def test_for_unrecognized_values(self):
"""qiime_config has no extra values"""
error_msg_fragment = (" contains unrecognized values:\n%s\nYou can "
"safely remove these values from your QIIME "
"config file as they will be ignored by QIIME.")
qiime_project_dir = get_qiime_project_dir()
orig_config = parse_qiime_config_file(open(qiime_project_dir +
'/qiime/support_files/qiime_config'))
# check the env qiime_config
qiime_config_env_filepath = getenv('QIIME_CONFIG_FP')
if qiime_config_env_filepath:
qiime_config_via_env = parse_qiime_config_file(
open(qiime_config_env_filepath))
extra_vals = []
for key in qiime_config_via_env:
if key not in orig_config:
extra_vals.append(key)
if extra_vals:
self.fail("The QIIME config file set via the QIIME_CONFIG_FP "
"environment variable" +
error_msg_fragment % ", ".join(extra_vals))
# check the qiime_config in $HOME/.qiime_config
home_dir = getenv('HOME')
if (exists(home_dir + "/.qiime_config")):
qiime_config_home = parse_qiime_config_file(
open(home_dir + "/.qiime_config"))
extra_vals = []
for key in qiime_config_home:
if key not in orig_config:
extra_vals.append(key)
if extra_vals:
self.fail("The .qiime_config in your HOME" +
error_msg_fragment % ", ".join(extra_vals))
def test_for_obsolete_values(self):
"""local qiime_config has no extra params"""
qiime_project_dir = get_qiime_project_dir()
orig_config = parse_qiime_config_file(open(qiime_project_dir +
'/qiime/support_files/qiime_config'))
#check the env qiime_config
qiime_config_env_filepath = getenv('QIIME_CONFIG_FP')
if qiime_config_env_filepath:
qiime_config_via_env= parse_qiime_config_file(open(qiime_config_env_filepath))
extra_vals = []
for key in qiime_config_via_env:
if key not in orig_config:
extra_vals.append(key)
if extra_vals:
self.fail("The qiime_config file set via QIIME_CONFIG_FP"+
"enviroment variable contains obsolete parameters:\n"+
", ".join(extra_vals))
# check the qiime_config in $HOME/.qiime_config
home_dir = getenv('HOME')
if (exists(home_dir+"/.qiime_config")):
qiime_config_home = parse_qiime_config_file(open(home_dir+"/.qiime_config"))
extra_vals = []
for key in qiime_config_home:
if key not in orig_config:
extra_vals.append(key)
if extra_vals:
self.fail("The .qiime_config in your HOME contains obsolete "+
"parameters:\n" + ", ".join(extra_vals))
def test_for_obsolete_values(self):
"""local qiime_config has no extra params"""
qiime_project_dir = get_qiime_project_dir()
orig_config = parse_qiime_config_file(open(qiime_project_dir +
'/qiime/support_files/qiime_config'))
#check the env qiime_config
qiime_config_env_filepath = getenv('QIIME_CONFIG_FP')
if qiime_config_env_filepath:
qiime_config_via_env= parse_qiime_config_file(open(qiime_config_env_filepath))
extra_vals = []
for key in qiime_config_via_env:
if key not in orig_config:
extra_vals.append(key)
if extra_vals:
self.fail("The qiime_config file set via QIIME_CONFIG_FP"+
"enviroment variable contains obsolete parameters:\n"+
", ".join(extra_vals))
# check the qiime_config in $HOME/.qiime_config
home_dir = getenv('HOME')
if (exists(home_dir+"/.qiime_config")):
qiime_config_home = parse_qiime_config_file(open(home_dir+"/.qiime_config"))
extra_vals = []
for key in qiime_config_home:
if key not in orig_config:
extra_vals.append(key)
if extra_vals:
self.fail("The .qiime_config in your HOME contains obsolete "+
"parameters:\n" + ", ".join(extra_vals))
def test_for_unrecognized_values(self):
"""qiime_config has no extra values"""
error_msg_fragment = (" contains unrecognized values:\n%s\nYou can "
"safely remove these values from your QIIME "
"config file as they will be ignored by QIIME.")
qiime_project_dir = get_qiime_project_dir()
orig_config = parse_qiime_config_file(
open(qiime_project_dir + '/qiime/support_files/qiime_config'))
# check the env qiime_config
qiime_config_env_filepath = getenv('QIIME_CONFIG_FP')
if qiime_config_env_filepath:
qiime_config_via_env = parse_qiime_config_file(
open(qiime_config_env_filepath))
extra_vals = []
for key in qiime_config_via_env:
if key not in orig_config:
extra_vals.append(key)
if extra_vals:
self.fail("The QIIME config file set via the QIIME_CONFIG_FP "
"environment variable" +
error_msg_fragment % ", ".join(extra_vals))
# check the qiime_config in $HOME/.qiime_config
home_dir = getenv('HOME')
if (exists(home_dir + "/.qiime_config")):
qiime_config_home = parse_qiime_config_file(
open(home_dir + "/.qiime_config"))
extra_vals = []
for key in qiime_config_home:
if key not in orig_config:
extra_vals.append(key)
if extra_vals:
self.fail("The .qiime_config in your HOME" +
error_msg_fragment % ", ".join(extra_vals))
