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"""Test input file READ section parsing."""
import logging
import pytest
from apbs.input_file.read import Read
_LOGGER = logging.getLogger(__name__)
GOOD_INPUT = [
"""# Typical input with PQR molecules
molecules:
- alias: molecule 1
format: pqr
path: mol1.pqr
- alias: molecule 2
format: pqr
path: mol2.pqr
- alias: complex between 1 & 2
format: pqr
path: complex.pqr
""",
"""# PDB input with parameter file
molecules:
- alias: molecule 1
format: pdb
path: mol1.pdb
- alias: molecule 2
format: pdb
path: mol2.pdb
- alias: the complex
format: pdb
path: mol1.pdb
parameters:
- alias: my parameters
format: flat
path: custom_parms.txt
""",
"""# PQR input with map for boundary conditions
molecules:
- alias: molecule
format: pqr
path: mol.pqr
potential maps:
- alias: potential
format: dx
path: potential.dx
""",
"""# All-map input
charge density maps:
- alias: charge density
format: dx
path: charge.dx
ion accessibility maps:
- alias: ion accessibility
format: dx
path: ions.dx
dielectric maps:
- alias: the dielectric maps
format: dx
x-shifted path: dielx.dx
y-shifted path: diely.dx
z-shifted path: dielz.dx
""",
]
BAD_INPUT = [
"""# Typical input with PQR molecules with BAD format
molecules:
- alias: molecule 1
format: BAD
path: mol1.pqr
- alias: molecule 2
format: pqr
path: mol2.pqr
- alias: complex between 1 & 2
format: pqr
path: complex.pqr
""",
"""# PDB input WITHOUT parameter file
molecules:
- alias: molecule 1
format: pdb
path: mol1.pdb
- alias: molecule 2
format: pdb
path: mol2.pdb
- alias: the complex
format: pdb
path: mol1.pdb
""",
"""# PQR input with map for boundary conditions WITHOUT path
molecules:
- alias: molecule
format: pqr
path: mol.pqr
potential maps:
- alias: potential
format: dx
""",
"""# All-map input with MISSING path
charge density maps:
- alias: charge density
format: dx
path: charge.dx
ion accessibility maps:
- alias: ion accessibility
format: dx
path: ions.dx
dielectric maps:
- alias: the dielectric maps
format: dx
x-shifted path: dielx.dx
z-shifted path: dielz.dx
""",
]
def id_function(test_string) -> str:
"""Turn test strings into labels."""
label = test_string.splitlines()[0]
return label[2:]
@pytest.mark.parametrize("input_", GOOD_INPUT, ids=id_function)
def test_good_input(input_):
"""Test input file READ sections."""
read = Read()
_LOGGER.debug(f"YAML input: {input_}")
read.from_yaml(input_)
read.validate()
new_dict = read.to_dict()
_LOGGER.debug(f"Object dictionary: {new_dict}")
read.from_dict(new_dict)
read.validate()
@pytest.mark.parametrize("input_", BAD_INPUT, ids=id_function)
def test_bad_input(input_):
"""Test input file READ sections."""
with pytest.raises((KeyError, ValueError)):
read = Read()
_LOGGER.debug(input_)
read.from_yaml(input_)
read.validate()
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