def test_add_sim_print_sim_and_delete_sim(capsys):
common_test_helpers.skip_if_outside_sim_db()
db_id = command_line_tool("sim_db", [
"add_sim", "--filename", "{0}/params_python_program.txt".format(
common_test_helpers.get_test_dir())
],
print_ids_added=False)
command_line_tool(
"sim_db", "print --id {0} -v --no_headers --columns name test_param1 "
"test_param2 test_param3 test_param4 test_param5 test_param6 "
"test_param7 test_param8 test_param9 test_param10 test_param11 "
"test_param12 test_param13".format(db_id).split())
output_print_sim, err = capsys.readouterr()
command_line_tool(
"sim_db",
["delete_sim", "--id", str(db_id), "--no_checks"])
command_line_tool("sim_db", "print -n 1 --no_headers --columns id".split())
output_after_delete, err = capsys.readouterr()
with capsys.disabled():
print("\nTest add_sim, print_sim and delete_sim...")
__assert_output_print_sim_after_add_sim(output_print_sim)
# Test that the added simulation parameters are deleted
assert (
len(output_after_delete) == 0
or output_after_delete.splitlines()[-1].strip() != "{0}".format(db_id))
def test_add_and_run(capsys):
common_test_helpers.skip_if_outside_sim_db()
db_id = command_line_tool("sim_db", [
"add_and_run", "--filename", "{0}/params_python_program.txt".format(
common_test_helpers.get_test_dir())
],
print_ids_added=False)
assert db_id != None
output_program, err = capsys.readouterr()
command_line_tool(
"sim_db",
"print_sim --id {0} -v --no_headers --columns name test_param1 "
"test_param2 test_param3 test_param4 test_param5 test_param6 "
"test_param7 test_param8 test_param9 test_param10 test_param11 "
"test_param12 test_param13".format(db_id).split())
output_print_sim_after_add_sim, err = capsys.readouterr()
command_line_tool(
"sim_db",
"print_sim --id {0} -v --columns new_test_param1 new_test_param2 "
"new_test_param3 new_test_param4 new_test_param5 new_test_param6 "
"new_test_param7 new_test_param8 new_test_param9 new_test_param10 "
"results_dir time_started used_walltime --no_headers".format(
db_id).split())
output_print_sim_after_run_sim, err = capsys.readouterr()
command_line_tool(
"sim_db",
["delete_sim", "--id", str(db_id), "--no_checks"])
with capsys.disabled():
print("\nTest add_and_run...")
__assert_output_print_sim_after_add_sim(output_print_sim_after_add_sim)
common_test_helpers.assert_output_python_program(output_program, db_id)
common_test_helpers.assert_output_print_sim_after_run_sim(
output_print_sim_after_run_sim, True)
def test_add_and_submit(capsys):
common_test_helpers.skip_if_outside_sim_db()
settings_no_set, job_scheduler, n_cpus_per_node, memory_per_node = \
__read_job_scheduler_settings()
with capsys.disabled():
print("\nTest add_and_submit...")
for no_set in settings_no_set:
print(
"WARNING: In settings.txt '{0}' is NOT set, but must be to test "
"add_and_submit.".format(no_set))
if len(settings_no_set) == 0:
db_id, job_script_name, job_id = command_line_tool(
"sim_db", [
"add_and_submit", "--filename",
"{0}/params_python_program.txt".format(
common_test_helpers.get_test_dir()), "--n_nodes", "2",
"--max_walltime", "03:34:00", "--do_not_submit_job_script"
],
print_ids_added=False)
command_line_tool("sim_db",
["delete_sim", "--id",
str(db_id), "--no_checks"])
job_script_file = open(job_script_name, 'r')
lines = job_script_file.readlines()
job_script_file.close()
os.remove(job_script_name)
__assert_lines_job_script(lines, job_scheduler, n_cpus_per_node,
memory_per_node)
def test_extract_params(capsys):
common_test_helpers.skip_if_outside_sim_db()
db_id = command_line_tool("sim_db", [
"add_sim", "--filename", "{0}/params_python_program.txt".format(
common_test_helpers.get_test_dir())
],
print_ids_added=False)
command_line_tool("sim_db",
"extract_params --id {0}".format(db_id).split())
output_extract_params, err = capsys.readouterr()
command_line_tool(
"sim_db",
["delete_sim", "--id", str(db_id), "--no_checks"])
lines_extract_params = output_extract_params.split('\n')
with capsys.disabled():
print("\nTest extract_params...")
assert "name (string): test_sim" == lines_extract_params[0]
assert "test_param1 (int): 3" == lines_extract_params[6]
assert "test_param2 (float): -5000000000.0" == lines_extract_params[8]
assert "test_param3 (string): hei" == lines_extract_params[10]
assert "test_param4 (bool): True" == lines_extract_params[12]
assert "test_param5 (int array): [1, 2, 3]" == lines_extract_params[14]
assert "test_param6 (float array): [1.5, 2.5, 3.5]" == lines_extract_params[
16]
assert "test_param7 (string array): [a, b, c]" == lines_extract_params[18]
assert "test_param8 (bool array): [True, False, True]" == lines_extract_params[
20]
assert "test_param9 (int): 9" == lines_extract_params[22]
assert "test_param10 (int): 11" == lines_extract_params[24]
def test_list_commands(capsys):
common_test_helpers.skip_if_outside_sim_db()
command_line_tool("sim_db", ["list_commands"])
output_list_commands, err = capsys.readouterr()
with capsys.disabled():
print("\nTest list_commands...")
output_lines = output_list_commands.split('\n')
assert output_lines[2] == "add_and_run"
assert output_lines[3] == "add_and_submit"
assert output_lines[4] == "add_column"
assert output_lines[5] == "add_comment"
assert output_lines[6] == "add_range / add_range_sim"
assert output_lines[7] == "add / add_sim"
assert output_lines[8] == "cd_res / cd_results_dir"
assert output_lines[9] == "combine_dbs"
assert output_lines[10] == "delete_empty_columns"
assert output_lines[11] == "delete_results_dir"
assert output_lines[12] == "delete / delete_sim"
assert output_lines[13] == "duplicate_and_run"
assert output_lines[14] == "ddr / duplicate_delete_and_run"
assert output_lines[15] == "duplicate / duplicate_sim"
assert output_lines[16] == "extract_params"
assert output_lines[17] == "get"
assert output_lines[18] == "init"
assert output_lines[19] == "list_commands"
assert output_lines[20] == "list_print_configs"
assert output_lines[21] == "print / print_sim"
assert output_lines[22] == "run_serial / run_serial_sims"
assert output_lines[23] == "run / run_sim"
assert output_lines[24] == "settings"
assert output_lines[25] == "submit / submit_sim"
assert output_lines[26] == "update / update_sim"
def test_delete_results_dir(capsys):
common_test_helpers.skip_if_outside_sim_db()
with capsys.disabled():
print("\nTest delete_results_dir...")
for entry in os.listdir(common_test_helpers.get_test_dir() + '/results'):
print(common_test_helpers.get_test_dir() + '/results/' + entry)
assert not os.path.isdir(common_test_helpers.get_test_dir() +
'/results/' + entry)
def test_combine_dbs(capsys):
common_test_helpers.skip_if_outside_sim_db()
path_db_1 = common_test_helpers.get_test_dir() + "/sim1_test_comb.db"
path_db_2 = common_test_helpers.get_test_dir() + "/sim2_test_comb.db"
path_comb_db = common_test_helpers.get_test_dir() + "/new_comb_sim.db"
if os.path.exists(path_comb_db):
os.remove(path_comb_db)
command_line_tool("sim_db",
["combine_dbs", path_db_1, path_db_2, path_comb_db])
comb_sim_db = helpers.connect_sim_db(path_comb_db)
comb_sim_db_cursor = comb_sim_db.cursor()
db_1 = helpers.connect_sim_db(path_db_1)
db_1_cursor = db_1.cursor()
db_2 = helpers.connect_sim_db(path_db_2)
db_2_cursor = db_2.cursor()
column_names_1, column_types_1 = helpers.get_db_column_names_and_types(
db_1_cursor)
column_names_2, column_types_2 = helpers.get_db_column_names_and_types(
db_2_cursor)
column_names_comb, column_types_comb = helpers.get_db_column_names_and_types( \
comb_sim_db_cursor)
old_run_commands = []
db_1_cursor.execute("SELECT run_command FROM runs WHERE id=1;")
old_run_commands.append(db_1_cursor.fetchall()[0][0])
db_1_cursor.execute("SELECT run_command FROM runs WHERE id=2;")
old_run_commands.append(db_1_cursor.fetchall()[0][0])
db_2_cursor.execute("SELECT run_command FROM runs WHERE id=1;")
old_run_commands.append(db_2_cursor.fetchall()[0][0])
db_2_cursor.execute("SELECT run_command FROM runs WHERE id=2;")
old_run_commands.append(db_2_cursor.fetchall()[0][0])
new_run_commands = []
comb_sim_db_cursor.execute("SELECT run_command FROM runs WHERE id=1;")
new_run_commands.append(comb_sim_db_cursor.fetchall()[0][0])
comb_sim_db_cursor.execute("SELECT run_command FROM runs WHERE id=2;")
new_run_commands.append(comb_sim_db_cursor.fetchall()[0][0])
comb_sim_db_cursor.execute("SELECT run_command FROM runs WHERE id=3;")
new_run_commands.append(comb_sim_db_cursor.fetchall()[0][0])
comb_sim_db_cursor.execute("SELECT run_command FROM runs WHERE id=4;")
new_run_commands.append(comb_sim_db_cursor.fetchall()[0][0])
with capsys.disabled():
print("\nTest combine_dbs...")
comb_sim_db.commit()
comb_sim_db_cursor.close()
comb_sim_db.close()
os.remove(path_comb_db)
for column_name in column_names_1:
assert column_name in column_names_comb
for column_name in column_names_2:
assert column_name in column_names_comb
for (old_command, new_command) in zip(old_run_commands, new_run_commands):
assert old_command == new_command
def test_list_print_configs(capsys):
common_test_helpers.skip_if_outside_sim_db()
command_line_tool("sim_db", ["list_print_configs"])
output_list_commands, err = capsys.readouterr()
with capsys.disabled():
print("\nTest list_print_configs...")
settings = helpers.Settings()
for print_config, output in zip(settings.read('print_config'),
output_list_commands.split('\n')):
assert print_config == output
def test_python_multithreading(capsys):
common_test_helpers.skip_if_outside_sim_db()
with capsys.disabled():
print("\nTest python multithreading and processing...")
path_script = os.path.join(common_test_helpers.get_test_dir(),
"multithreading_and_processing.py")
output = subprocess.check_output(["python", path_script],
universal_newlines=True)
last_line = output.splitlines()[-1]
assert last_line.strip() == "finished"
def test_init(capsys):
common_test_helpers.skip_if_outside_sim_db()
command_line_tool(
"sim_db",
["init", "--path", "{0}".format(common_test_helpers.get_test_dir())])
with capsys.disabled():
print("\nTest init...")
assert os.path.isdir(common_test_helpers.get_test_dir() + '/.sim_db')
assert os.path.isfile(common_test_helpers.get_test_dir() +
'/.sim_db/settings.txt')
shutil.rmtree(common_test_helpers.get_test_dir() + '/.sim_db')
def test_add_column_and_delete_empty_columns(capsys):
common_test_helpers.skip_if_outside_sim_db()
with capsys.disabled():
print("\nTest add_column and delete_empty_columns...")
command_line_tool("sim_db",
"add_column --column new_column --type 'TEXT'".split())
db = helpers.connect_sim_db()
db_cursor = db.cursor()
column_names, column_types = helpers.get_db_column_names_and_types(
db_cursor)
assert "new_column" in column_names
command_line_tool("sim_db", ["delete_empty_columns"])
column_names, column_types = helpers.get_db_column_names_and_types(
db_cursor)
assert "new_column" not in column_names
def test_add_sim_with_alias_error(capsys):
common_test_helpers.skip_if_outside_sim_db()
with pytest.raises(SystemExit) as pytest_wrapped_e:
command_line_tool("sim_db", [
"add_sim", "--filename", "{0}/params_alias_error.txt".format(
common_test_helpers.get_test_dir())
],
print_ids_added=False)
output_sim_add, err = capsys.readouterr()
with capsys.disabled():
print("\nTest that add_sim catches alias error...")
assert pytest_wrapped_e.type == SystemExit
assert (
output_sim_add.splitlines()[0] == "ERROR: Alias name on line no. 0 "
"in the parameter file MUST start and end with curly brackets.")
def test_add_range_sim(capsys):
common_test_helpers.skip_if_outside_sim_db()
db_ids = command_line_tool(
"sim_db",
"add_range_sim --filename".split() + [
"{0}/params_python_program.txt".format(
common_test_helpers.get_test_dir())
] + "--columns test_param1 test_param2 --lin_steps 0 2 --exp_steps "
"3 1 --end_steps 27 -4999999999 --n_steps 0 2".split(),
print_ids_added=False)
db_ids_string = ""
for db_id in db_ids:
db_ids_string = db_ids_string + " " + str(db_id)
command_line_tool(
"sim_db", "print_sim --id {0} -v --no_headers --columns "
"test_param1 test_param2".format(db_ids_string).split())
output_print_sim, err = capsys.readouterr()
command_line_tool(
"sim_db",
["delete_sim", "--id", str(db_id), "--no_checks"])
command_line_tool("sim_db",
"print_sim -n 1 --no_headers --columns id".split())
output_after_delete, err = capsys.readouterr()
with capsys.disabled():
print("\nTest add_range_sim...")
test_param1_list, test_param2_list = output_print_sim.split('\n', 1)
test_param1_list = test_param1_list.split()
test_param2_list = test_param2_list.split()
assert (test_param1_list[0] == "3" and test_param1_list[1] == "3"
and test_param1_list[2] == "3")
assert (test_param1_list[3] == "9" and test_param1_list[4] == "9"
and test_param1_list[5] == "9")
assert (test_param1_list[6] == "27" and test_param1_list[7] == "27"
and test_param1_list[8] == "27")
param2_start = -5000000000.0
assert (test_param2_list[0] == str(param2_start)
and test_param2_list[3] == str(param2_start)
and test_param2_list[6] == str(param2_start))
assert (test_param2_list[1] == str(param2_start + 2)
and test_param2_list[4] == str(param2_start + 2)
and test_param2_list[7] == str(param2_start + 2))
assert (test_param2_list[2] == str(param2_start + 4)
and test_param2_list[5] == str(param2_start + 4)
and test_param2_list[8] == str(param2_start + 4))
# Test that the added simulation parameters are deleted
assert (len(output_after_delete) == 0
or output_after_delete != "{0}".format(db_id))
def test_c_multithreading(capsys):
common_test_helpers.skip_if_outside_sim_db()
with capsys.disabled():
print("\nTest C multithreading and processing...")
path_tests_dir = common_test_helpers.get_test_dir()
path_sim_db_root = os.path.join(path_tests_dir, os.pardir)
path_build = os.path.join(path_tests_dir, "build")
path_c_mtap = os.path.join(os.path.join(path_tests_dir, "build"), "c_mtap")
subprocess.call([
"cmake", "-H{0}".format(path_sim_db_root), "-B{0}".format(path_build),
"-DCMAKE_BUILD_TYPE=Debug"
])
subprocess.call(["cmake", "--build", path_build, "--target", "c_mtap"])
output = subprocess.check_output([path_c_mtap], universal_newlines=True)
last_line = output.splitlines()[-1]
assert last_line.strip() == "finished"
def test_run_serial_sims(capsys):
common_test_helpers.skip_if_outside_sim_db()
id_1 = command_line_tool("sim_db", [
"add_sim", "--filename",
common_test_helpers.get_test_dir() + "/params_python_program.txt"
],
print_ids_added=False)
id_2 = command_line_tool("sim_db", [
"add_sim", "--filename",
common_test_helpers.get_test_dir() + "/params_c_program.txt"
],
print_ids_added=False)
id_3 = command_line_tool("sim_db", [
"add_sim", "--filename",
common_test_helpers.get_test_dir() + "/params_cpp_program.txt"
],
print_ids_added=False)
command_line_tool(
"sim_db",
["run_serial_sims", "--id",
str(id_1), str(id_2),
str(id_3)])
output_serial_run, err = capsys.readouterr()
command_line_tool(
"sim_db", "print_sim --id {0} {1} {2} -v --no_headers --columns name "
"test_param1 ".format(id_1, id_2, id_3).split())
output_print_sim, err = capsys.readouterr()
command_line_tool(
"sim_db",
["delete_sim", "--id",
str(id_1),
str(id_2),
str(id_3), "--no_checks"])
command_line_tool("sim_db",
"print_sim -n 1 --no_headers --columns id".split())
output_after_delete, err = capsys.readouterr()
with capsys.disabled():
print("\nTest run_serial_sims...")
printed_params = output_print_sim.split('\n')[0::2]
printed_names = printed_params[0].split()
printed_params_1 = printed_params[1].split()
assert printed_names[0] == printed_names[1] == printed_names[2]
assert printed_params_1[0] == printed_params_1[1] == printed_params_1[2]
# Test that the added simulation parameters are deleted
assert (len(output_after_delete) == 0
or output_after_delete != "{0}".format(id_3))
def test_duplicate_delete_and_run(capsys):
common_test_helpers.skip_if_outside_sim_db()
db_id = command_line_tool("sim_db", [
"add_sim", "--filename", "{0}/params_python_program.txt".format(
common_test_helpers.get_test_dir())
],
print_ids_added=False)
new_id = command_line_tool(
"sim_db",
["duplicate_delete_and_run", "--id",
str(db_id), "--no_checks"],
print_ids_added=False)
output_program, err = capsys.readouterr()
command_line_tool(
"sim_db",
"print_sim --id {0} -v --no_headers --columns name test_param1 "
"test_param2 test_param3 test_param4 test_param5 test_param6 "
"test_param7 test_param8 test_param9 test_param10 test_param11 "
"test_param12 test_param13".format(new_id).split())
output_print_sim_after_duplicate_sim, err = capsys.readouterr()
command_line_tool(
"sim_db",
"print_sim --id {0} -v --columns new_test_param1 new_test_param2 "
"new_test_param3 new_test_param4 new_test_param5 new_test_param6 "
"new_test_param7 new_test_param8 new_test_param9 new_test_param10 "
"results_dir time_started used_walltime --no_headers".format(
new_id).split())
output_print_sim_after_run_sim, err = capsys.readouterr()
command_line_tool("sim_db",
["delete_sim", "--id",
str(new_id), "--no_checks"])
command_line_tool("sim_db", "print -n 1 --no_headers --columns id".split())
output_after_delete, err = capsys.readouterr()
with capsys.disabled():
print("\nTest duplicate_delete_and_run...")
__assert_output_print_sim_after_add_sim(
output_print_sim_after_duplicate_sim)
common_test_helpers.assert_output_python_program(output_program, new_id)
common_test_helpers.assert_output_print_sim_after_run_sim(
output_print_sim_after_run_sim, True)
# Test that the added simulation parameters are deleted
assert (
len(output_after_delete) == 0
or output_after_delete.splitlines()[-1].strip() != "{0}".format(db_id))
def test_settings(capsys):
common_test_helpers.skip_if_outside_sim_db()
command_line_tool(
"sim_db",
["init", "--path", "{0}".format(common_test_helpers.get_test_dir())])
output_program, err = capsys.readouterr()
cwd = os.getcwd()
os.chdir(common_test_helpers.get_test_dir())
command_line_tool("sim_db",
["settings", "print", "--setting", "parameter_files"])
output_setting_print_original, err = capsys.readouterr()
command_line_tool("sim_db", [
"settings", "add", "--setting", "parameter_files", "--line",
"test_settings.txt"
])
command_line_tool("sim_db",
["settings", "print", "--setting", "parameter_files"])
output_setting_print_after_add, err = capsys.readouterr()
command_line_tool("sim_db", [
"settings", "remove", "--setting", "parameter_files", "--line",
"sim_params.txt"
])
command_line_tool("sim_db",
["settings", "print", "--setting", "parameter_files"])
output_setting_print_after_remove, err = capsys.readouterr()
command_line_tool("sim_db", ["settings", "reset_to_default"])
output, err = capsys.readouterr()
command_line_tool("sim_db",
["settings", "print", "--setting", "parameter_files"])
output_setting_print_after_reset, err = capsys.readouterr()
with capsys.disabled():
print("\nTest settings...")
os.chdir(cwd)
shutil.rmtree(common_test_helpers.get_test_dir() + '/.sim_db')
assert output_setting_print_original.strip() == 'sim_params.txt'
assert output_setting_print_after_add.split(
'\n')[0].strip() == 'sim_params.txt'
assert output_setting_print_after_add.split(
'\n')[1].strip() == 'test_settings.txt'
assert output_setting_print_after_remove.strip() == 'test_settings.txt'
assert output_setting_print_after_reset.strip() == 'sim_params.txt'
def test_add_comment(capsys):
common_test_helpers.skip_if_outside_sim_db()
db_id = command_line_tool("sim_db", [
"add_sim", "--filename", "{0}/params_python_program.txt".format(
common_test_helpers.get_test_dir())
],
print_ids_added=False)
command_line_tool("sim_db", [
"add_comment", "--id", "{0}".format(db_id), "--comment",
"This is a test comment."
])
command_line_tool(
"sim_db", "print_sim --id {0} --columns comment --no_headers".format(
db_id).split())
output_print_sim, err = capsys.readouterr()
command_line_tool(
"sim_db",
["delete_sim", "--id", str(db_id), "--no_checks"])
with capsys.disabled():
print("\nTest add_comment...")
assert output_print_sim.strip() == "This is a test comment."
def test_get_and_cd_results_dir(capsys):
common_test_helpers.skip_if_outside_sim_db()
db_id = command_line_tool("sim_db", [
"add_and_run", "--filename", "{0}/params_python_program.txt".format(
common_test_helpers.get_test_dir())
])
output_program, err_program = capsys.readouterr()
results_dir = command_line_tool(
"sim_db", "get results_dir --id {0}".format(db_id).split())
command_line_tool(
"sim_db",
"print_sim --id {0} -v --columns results_dir --no_headers".format(
db_id).split())
output_print_sim, err_print_sim = capsys.readouterr()
with capsys.disabled():
print("\nTest get and cd_results_dir...")
assert os.path.isdir(results_dir)
command_line_tool(
"sim_db",
["delete_sim", "--id", str(db_id), "--no_checks"])
assert not os.path.isdir(results_dir)
def test_duplicate_sim(capsys):
common_test_helpers.skip_if_outside_sim_db()
db_id = command_line_tool("sim_db", [
"add_sim", "--filename",
common_test_helpers.get_test_dir() + "/params_python_program.txt"
],
print_ids_added=False)
command_line_tool(
"sim_db",
["update_sim", "--id",
str(db_id), "-c", "status", "-v", "finished"])
db_id_duplicated = command_line_tool(
"sim_db",
["duplicate_sim", "--id", str(db_id)], print_ids_added=False)
command_line_tool(
"sim_db", "print_sim -i {0} --no_headers -v -c id status name "
"--params --results".format(db_id).split())
output_original_sim, err = capsys.readouterr()
command_line_tool(
"sim_db", "print_sim -i {0} --no_headers -v -c id status name "
"--params --results".format(db_id_duplicated).split())
output_duplicated_sim, err = capsys.readouterr()
command_line_tool(
"sim_db",
["delete_sim", "--id", str(db_id), "--no_checks"])
command_line_tool(
"sim_db", ["delete_sim", "--id",
str(db_id_duplicated), "--no_checks"])
with capsys.disabled():
print("\nTest duplicate_sim...")
assert (output_original_sim.split('\n')[0].strip() !=
output_duplicated_sim.split('\n')[0].strip())
assert output_duplicated_sim.split('\n')[2].strip() == 'new'
assert (output_original_sim.split('\n',
3)[3] == output_duplicated_sim.split(
'\n', 3)[3])
def test_cpp_functions_without_storing_metadata(capsys):
common_test_helpers.skip_if_outside_sim_db()
__cpp_functions(capsys, False)
def test_cpp_functions(capsys):
common_test_helpers.skip_if_outside_sim_db()
__cpp_functions(capsys, True)
