comparison tests/run-tests.py @ 9:6cc488e11544 draft

"planemo upload for repository https://github.com/galaxyproject/dunovo commit 5a2e08bc1213b0437d0adcb45f7f431bd3c735f4"

8:411adeff1eec

#!/usr/bin/env python
import os
import sys
import subprocess

SCRIPT_NAME = 'allele-counts.py'

  test_dir = os.path.dirname(os.path.realpath(__file__))
  script_dir = os.path.relpath(os.path.dirname(test_dir))
  test_dir = os.path.relpath(test_dir)

  if do_print_xml:
    print XML.get('tests_start')

  for dataset in DATASETS:
    infile  = os.path.join(test_dir, dataset+IN_EXT)
    outfile = os.path.join(test_dir, dataset+OUT_EXT)

      print_xml(infile, outfile, options, XML, PARAMS, PARAM_ARG)
    else:
      run_tests(infile, outfile, options, script_dir)

  if do_print_xml:
    print XML.get('tests_end')


def run_tests(infile, outfile, options, script_dir):
  script_cmd = os.path.join(script_dir, SCRIPT_NAME)+' '+options+' -i '+infile
  bash_cmd = 'diff '+outfile+' <('+script_cmd+')'
  print script_cmd
  subprocess.call(['bash', '-c', bash_cmd])


def print_xml(infile, outfile, options_str, xml, params, param_arg):
  infile = os.path.basename(infile)
  outfile = os.path.basename(outfile)

  options = options_str.split()  # on whitespace

  print xml.get('test_start')
  print xml.get('input') % infile

  # read in options one at a time, print <param> line
  i = 0
  while i < len(options):
    opt = options[i]
    if not params.has_key(opt) or not param_arg.has_key(opt):
      sys.stderr.write("Error: unknown option '"+opt+"' in ARGS list in file "
        +infile+"\n")
      sys.exit(1)
    # takes argument
    if param_arg[opt]:
      i+=1
      arg = options[i]
      print xml.get('param') % (params[opt], arg)
    # no argument (boolean)
    else:
      print xml.get('param') % (params[opt], 'true')
    i+=1

  print xml.get('output') % outfile
  print xml.get('test_end')


def read_options(infile):
  with open(infile, 'r') as infilehandle:
    for line in infilehandle:

9:6cc488e11544

#!/usr/bin/env python3
import os
import sys
import subprocess

SCRIPT_NAME = 'allele-counts.py'

  test_dir = os.path.dirname(os.path.realpath(__file__))
  script_dir = os.path.relpath(os.path.dirname(test_dir))
  test_dir = os.path.relpath(test_dir)

  if do_print_xml:
    print(XML.get('tests_start'))

  for dataset in DATASETS:
    infile  = os.path.join(test_dir, dataset+IN_EXT)
    outfile = os.path.join(test_dir, dataset+OUT_EXT)

      print_xml(infile, outfile, options, XML, PARAMS, PARAM_ARG)
    else:
      run_tests(infile, outfile, options, script_dir)

  if do_print_xml:
    print(XML.get('tests_end'))


def run_tests(infile, outfile, options, script_dir):
  script_cmd = os.path.join(script_dir, SCRIPT_NAME)+' '+options+' -i '+infile
  bash_cmd = 'diff '+outfile+' <('+script_cmd+')'
  print(script_cmd)
  subprocess.call(['bash', '-c', bash_cmd])


def print_xml(infile, outfile, options_str, xml, params, param_arg):
  infile = os.path.basename(infile)
  outfile = os.path.basename(outfile)

  options = options_str.split()  # on whitespace

  print(xml.get('test_start'))
  print(xml.get('input') % infile)

  # read in options one at a time, print <param> line
  i = 0
  while i < len(options):
    opt = options[i]
    if opt not in params or opt not in param_arg:
      sys.stderr.write("Error: unknown option '"+opt+"' in ARGS list in file "+infile+"\n")
      sys.exit(1)
    # takes argument
    if param_arg[opt]:
      i+=1
      arg = options[i]
      print(xml.get('param') % (params[opt], arg))
    # no argument (boolean)
    else:
      print(xml.get('param') % (params[opt], 'true'))
    i+=1

  print(xml.get('output') % outfile)
  print(xml.get('test_end'))


def read_options(infile):
  with open(infile, 'r') as infilehandle:
    for line in infilehandle: