerCheck and captures Errors and associated lines
-# Results : http://hgwdev.cse.ucsc.edu/qa/test-results/joinerCheck_monitor/keys/
+# Results : http://genecats.cse.ucsc.edu/qa/test-results/joinerCheck_monitor/keys/
 # Author  : Jennifer Jackson
 # Int Date: 2005-03-04
 # Rev Date: 2005-11-XX
 # Author  : Ann Zweig
 # Rev Date: 2006-02-13 - added results to HTML page
-# Results : http://hgwdev.cse.ucsc.edu/qa/test-results/joinerCheck_monitor/keys/joinerKeyErrors.YYMMDD
+# Results : http://genecats.cse.ucsc.edu/qa/test-results/joinerCheck_monitor/keys/joinerKeyErrors.YYMMDD
 
 use File::Copy;
 
 
 if ($#ARGV != 0) { die
 "\nUSAGE: $0 /hive/groups/qa/joinerCheck/keys/YYYYMM 
 	run on dev, use path exactly as shown in usage (YYYYMM ex: 200503)
         parses output of 'joinerCheck -keys' and captures errors and associated lines
 	parses all files in dir, input/ingored file names are listed in output file report 
        	report is in target directory: joinerKeyErrors.YYMMDD 
 	STDERR is sent to screen
 	reports can be viewed online at:
-	http://hgwdev.cse.ucsc.edu/qa/test-results/joinerCheck_monitor/keys/YYYYMM/*\n\n";}
+	http://genecats.cse.ucsc.edu/qa/test-results/joinerCheck_monitor/keys/YYYYMM/*\n\n";}
 
 # State the program has started
 print STDERR "PROCESSING: $0 program started, locating directory & input files\n";
 
 
 # get input file names     
 chomp($in_dir = $ARGV[0]);
 if ($in_dir =~ /\/hive\/groups\/qa\/joinerCheck\/keys\/[0-9]{6}/) {
    $path = $in_dir;
 }  else {
    die "ERROR: Path to directory incorrectly formatted $in_dir\n";
 }
 
 # get date
 ($day,$month,$year) = (localtime)[3,4,5];
 $f_month = ($month+1);
 $f_year  = (($year+1900)-2000);
 if (length($day) != 2) { $p_day = "0$day"; } else { $p_day = $day; } 
 if (length($f_year) != 2) { $p_year = "0$f_year"; } else {$p_year = $f_year; }
 if (length($f_month) != 2) { $p_month = "0$f_month"; } else {$p_month = $f_month; }
 #print "$p_year$p_month$p_day\n";
 
 
 # open outfile for writing
 $outfile = "$path/joinerKeyErrors.$p_year$p_month$p_day";
 open OUT, ">$outfile" || die "ERROR: Cannot open $outfile for writing\n";
 print OUT "$outfile\n\n";
 print OUT "Files evaluated and associated errors----------\n\n";
 
 $skipped_count     = 0;
 $not_skipped_count = 0;
 
 
 # open dir, open each file and extract error info
 opendir(DIR, $path) || die "ERROR: Cannot open $path for reading\n";
 
 while (defined($file = readdir(DIR))) {
 
 if (($file =~ /^\./) || ($file =~ /^$/)) {
   next;
 } else { 
  open(FILE,"$path/$file"); 
 
  $line        = 0;
  $errors      = 0;
  $non_errors  = 0;
  $examples    = 0;
  $skipped     = "";
  $not_skipped = "";
  $loops       = 0;
  $noloop      = 0;
  $notfirst    = 0;
  
  while(<FILE>) {
   chomp;
   s/^ //;
   @row = split(/ /, $_);
   $line++; 
   
   if (($line == 1) && ($row[0] eq "Checking")) {
      print OUT "\n$file errors found (if any):\n"; 
      $skipped = 1;
      $not_skipped_count++;
    } elsif (($line == 1) && ($row[0] ne "Checking")) {
      print OUT "\n$file skipped (not joinerCheck output)\n";
      $skipped = 2;
      $skipped_count++;
    } else {
      $notfirst++;
    }
 
 
   if (($line > 1) && ($skipped == 1)) {
       $loops++;
       if ($row[0] eq "Error:") {
          $last_error_line = $line;
          $errors++;
          print OUT "  $_\n";
        } elsif (($line == ($last_error_line + 1)) && ($row[0] eq "Example")) {
          $examples++;    
          print OUT "  $_\n";
        } else {
          $non_errors++;
        }
     } else {
       $noloop++;
     } 
   
   next;
  }
 
  if ($skipped == 1) {  
  print OUT "Total lines(including header):$line, errors:$errors, examples:$examples, non-errors:$non_errors\n\n";
  #print OUT "Loops:$loops, Ingored Lines in skipped files:$noloop, Not first: $notfirst\n\n";    
  }
 }
 }
 
 print OUT "\n\nTotal number of files evaluated for errors: $not_skipped_count\n";
 print OUT "Total number of files not evaluated (skipped): $skipped_count\n";
 
 
 print STDERR "PROCESSING: $0 program completed successfully.\nOutput: $outfile\n";
 
 closedir(DIR);
 
 # copy results to html location
 $oldlocation = "joinerKeyErrors.$p_year$p_month$p_day";
-$newlocation = "/usr/local/apache/htdocs/qa/test-results/joinerCheck_monitor/keys/joinerKeyErrors.$p_year$p_month$p_day";
+$newlocation = "/usr/local/apache/htdocs-genecats/qa/test-results/joinerCheck_monitor/keys/joinerKeyErrors.$p_year$p_month$p_day";
 copy($oldlocation, $newlocation);