def test_update_config_file_to_version5(self):
config_file = "yarss2_v4.conf"
filename = yarss2.util.common.get_resource(config_file, path="tests/data/")
tmp_dir = common.get_tmp_dir()
shutil.copy(filename, tmp_dir)
self.config = common.get_test_config(config_filename=config_file, config_dir=tmp_dir, verify_config=False)
# Call the function that makes the changes
self.config.config.run_converter((4, 4), 5, self.config.update_config_to_version5)
# Test changes for "add_torrents_in_paused_state_to_GeneralSubsConf"
self.assertEquals(self.config.config["subscriptions"]["0"]["add_torrents_in_paused_state"], GeneralSubsConf.DISABLED)
self.assertEquals(self.config.config["subscriptions"]["1"]["add_torrents_in_paused_state"], GeneralSubsConf.ENABLED)
for key in self.config.config["subscriptions"].keys():
# last_update replaced with last_match
self.assertFalse("last_update" in self.config.config["subscriptions"][key])
self.assertTrue("last_match" in self.config.config["subscriptions"][key])
# Add in paused state should be unicode
self.assertEquals(type(self.config.config["subscriptions"][key]["add_torrents_in_paused_state"]), unicode)
self.assertTrue("max_upload_slots" in self.config.config["subscriptions"][key])
self.assertTrue("max_connections" in self.config.config["subscriptions"][key])
self.assertTrue("max_upload_speed" in self.config.config["subscriptions"][key])
self.assertTrue("prioritize_first_last_pieces" in self.config.config["subscriptions"][key])
self.assertTrue("auto_managed" in self.config.config["subscriptions"][key])
self.assertTrue("sequential_download" in self.config.config["subscriptions"][key])
# Test changes for "change_value_from_list_to_dict"
for cookie in self.config.config["cookies"].values():
self.assertEquals(type(cookie["value"]), dict)
def test_update_config_file_from_1_2_beta(self):
tmp_dir = common.get_tmp_dir()
config_file = "yarss2_v1.2.beta.conf"
filename = yarss2.util.common.get_resource(config_file, path="tests/data/")
shutil.copy(filename, tmp_dir)
self.config = common.get_test_config(config_filename=config_file, config_dir=tmp_dir, verify_config=False)
self.assertEquals(self.config.config._Config__version["format"], 1)
self.assertEquals(self.config.config._Config__version["file"], 2)
# Verify that the old values are what we expect
for key in self.config.config["cookies"].keys():
self.assertEquals(type(self.config.config["cookies"][key]["value"]), dict)
# Update the config
self.config._verify_config()
config_dict = self.config.config.config
config_file = "yarss2_v5.conf"
filename = yarss2.util.common.get_resource(config_file, path="tests/data/")
shutil.copy(filename, tmp_dir)
self.config = common.get_test_config(config_filename=config_file, config_dir=tmp_dir, verify_config=False)
config_dict_v5 = self.config.config.config
# Verify that the 1.2 beta config equals the config updated from earlier versions
self.assertTrue(yarss2.util.common.dicts_equals(config_dict_v5, config_dict))
def initialize(self):
self.info("[US1608][BI] : Allow RSA and DSA SSH keys - CLI")
self.user_email = self.config.OPENSHIFT_user_email
self.user_passwd = self.config.OPENSHIFT_user_passwd
self.app_type = common.app_types["php"]
self.app_name = "php"+common.getRandomString(7)
self.backup_dir = os.path.join(common.get_tmp_dir(),common.getRandomString(10))
self.ssh_keyname="id_rsa"
self.ssh_key = os.path.join(os.path.expanduser("~"),".ssh", self.ssh_keyname)
common.env_setup()
def gen_dsa_key(self):
key_path=os.path.join(common.get_tmp_dir(), self.ssh_keyname)
try:
os.remove(key_path)
except:
pass
cmd = "ssh-keygen -t dsa -N '' -f %s "%(key_path)
r = common.cmd_get_status(cmd, quiet=True)
if r == 0:
os.rename(key_path, self.ssh_key)
os.rename(key_path+".pub", self.ssh_key+".pub")
return 0
else:
self.error("Unable to generate new DSA key")
return 1
def test_update_config_file_to_version2(self):
config_file = "yarss2_v1.conf"
filename = yarss2.util.common.get_resource(config_file, path="tests/data/")
tmp_dir = common.get_tmp_dir()
shutil.copy(filename, tmp_dir)
self.config = common.get_test_config(config_filename=config_file, config_dir=tmp_dir, verify_config=False)
# Call the function that makes the changes
self.config.config.run_converter((0, 1), 2, self.config.update_config_to_version2)
# 1 - search field from subscription was removed
# 2 - Added field 'custom_text_lines'
subscriptions = self.config.config["subscriptions"]
for key in subscriptions:
self.assertFalse(subscriptions[key].has_key("search"), "Field 'search still exists'")
self.assertTrue(subscriptions[key].has_key("custom_text_lines"), "Field 'custom_text_lines' does not exist!")
def test_update_config_file_to_version4(self):
config_file = "yarss2_v3.conf"
filename = yarss2.util.common.get_resource(config_file, path="tests/data/")
tmp_dir = common.get_tmp_dir()
shutil.copy(filename, tmp_dir)
self.config = common.get_test_config(config_filename=config_file, config_dir=tmp_dir, verify_config=False)
subscription_keys = self.config.config["subscriptions"].keys()
last_update_values = [self.config.config["subscriptions"][key]["last_update"] for key in subscription_keys]
# Call the function that makes the changes
self.config.config.run_converter((3, 3), 4, self.config.update_config_to_version4)
for i, key in enumerate(subscription_keys):
# Test changes for "replace_last_update_with_last_match"
self.assertTrue(self.config.config["subscriptions"][key].has_key("last_match"))
self.assertFalse(self.config.config["subscriptions"][key].has_key("last_update"))
self.assertEquals(self.config.config["subscriptions"][key]["last_match"], last_update_values[i])
def run_ase(self, job):
(mystr, _) = self.coords2xyz(job.v)
tmp_dir = common.get_tmp_dir()
job_base_name = "asejob" + str(self.__get_job_counter())
mol_geom_file = os.path.join(tmp_dir, job_base_name + ".xyz")
ase_stdout_file = os.path.join(tmp_dir, job_base_name + ".stdout")
results_file = os.path.join(tmp_dir,
job_base_name + common.LOGFILE_EXT)
# write input file as xyz format
f = open(mol_geom_file, "w")
f.write(mystr)
f.close()
# p = Popen(["./aseisolator.py", self.ase_settings_file, mol_geom_file], stdout=open(ase_stdout_file, "w"))
cmd = [
"python", "-m", "aseisolator", self.ase_settings_file,
mol_geom_file
]
p = Popen(cmd, stdout=open(ase_stdout_file, "w"))
(_, ret_val) = os.waitpid(p.pid, 0)
if ret_val != 0:
# raise MolInterfaceException("aseisolator.py returned with " +
# str(ret_val) + " when attempting: " + "./aseisolator.py " +
# self.ase_settings_file + " " + mol_geom_file)
# additions from Alexei
raise MolInterfaceException("aseisolator.py returned with " +
str(ret_val) +
"\nwhen attempting to run " +
' '.join(cmd) +
"\nMake sure $PYTHONPATH contains " +
sys.path[0])
# load results from file
(e, g) = pickle.load(open(results_file, "r"))
grads_opt = self.__transform(g, job.v, "dummy")
return common.Result(job.v, e, grads_opt)
def test_update_config_file_to_version3(self):
config_file = "yarss2_v2.conf"
filename = yarss2.util.common.get_resource(config_file, path="tests/data/")
tmp_dir = common.get_tmp_dir()
shutil.copy(filename, tmp_dir)
self.config = common.get_test_config(config_filename=config_file, config_dir=tmp_dir, verify_config=False)
# Call the function that makes the changes
self.config.config.run_converter((2, 2), 3, self.config.update_config_to_version3)
# Added field 'download_location'
for key in self.config.config["subscriptions"]:
self.assertTrue(self.config.config["subscriptions"][key].has_key("download_location"), "Field 'download_location' does not exist!")
for key in self.config.config["rssfeeds"]:
self.assertTrue(self.config.config["rssfeeds"][key].has_key("obey_ttl"), "Field 'obey_ttl' does not exist!")
for key in self.config.config["email_configurations"].keys():
self.assertTrue(not type(self.config.config["email_configurations"][key]) is str, "Field in str!")
def test_update_config_file_from_1_0(self):
tmp_dir = common.get_tmp_dir()
# Copy the yarss2_v1.conf file to test dir to avoid changes to the file.
config_file = "yarss2_v1.conf"
filename = yarss2.util.common.get_resource(config_file, path="tests/data/")
shutil.copy(filename, tmp_dir)
self.config = common.get_test_config(config_filename=config_file, config_dir=tmp_dir, verify_config=False)
self.assertEquals(self.config.config._Config__version["format"], 1)
self.assertEquals(self.config.config._Config__version["file"], 1)
# Verify that the old values are what we expect
for key in self.config.config["cookies"].keys():
self.assertEquals(type(self.config.config["cookies"][key]["value"]), list)
# Update the config
self.config._verify_config()
for key in self.config.config["cookies"].keys():
self.assertEquals(type(self.config.config["cookies"][key]["value"]), dict)
for key in self.config.config["subscriptions"].keys():
# last_update replaced with last_match
self.assertFalse("last_update" in self.config.config["subscriptions"][key])
self.assertTrue("last_match" in self.config.config["subscriptions"][key])
# Add in paused state should be string
self.assertEquals(type(self.config.config["subscriptions"][key]["add_torrents_in_paused_state"]), unicode)
self.assertTrue("max_upload_slots" in self.config.config["subscriptions"][key])
self.assertTrue("max_connections" in self.config.config["subscriptions"][key])
self.assertTrue("max_upload_speed" in self.config.config["subscriptions"][key])
self.assertTrue("prioritize_first_last_pieces" in self.config.config["subscriptions"][key])
self.assertTrue("auto_managed" in self.config.config["subscriptions"][key])
self.assertTrue("sequential_download" in self.config.config["subscriptions"][key])
# Test cookie type
for cookie in self.config.config["cookies"].values():
self.assertEquals(type(cookie["value"]), dict)
self.assertEquals(self.config.config._Config__version["format"], 1)
self.assertEquals(self.config.config._Config__version["file"], 5)
def run_ase(self, job):
(mystr, _) = self.coords2xyz(job.v)
tmp_dir = common.get_tmp_dir()
job_base_name = "asejob" + str(self.__get_job_counter())
mol_geom_file = os.path.join(tmp_dir, job_base_name + ".xyz")
ase_stdout_file = os.path.join(tmp_dir, job_base_name + ".stdout")
results_file = os.path.join(tmp_dir, job_base_name + common.LOGFILE_EXT)
# write input file as xyz format
f = open(mol_geom_file, "w")
f.write(mystr)
f.close()
# p = Popen(["./aseisolator.py", self.ase_settings_file, mol_geom_file], stdout=open(ase_stdout_file, "w"))
cmd = ["python", "-m", "aseisolator", self.ase_settings_file, mol_geom_file]
p = Popen(cmd, stdout=open(ase_stdout_file, "w"))
(_, ret_val) = os.waitpid(p.pid, 0)
if ret_val != 0:
# raise MolInterfaceException("aseisolator.py returned with " +
# str(ret_val) + " when attempting: " + "./aseisolator.py " +
# self.ase_settings_file + " " + mol_geom_file)
# additions from Alexei
raise MolInterfaceException("aseisolator.py returned with " + str(ret_val)
+ "\nwhen attempting to run " + ' '.join(cmd)
+ "\nMake sure $PYTHONPATH contains " + sys.path[0] )
# load results from file
(e, g) = pickle.load(open(results_file, "r"))
grads_opt = self.__transform(g, job.v, "dummy")
return common.Result(job.v, e, grads_opt)
def main(argv=None):
if argv is None:
argv = sys.argv
try:
try:
opts, args = getopt.getopt(argv[1:], "ho", ["help", "optimise"])
except getopt.error, msg:
raise ASEIsolatorException(msg)
mode = "calc_eg"
for o, a in opts:
if o in ("-h", "--help"):
usage()
return 0
if o in ("-o", "--optimise"):
mode = "optimise"
else:
usage()
return -1
if len(args) != 2:
raise ASEIsolatorException("Exactly two input files must be given.")
ase_job_settings = os.path.abspath(args[0])
molecule = os.path.abspath(args[1])
# create atoms object based on molecular geometry in file
atoms = ase.io.read(molecule)
jobname = os.path.splitext(molecule)[0]
# setup directories, filenames
isolation_dir = os.path.basename(jobname)
print isolation_dir
old_dir = os.getcwd()
# if a tmp directory is specified, then use it
tmp_dir = common.get_tmp_dir()
os.chdir(tmp_dir)
# Create/change into isolation directory. This directory holds temporary files
# specific to a computation, not including input and output files.
if not os.path.exists(isolation_dir):
os.mkdir(isolation_dir)
os.chdir(isolation_dir)
# set up calculators, etc.
exec open(ase_job_settings).read()
# Based on what was found in ase_job_settings, perform further
# setup for 'atoms'
if 'mycell' in locals():
atoms.set_cell(mycell)
if 'mypbc' in locals():
atoms.set_pbc(mypbc)
if not 'mycalc' in locals():
raise ASEIsolatorException("'mycalc' not defined in " + ase_job_settings)
atoms.set_calculator(mycalc)
result_file = os.path.join(tmp_dir, jobname + common.LOGFILE_EXT)
if mode == "calc_eg":
# run job using ASE calculator
g = atoms.get_forces().flatten()
e = atoms.get_potential_energy()
os.chdir(old_dir)
result = (e, g)
pickle.dump(result, open(result_file, "w"), protocol=2)
# just for testing...
#print pickle.load(open(result_file, "r"))
elif mode == "optimise":
optim = ase.LBFGS(atoms, trajectory='opt.traj')
optim.run()
os.chdir(old_dir)
ase.io.write(result_file, atoms, format="traj")
else:
raise ASEIsolatorException("Unrecognised mode: " + mode)
def main(argv=None):
if argv is None:
argv = sys.argv
try:
try:
opts, args = getopt.getopt(argv[1:], "ho", ["help", "optimise"])
except getopt.error, msg:
raise ASEIsolatorException(msg)
mode = "calc_eg"
for o, a in opts:
if o in ("-h", "--help"):
usage()
return 0
if o in ("-o", "--optimise"):
mode = "optimise"
else:
usage()
return -1
if len(args) != 2:
raise ASEIsolatorException(
"Exactly two input files must be given.")
ase_job_settings = os.path.abspath(args[0])
molecule = os.path.abspath(args[1])
# create atoms object based on molecular geometry in file
atoms = ase.io.read(molecule)
jobname = os.path.splitext(molecule)[0]
# setup directories, filenames
isolation_dir = os.path.basename(jobname)
print isolation_dir
old_dir = os.getcwd()
# if a tmp directory is specified, then use it
tmp_dir = common.get_tmp_dir()
os.chdir(tmp_dir)
# Create/change into isolation directory. This directory holds temporary files
# specific to a computation, not including input and output files.
if not os.path.exists(isolation_dir):
os.mkdir(isolation_dir)
os.chdir(isolation_dir)
# set up calculators, etc.
exec open(ase_job_settings).read()
# Based on what was found in ase_job_settings, perform further
# setup for 'atoms'
if 'mycell' in locals():
atoms.set_cell(mycell)
if 'mypbc' in locals():
atoms.set_pbc(mypbc)
if not 'mycalc' in locals():
raise ASEIsolatorException("'mycalc' not defined in " +
ase_job_settings)
atoms.set_calculator(mycalc)
result_file = os.path.join(tmp_dir, jobname + common.LOGFILE_EXT)
if mode == "calc_eg":
# run job using ASE calculator
g = atoms.get_forces().flatten()
e = atoms.get_potential_energy()
os.chdir(old_dir)
result = (e, g)
pickle.dump(result, open(result_file, "w"), protocol=2)
# just for testing...
#print pickle.load(open(result_file, "r"))
elif mode == "optimise":
optim = ase.LBFGS(atoms, trajectory='opt.traj')
optim.run()
os.chdir(old_dir)
ase.io.write(result_file, atoms, format="traj")
else:
raise ASEIsolatorException("Unrecognised mode: " + mode)