def test_read_aid_no_regex_with_prefix(self):
t1 = AtomsCollection("t1", "./tests/store")
fn1 = "../homer/ni.p454.out"
prefix = "Test"
a5 = t1._read_aid(fn1, None, prefix)
assert a5 == "test_ni.p454.out"
shutil.rmtree("./tests/store")
def test_read_aid(self):
t1 = AtomsCollection("t1", "./tests/store")
rxid = r'ni.p(?P<gbid>\d+).out'
import re
c_rxid = re.compile(rxid)
fn1 = "../homer/ni.p454.out"
a1 = t1._read_aid(fn1, c_rxid)
assert a1 == "454"
shutil.rmtree("./tests/store")
def test_get(self):
my_col = AtomsCollection("A", "./tests/results")
result = "Random test result"
desc = "test"
aid = "12"
my_col.store.store(result, desc, aid, arg_a=1, arg_b=2)
ret_val3 = my_col.get(desc, aid, arg_a=1, arg_b=2)
assert ret_val3 == result
shutil.rmtree("./tests/results")
def test_read_aid_with_prefix(self):
t1 = AtomsCollection("t1", "./tests/store")
rxid = r'ni.p(?P<gbid>\d+).out'
import re
c_rxid = re.compile(rxid)
fn1 = "../homer/ni.p454.out"
prefix = "Pre"
a2 = t1._read_aid(fn1, c_rxid, prefix)
assert a2 == "pre_454"
shutil.rmtree("./tests/store")
def test_read_single_file(self):
t1 = AtomsCollection("Test_1", "./tests/store")
# read single file
t1.read("./tests/test_data/ni.p455.out",
28,
"lammps-dump-text",
rxid=r'ni.p(?P<gbid>\d+).out',
prefix="TEST")
assert 1 == len(t1)
shutil.rmtree("./tests/store")
def _initialize_collection_and_read(aids):
'''initialize collection and read specified atoms files'''
my_col = AtomsCollection("Test", "tests/results")
data_path = 'tests/test_data/ni.p{0:s}.out'
for aid in aids:
my_col.read(data_path.format(aid),
28,
'lammps-dump-text',
rxid=r'ni.p(?P<aid>\d+).out')
return my_col
def test_read_empty_list(self):
t1 = AtomsCollection("Test_1", "./tests/store")
# empty list
t1.read([],
28,
"lammps-dump-text",
rxid=r'ni.p(?P<gbid>\d+).out',
prefix="TEST")
assert 0 == len(t1)
shutil.rmtree("./tests/store")
def test_read_empty_dir_with_file(self):
t1 = AtomsCollection("Test_1", "./tests/store")
# empty directory / directory and file
t1.read(["./tests/test_data/ni.p456.out", "./tests/test_data/empty"],
28,
"lammps-dump-text",
rxid=r'ni.p(?P<gbid>\d+).out',
prefix="TEST")
assert 1 == len(t1)
shutil.rmtree("./tests/store")
def test_read_directory(self):
t1 = AtomsCollection("Test_1", "./tests/store")
# read directory
t1.read("./tests/test_data/sub1/",
28,
"lammps-dump-text",
rxid=r'ni.p(?P<gbid>\d+).out',
prefix="TEST")
assert 2 == len(t1)
shutil.rmtree("./tests/store")
def test_aids(self):
t1 = AtomsCollection("Test_1", "./tests/test_paths")
t1.read(
["./tests/test_data/ni.p454.out", "./tests/test_data/ni.p453.out"],
28,
"lammps-dump-text",
rxid=r'ni.p(?P<gbid>\d+).out')
aid_list = t1.aids()
assert type(aid_list) is list
assert int(aid_list[0]) == int("453")
assert len(aid_list) is 2
def test_read_list(self):
t1 = AtomsCollection("Test_1", "./tests/store")
# list of input files
t1.read(
["./tests/test_data/ni.p454.out", "./tests/test_data/ni.p453.out"],
28,
"lammps-dump-text",
rxid=r'ni.p(?P<gbid>\d+).out',
prefix="TEST")
assert 2 == len(t1)
assert "test_454" == list(t1)[0]
shutil.rmtree("./tests/store")
def test_read_list_with_atomic_num_list(self):
t1 = AtomsCollection("Test_1", "./tests/store")
# list of input files with atomic num list (corresponding to one file)
t1.read(
["./tests/test_data/ni.p454.out", "./tests/test_data/ni.p453.out"],
[28, 28],
"lammps-dump-text",
rxid=r'ni.p(?P<gbid>\d+).out',
prefix="TEST")
assert 2 == len(t1)
assert "test_454" == list(t1)[0]
shutil.rmtree("./tests/store")
def test_read_aid_invalid_regex(self):
t1 = AtomsCollection("t1", "./tests/store")
fn1 = "../homer/ni.p454.out"
prefix = "Test"
output2 = io.StringIO()
sys.stdout = output2
import re
c_rxid3 = re.compile(r'ni.p(P<gbid>\d+).out')
a6 = t1._read_aid(fn1, c_rxid3, prefix)
assert "Regex found no pattern. Resolving to filename as aid.\n" == output2.getvalue(
)
assert a6 == "test_ni.p454.out"
shutil.rmtree("./tests/store")
def test_read_nonexistent_directory(self):
# non-existent directory
t1 = AtomsCollection("Test_1", "./tests/store")
output = io.StringIO()
sys.stdout = output
t1.read("definitely_wrong",
28,
"lammps-dump-text",
rxid=r'ni.p(?P<gbid>\d+).out',
prefix="TEST")
assert "Invalid file path, definitely_wrong was not read.\n" == output.getvalue(
)
shutil.rmtree("./tests/store")
def test_get_no_aid(self):
my_col = AtomsCollection("A", "./tests/results")
result = "Random test result"
desc = "test"
aid = "12"
aid2 = "13"
my_col["12"] = "test"
my_col["13"] = "test2"
my_col.store.store(result, desc, aid, arg_a=1, arg_b=2)
my_col.store.store(result, desc, aid2, arg_a=1, arg_b=2)
ret_val3 = my_col.get(desc, arg_a=1, arg_b=2)
assert type(ret_val3) is dict
assert len(ret_val3) is 2
shutil.rmtree("./tests/results")
def test_generate_file_name_with_collection(self):
my_col = AtomsCollection("A", ".")
f = my_col.store._generate_file_name("ler",
'U',
collection=my_col,
eps=0.025,
rcut=5.0,
nmax=9,
lmax=9,
metric="euclidean",
n_trees=10,
search_k=-1)
assert f == "ler__U___collection_a___eps_0.025___lmax_9___metric_euclidean___n_trees_10___nmax_9___rcut_5.0___search_k_-1.pkl"
def test_read_ASE_read_error(self):
t1 = AtomsCollection("Test_1", "./tests/store")
# ASE io.read() cannot automatically determine filetype
self.assertRaises(StopIteration,
AtomsCollection.read,
t1,
"./tests/test_data/ni.p457.out",
28,
rxid=r'ni.p(?P<gbid>\d+).out',
prefix="TEST")
# missing parameter
self.assertRaises(StopIteration,
AtomsCollection.read,
t1,
"./tests/test_data/ni.p456.out",
"lammps-dump-text",
rxid=r'ni.p(?P<gbid>\d+).out',
prefix="TEST")
shutil.rmtree("./tests/store")
def test_read_repeat_file(self):
# will not read previously read file
t1 = AtomsCollection("Test_1", "./tests/store")
t1.read("./tests/test_data/ni.p456.out",
28,
"lammps-dump-text",
rxid=r'ni.p(?P<gbid>\d+).out',
prefix="TEST")
t1.read("./tests/test_data/ni.p456.out",
28,
"lammps-dump-text",
rxid=r'ni.p(?P<gbid>\d+).out',
prefix="TEST")
assert 1 == len(t1)
shutil.rmtree("./tests/store")
def test_read_aid_no_regex(self):
t1 = AtomsCollection("t1", "./tests/store")
fn1 = "../homer/ni.p454.out"
a4 = t1._read_aid(fn1, None)
assert a4 == "ni.p454.out"
shutil.rmtree("./tests/store")