def test_process_options(self):
#Test the process_options
options = config_util.AMPLEConfigOptions()
options.d = {'fasta' : 'foo',
'side_chain_treatments' : [],
'rcdir' : os.path.join(os.sep, 'foo', 'bar'),
'nproc' : 1,
'submit_qtype' : False,
'shelxe_rebuild' : True,
'shelxe_rebuild_arpwarp' : False,
'shelxe_rebuild_buccaneer' : False,
'classic_mode' : False,
'devel_mode' : False,
'quick_mode' : False,
'thin_clusters' : False,
'webserver_uri' : False,
}
expected = {'ample_version' : version.__version__,
'fasta' : os.path.join(os.getcwd(), 'foo'),
'rcdir' : os.path.join(os.sep, 'foo', 'bar'),
'side_chain_treatments' : ['polyAla', 'reliable', 'allatom'],
'nproc' : 1,
'submit_qtype' : False,
'shelxe_rebuild' : True,
'shelxe_rebuild_arpwarp' : True,
'shelxe_rebuild_buccaneer' : True,
'classic_mode' : False,
'devel_mode' : False,
'quick_mode' : False,
'thin_clusters' : False,
'webserver_uri' : False,
}
options._process_options()
self.assertItemsEqual(options.d, expected)
def test_roundtrip_config_file(self):
"""Test we can read in and write out a config file with no changes"""
options = config_util.AMPLEConfigOptions()
# All files are run through abspath on reading by the config parser so we need to convert the names
# We can't test [Files] as these are hashed out on writing and ignored on reading
inputd = { 'nr' : os.path.abspath('nr'),
'rosetta_db' : os.path.abspath('rosetta_db'),
'blast_dir' : os.path.abspath('blast_dir'),
'fast_protein_cluster_exe' : os.path.abspath('fpc.exe'),
}
input_str = """[AMPLE_info]
[Databases]
nr = {nr}
rosetta_db = {rosetta_db}
[Executables]
blast_dir = {blast_dir}
fast_protein_cluster_exe = {fast_protein_cluster_exe}
[Files]
[Molecular_Replacement]
F = None
FREE = None
arpwarp_cycles = 10
ensemble_options = None
[Unspecified]
""".format(**inputd)
f1 = tempfile.NamedTemporaryFile("w", delete=False)
f1.write(input_str)
f1.close()
# Read in the file from disk
options._read_config_file(f1.name)
f2 = tempfile.NamedTemporaryFile("w", delete=False)
f2.close()
# Write back out to disk
options.write_config_file(config_file=f2.name)
# Read in and make sure the strings are the same
with open(f2.name) as f2: output_str = f2.read()
self.assertItemsEqual(output_str, input_str)
os.unlink(f1.name)
os.unlink(f2.name)
