old_contents: 
  import os, sys
  import gzip
  
  import json
  import os
  script_dir = os.getcwd()
  current_dir = os.getcwd().split('/')
  #remove just one path and add mendel,md
  current_dir[-1] = 'mendelmd_source'
  
  proj_path = "/".join(current_dir)
  # This is so Django knows where to find stuff.
  os.environ.setdefault("DJANGO_SETTINGS_MODULE", "mendelmd.settings")
  sys.path.append(proj_path)
  
  # This is so my local_settings.py gets loaded.
  os.chdir(proj_path)
  
  # This is so models get loaded.
  from django.core.wsgi import get_wsgi_application
  application = get_wsgi_application()
  
  from individuals.models import Individual
  from django.contrib.auth.models import User
  from django.core.files import File
  from django.utils.text import slugify
  from individuals.tasks import VerifyVCF
  from django.conf import settings
  import argparse
  
  parser = argparse.ArgumentParser()
  parser.add_argument('-i', '--input', default='input', required=True)
  args = parser.parse_args()
  
  # print(args)
  
  
  individuals = Individual.objects.all()
  
  user = User.objects.first()
  
  print(user)
  individual = Individual.objects.create(user=user, status='new')
  
  # filepath = '/home/raony/dev/mendelmd/examples/miller.vcf.gz'
  filepath = args.input
  
  filename = os.path.basename(filepath)
  dirname = os.path.dirname(filepath)
  print(dirname)
  print(filename)
  
  command = 'cp %s .' % (filepath)
  os.system(command)
  
  if filename.endswith('.gz'):
      file = gzip.open('%s' % (filename))
  else:
      file = open('%s' % (filename))
  
  individual.vcf_file = File(file)
  
  # print(individual.vcf_file.file)
  
  command = 'rm %s' % (filename)
  os.system(command)
  
  individual.name = str(os.path.splitext(individual.vcf_file.name)[0]).replace('.vcf', '').replace('.gz', '').replace('.rar', '').replace('.zip', '').replace('._', ' ').replace('.', ' ')
  individual.save()
  os.chmod("%s/genomes/%s/%s" % (settings.BASE_DIR, slugify(individual.user), individual.id), 0o777)
  
  VerifyVCF.delay(individual.id)
new_contents: 
  import os, sys
  import gzip
  
  import json
  import os
  script_dir = os.getcwd()
  current_dir = os.getcwd().split('/')
  #remove just one path and add mendel,md
  current_dir[-1] = 'mendelmd_source'
  
  proj_path = "/".join(current_dir)
  # This is so Django knows where to find stuff.
  os.environ.setdefault("DJANGO_SETTINGS_MODULE", "mendelmd.settings")
  sys.path.append(proj_path)
  
  # This is so my local_settings.py gets loaded.
  os.chdir(proj_path)
  
  # This is so models get loaded.
  from django.core.wsgi import get_wsgi_application
  application = get_wsgi_application()
  
  from individuals.models import Individual
  from django.contrib.auth.models import User
  from django.core.files import File
  from django.utils.text import slugify
  from individuals.tasks import VerifyVCF
  from django.conf import settings
  import argparse
  
  parser = argparse.ArgumentParser()
  parser.add_argument('-i', '--input', default='input', required=True)
  args = parser.parse_args()
  
  # print(args)
  
  
  individuals = Individual.objects.all()
  
  user = User.objects.first()
  
  print(user)
  individual = Individual.objects.create(user=user, status='new')
  
  # filepath = '/home/raony/dev/mendelmd/examples/miller.vcf.gz'
  filepath = args.input
  
  filename = os.path.basename(filepath)
  dirname = os.path.dirname(filepath)
  print(dirname)
  print(filename)
  
  command = 'cp %s .' % (filepath)
  os.system(command)
  
  if filename.endswith('.gz'):
      file = gzip.GzipFile(fileobj='%s' % (filename))
  else:
      file = open('%s' % (filename))
  
  individual.vcf_file = File(file)
  
  # print(individual.vcf_file.file)
  
  command = 'rm %s' % (filename)
  os.system(command)
  
  individual.name = str(os.path.splitext(individual.vcf_file.name)[0]).replace('.vcf', '').replace('.gz', '').replace('.rar', '').replace('.zip', '').replace('._', ' ').replace('.', ' ')
  individual.save()
  os.chmod("%s/genomes/%s/%s" % (settings.BASE_DIR, slugify(individual.user), individual.id), 0o777)
  
  VerifyVCF.delay(individual.id)
subject: fix indivdual add