[WORK IN PROGRESS] - preparsing job recognises uploaded archive better

app/workers/preparsing.rb

@@ -1,5 +1,7 @@
 # frozen_string_literal: true
 require 'zip'
+require 'zlib'
+require 'rubygems/package'
 require 'digest'
 
 class Preparsing
@@ -10,11 +12,41 @@ class Preparsing
   def perform(genotype_id)
     genotype = Genotype.find(genotype_id)
 
-    logger.info "Starting preparse"
-    biggest = ''
-    biggest_size = 0
-    begin
-      Zip::File.open(genotype.genotype.path) do |zipfile|
+    logger.info "Starting preparse on #{genotype.genotype.path}"
+    # First, we need to find out which archive or flat text our uploaded file is!
+    # We use the bash tool file for that
+    #
+    # There are two possible outcomes - file is a collection of files (tar, tar.gz, zip)
+    # or file is a single file (ASCII, gz)
+    filetype = %x{file #{genotype.genotype.path}}
+    case filetype
+    when /ASCII text/
+      logger.info "File is flat text"
+      reader = File.method("open")
+      is_collection = false
+    when /gzip compressed data, was/
+      reader = Zlib::GzipReader.method("open")
+      logger.info "File is gz"
+      is_collection = false
+    when /gzip compressed data, last modified/
+      reader = lambda { |zipfile| Gem::Package::TarReader.new(Zlib::GzipReader.open(zipfile)) }
+      is_collection = true
+    when /POSIX tar archive/
+      logger.info "File is tar"
+      reader = Gem::Package::TarReader.method("new")
+      is_collection = true
+    when /Zip archive data/
+      logger.info "File is zip"
+      reader = Zip::File.method("open")
+      is_collection = true
+    end
+
+
+    if is_collection
+      # Find the biggest file in the archive
+      biggest = ''
+      biggest_size = 0
+      reader.call genotype.genotype.path do |zipfile|
         # find the biggest file, since that's going to be the genotyping
         zipfile.each do |entry|
           if entry.size > biggest_size
@@ -27,14 +59,13 @@ def perform(genotype_id)
         system("mv #{Rails.root}/tmp/#{genotype.fs_filename}.csv #{Rails.root}/public/data/#{genotype.fs_filename}")
         logger.info "copied file"
       end
-
-    rescue
-      logger.info "nothing to unzip, seems to be a text-file in the first place"
+    else
+      system("cp #{genotype.genotype.path} #{Rails.root}/public/data/#{genotype.fs_filename}")
     end
 
     # now that they are unzipped, check if they're actually proper files
     file_is_ok = false
-    fh = File.open(genotype.genotype.path)
+    fh = File.open "#{Rails.root}/public/data/#{genotype.fs_filename}"
     l = fh.readline()
     # some files, for some reason, start with the UTF-BOM-marker
     l = l.sub("\uFEFF","")