Tutorial :Compare many text files that contain duplicate “stubs” from the previous and next file and remove duplicate text automatically



Question:

I have a large number of text files (1000+) each containing an article from an academic journal. Unfortunately each article's file also contains a "stub" from the end of the previous article (at the beginning) and from the beginning of the next article (at the end).

I need to remove these stubs in preparation for running a frequency analysis on the articles because the stubs constitute duplicate data.

There is no simple field that marks the beginning and end of each article in all cases. However, the duplicate text does seem to formatted the same and on the same line in both cases.

A script that compared each file to the next file and then removed 1 copy of the duplicate text would be perfect. This seems like it would be a pretty common issue when programming so I am surprised that I haven't been able to find anything that does this.

The file names sort in order, so a script that compares each file to the next sequentially should work. E.G.

  bul_9_5_181.txt  bul_9_5_186.txt  

are two articles, one starting on page 181 and the other on page 186. Both of these articles are included bellow.

There is two volumes of test data located at [http://drop.io/fdsayre][1]

Note: I am an academic doing content analysis of old journal articles for a project in the history of psychology. I am no programmer, but I do have 10+ years experience with linux and can usually figure things out as I go.

Thanks for your help

FILENAME: bul_9_5_181.txt

SYN&STHESIA

ISI

the majority of Portugese words signifying black objects or ideas relating to black. This association is, admittedly, no true synsesthesia, but the author believes that it is only a matter of degree between these logical and spontaneous associations and genuine cases of colored audition. REFERENCES

DOWNEY, JUNE E. A Case of Colored Gustation. Amer. J. of Psycho!., 1911, 22, S28-539MEDEIROS-E-ALBUQUERQUE. Sur un phenomene de synopsie presente par des millions de sujets. / . de psychol. norm, et path., 1911, 8, 147-151. MYERS, C. S. A Case of Synassthesia. Brit. J. of Psychol., 1911, 4, 228-238.

AFFECTIVE PHENOMENA â€" EXPERIMENTAL BY PROFESSOR JOHN F. .SHEPARD University of Michigan

Three articles have appeared from the Leipzig laboratory during the year. Drozynski (2) objects to the use of gustatory and olfactory stimuli in the study of organic reactions with feelings, because of the disturbance of breathing that may be involved. He uses rhythmical auditory stimuli, and finds that when given at different rates and in various groupings, they are accompanied by characteristic feelings in each subject. He records the chest breathing, and curves from a sphygmograph and a water plethysmograph. Each experiment began with a normal record, then the stimulus was given, and this was followed by a contrast stimulus; lastly, another normal was taken. The length and depth of breathing were measured (no time line was recorded), and the relation of length of inspiration to length of expiration was determined. The length and height of the pulsebeats were also measured. Tabular summaries are given of the number of times the author finds each quantity to have been increased or decreased during a reaction period with each type of feeling. The feeling state accompanying a given rhythm is always complex, but the result is referred to that dimension which seemed to be dominant. Only a few disconnected extracts from normal and reaction periods are reproduced from the records. The author states that excitement gives increase in the rate and depth of breathing, in the inspiration-expiration ratio, and in the rate and size of pulse. There are undulations in the arm volume. In so far as the effect is quieting, it causes decrease in rate and depth of

182

JOHN F. SHEPARD

breathing, in the inspiration-expiration ratio, and in the pulse rate and size. The arm volume shows a tendency to rise with respiratory waves. Agreeableness shows


Solution:1

Here's is the beginning of another possible solution in Perl (It works as is but could probably be made more sophisticated if needed). It sounds as if all you are concerned about is removing duplicates across the corpus and don't really care if the last part of one article is in the file for the next one as long as it isn't duplicated anywhere. If so, this solution will strip out the duplicate lines leaving only one copy of any given line in the set of files as a whole.

You can either just run the file in the directory containing the text files with no argument or alternately specify a file name containing the list of files you want to process in the order you want them processed. I recommend the latter as your file names (at least in the sample files you provided) do not naturally list out in order when using simple commands like ls on the command line or glob in the Perl script. Thus it won't necessarily compare the correct files to one another as it just runs down the list (entered or generated by the glob command). If you specify the list, you can guarantee that they will be processed in the correct order and it doesn't take that long to set it up properly.

The script simply opens two files and makes note of the first three lines of the second file. It then opens a new output file (original file name + '.new') for the first file and writes out all the lines from the first file into the new output file until it finds the first three lines of the second file. There is an off chance that there are not three lines from the second file in the last one but in all the files I spot checked that seemed to be the case because of the journal name header and page numbers. One line definitely wasn't enough as the journal title was often the first line and that would cut things off early.

I should also note that the last file in your list of files entered will not be processed (i.e. have a new file created based off of it) as it will not be changed by this process.

Here's the script:

#!/usr/bin/perl  use strict;    my @files;  my $count = @ARGV;  if ($count>0){      open (IN, "$ARGV[0]");      @files = <IN>;      close (IN);  } else {      @files = glob "bul_*.txt";  }  $count = @files;  print "Processing $count files.\n";    my $lastFile="";  foreach(@files){      if ($lastFile ne ""){          print "Processing $_\n";          open (FILEB,"$_");          my @fileBLines = <FILEB>;          close (FILEB);          my $line0 = $fileBLines[0];              if ($line0 =~ /\(/ || $line0 =~ /\)/){                      $line0 =~ s/\(/\\\(/;                      $line0 =~ s/\)/\\\)/;              }          my $line1 = $fileBLines[1];          my $line2 = $fileBLines[2];          open (FILEA,"$lastFile");          my @fileALines = <FILEA>;          close (FILEA);          my $newName = "$lastFile.new";          open (OUT, ">$newName");          my $i=0;          my $done = 0;          while ($done != 1 and $i < @fileALines){              if ($fileALines[$i] =~ /$line0/                   && $fileALines[$i+1] == $line1                  && $fileALines[$i+2] == $line2) {                  $done=1;              } else {                  print OUT $fileALines[$i];                  $i++;              }          }          close (OUT);      }      $lastFile = $_;  }  

EDIT: Added a check for parenthesis in the first line that goes into the regex check for duplicity later on and if found escapes them so that they don't mess up the duplicity check.


Solution:2

It looks like a much simpler solution would actually work.

No one seems to be using the information provided by the filenames. If you do make use of this information, you may not have to do any comparisons between files to identify the area of overlap. Whoever wrote the OCR probably put some thought into this problem.

The last number in the file name tells you what the starting page number for that file is. This page number appears on a line by itself in the file as well. It also looks like this line is preceded and followed by blank lines. Therefore for a given file you should be able to look at the name of the next file in the sequence and determine the page number at which you should start removing text. Since this page number appears in your file just look for a line that contains only this number (preceded and followed by blank lines) and delete that line and everything after. The last file in the sequence can be left alone.

Here's an outline for an algorithm

  1. choose a file; call it: file1
  2. look at the filename of the next file; call it: file2
  3. extract the page number from the filename of file2; call it: pageNumber
  4. scan the contents of file1 until you find a line that contains only pageNumber
  5. make sure this line is preceded and followed by a blank line.
  6. remove this line and everything after
  7. move on to the next file in the sequence


Solution:3

You should probably try something like this (I've now tested it on the sample data you provided):

#!/usr/bin/ruby    class A_splitter      Title   = /^[A-Z]+[^a-z]*$/      Byline  = /^BY /      Number = /^\d*$/      Blank_line = /^ *$/      attr_accessor :recent_lines,:in_references,:source_glob,:destination_path,:seen_in_last_file      def initialize(src_glob,dst_path=nil)          @recent_lines = []          @seen_in_last_file = {}          @in_references = false          @source_glob = src_glob          @destination_path = dst_path          @destination = STDOUT          @buffer = []          split_em          end      def split_here          if destination_path              @destination.close if @destination              @destination = nil            else              print "------------SPLIT HERE------------\n"             end          print recent_lines.shift          @in_references = false          end      def at_page_break          ((recent_lines[0] =~ Title  and recent_lines[1] =~ Blank_line and recent_lines[2] =~ Number) or           (recent_lines[0] =~ Number and recent_lines[1] =~ Blank_line and recent_lines[2] =~ Title))          end      def print(*args)          (@destination || @buffer) << args          end      def split_em          Dir.glob(source_glob).sort.each { |filename|              if destination_path                  @destination.close if @destination                  @destination = File.open(File.join(@destination_path,filename),'w')                  print @buffer                  @buffer.clear                end              in_header = true              File.foreach(filename) { |line|                  line.gsub!(/\f/,'')                  if in_header and seen_in_last_file[line]                      #skip it                    else                       seen_in_last_file.clear if in_header                      in_header = false                      recent_lines << line                      seen_in_last_file[line] = true                    end                  3.times {recent_lines.shift} if at_page_break                  if recent_lines[0] =~ Title and recent_lines[1] =~ Byline                      split_here                    elsif in_references and recent_lines[0] =~ Title and recent_lines[0] !~ /\d/                      split_here                    elsif recent_lines.length > 4                      @in_references ||= recent_lines[0] =~ /^REFERENCES *$/                      print recent_lines.shift                    end                  }              }           print recent_lines          @destination.close if @destination          end      end    A_splitter.new('bul_*_*_*.txt','test_dir')  

Basically, run through the files in order, and within each file run through the lines in order, omitting from each file the lines that were present in the preceding file and printing the rest to STDOUT (from which it can be piped) unless a destination director is specified (called 'test_dir' in the example see the last line) in which case files are created in the specified directory with the same name as the file which contained the bulk of their contents.

It also removes the page-break sections (journal title, author, and page number).

It does two split tests:

  • a test on the title/byline pair
  • a test on the first title-line after a reference section

(it should be obvious how to add tests for additional split-points).

Retained for posterity:

If you don't specify a destination directory it simply puts a split-here line in the output stream at the split point. This should make it easier for testing (you can just less the output) and when you want them in individual files just pipe it to csplit (e.g. with

csplit -f abstracts - '---SPLIT HERE---' '{*}'  

or something) to cut it up.


Solution:4

You have a nontrivial problem. It is easy to write code to find the duplicate text at the end of file 1 and the beginning of file 2. But you don't want to delete the duplicate text---you want to split it where the second article begins. Getting the split right might be tricky---one marker is the all caps, another is the BY at the start of the next line.

It would have helped to have examples from consecutive files, but the script below works on one test case. Before trying this code, back up all your files. The code overwrites existing files.

The implementation is in Lua. The algorithm is roughly:

  1. Ignore blank lines at the end of file 1 and the start of file 2.
  2. Find a long sequence of lines common to end of file 1 and start of file 2.
    • This works by trying a sequence of 40 lines, then 39, and so on
  3. Remove sequence from both files and call it overlap.
  4. Split overlap at title
  5. Append first part of overlap to file1; prepend second part to file2.
  6. Overwrite contents of files with lists of lines.

Here's the code:

#!/usr/bin/env lua    local ext = arg[1] == '-xxx' and '.xxx' or ''  if #ext > 0 then table.remove(arg, 1) end      local function lines(filename)    local l = { }    for line in io.lines(filename) do table.insert(l, (line:gsub('', ''))) end    assert(#l > 0, "No lines in file " .. filename)    return l  end    local function write_lines(filename, lines)    local f = assert(io.open(filename .. ext, 'w'))    for i = 1, #lines do      f:write(lines[i], '\n')    end    f:close()  end    local function lines_match(line1, line2)    io.stderr:write(string.format("%q ==? %q\n", line1, line2))    return line1 == line2 -- could do an approximate match here  end    local function lines_overlap(l1, l2, k)    if k > #l2 or k > #l1 then return false end    io.stderr:write('*** k = ', k, '\n')    for i = 1, k do      if not lines_match(l2[i], l1[#l1 - k + i]) then        if i > 1 then          io.stderr:write('After ', i-1, ' matches: FAILED <====\n')        end        return false      end    end    return true  end    function find_overlaps(fname1, fname2)    local l1, l2 = lines(fname1), lines(fname2)    -- strip trailing and leading blank lines    while l1[#l1]:find '^[%s]*$' do table.remove(l1)    end    while l2[1]  :find '^[%s]*$' do table.remove(l2, 1) end    local matchsize  -- # of lines at end of file 1 that are equal to the same                      -- # at the start of file 2    for k = math.min(40, #l1, #l2), 1, -1 do      if lines_overlap(l1, l2, k) then        matchsize = k        io.stderr:write('Found match of ', k, ' lines\n')        break      end    end      if matchsize == nil then      return false -- failed to find an overlap    else      local overlap = { }      for j = 1, matchsize do        table.remove(l1) -- remove line from first set        table.insert(overlap, table.remove(l2, 1))      end      return l1, overlap, l2    end  end    local function split_overlap(l)    for i = 1, #l-1 do      if l[i]:match '%u' and not l[i]:match '%l' then -- has caps but no lowers        -- io.stderr:write('Looking for byline following ', l[i], '\n')        if l[i+1]:match '^%s*BY%s' then          local first = {}          for j = 1, i-1 do            table.insert(first, table.remove(l, 1))          end          -- io.stderr:write('Split with first line at ', l[1], '\n')          return first, l        end      end    end  end    local function strip_overlaps(filename1, filename2)    local l1, overlap, l2 = find_overlaps(filename1, filename2)    if not l1 then      io.stderr:write('No overlap in ', filename1, ' an  


Solution:5

Are the stubs identical to the end of the previous file? Or different line endings/OCR mistakes?

Is there a way to discern an article's beginning? Maybe an indented abstract? Then you could go through each file and discard everything before the first and after (including) the second title.


Solution:6

Are the titles & author always on a single line? And does that line always contain the word "BY" in uppercase? If so, you can probably do a fair job withn awk, using those criteria as the begin/end marker.

Edit: I really don't think that using diff is going to work as it is a tool for comparing broadly similar files. Your files are (from diff's point of view) actually completely different - I think it will get out of sync immediately. But then, I'm not a diff guru :-)


Solution:7

A quick stab at it, assuming that the stub is strictly identical in both files:

#!/usr/bin/perl    use strict;    use List::MoreUtils qw/ indexes all pairwise /;    my @files = @ARGV;    my @previous_text;    for my $filename ( @files ) {      open my $in_fh,  '<', $filename          or die;      open my $out_fh, '>', $filename.'.clean' or die;        my @lines = <$in_fh>;      print $out_fh destub( \@previous_text, @lines );      @previous_text = @lines;  }      sub destub {      my @previous = @{ shift() };      my @lines = @_;        my @potential_stubs = indexes { $_ eq $lines[0] } @previous;        for my $i ( @potential_stubs ) {          # check if the two documents overlap for that index          my @p = @previous[ $i.. $#previous ];          my @l = @lines[ 0..$#previous-$i ];            return @lines[ $#previous-$i + 1 .. $#lines ]                  if all { $_ } pairwise { $a eq $b } @p, @l;        }        # no stub detected      return @lines;  }  

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