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[WORK IN PROGRESS] - preparsing job recognises uploaded archive better #492

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[WORK IN PROGRESS] - preparsing job recognises uploaded archive better #492

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08e2c4b
First piece of work on the preparsing file recognition
philippbayer Mar 27, 2018
276b593
Fixed python True/False with ruby true/false
philippbayer Mar 27, 2018
2485376
Merge branch 'master' into fixUploadZip
philippbayer Mar 27, 2018
9369ad0
Accidentally left part of hack in
philippbayer Mar 27, 2018
610c56f
Satisfy hound
philippbayer Mar 27, 2018
b5b38a0
further hound satisfaction
philippbayer Mar 27, 2018
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54 changes: 42 additions & 12 deletions app/workers/preparsing.rb
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Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
# frozen_string_literal: true
require 'zip'
require 'zlib'
require 'rubygems/package'
require 'digest'

class Preparsing
Expand All @@ -10,11 +12,40 @@ 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 = `file #{genotype.genotype.path}`
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I saw some .docx files as well.. not sure if after extraction or before..

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Haha, yeah, some folks aren't great at uploading the right file types. I'd say we should reject anything that's not ASCII post-unzip :)

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That's true. I also saw a few post-genotype analyses from Promethease.

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 = -> (zipfile) { Gem::Package::TarReader.new(Zlib::GzipReader.open(zipfile)) }
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Do not use spaces between -> and opening brace in lambda literals

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
Expand All @@ -23,18 +54,17 @@ def perform(genotype_id)
end
end

zipfile.extract(biggest,"#{Rails.root}/tmp/#{genotype.fs_filename}.csv")
system("mv #{Rails.root}/tmp/#{genotype.fs_filename}.csv #{Rails.root}/public/data/#{genotype.fs_filename}")
logger.info "copied file"
zipfile.extract(biggest, Rails.root.join('tmp', "#{genotype.fs_filename}.csv"))
system("mv #{Rails.root.join('tmp', "#{genotype.fs_filename}.csv")} #{Rails.root.join('public', 'data',genotype.fs_filename)}")
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Please use Rails.root.join('path', 'to') instead.
Line is too long. [135/100]
Space missing after comma.

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.join('public', 'data', genotype.fs_filename)}")
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Please use Rails.root.join('path', 'to') instead.
Line is too long. [103/100]

end

# now that they are unzipped, check if they're actually proper files
file_is_ok = false
fh = File.open(genotype.genotype.path)
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How did this ever work?? It parses the original uploaded file the way this looks like, that can be anything before extraction

fh = File.open Rails.root.join('public', 'data', genotype.fs_filename)
l = fh.readline()
# some files, for some reason, start with the UTF-BOM-marker
l = l.sub("\uFEFF","")
Expand Down