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Updated tests
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@smelandr
smelandr committed Apr 11, 2017
1 parent 21ecd88 commit 51b1496
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Showing 3 changed files with 89 additions and 36 deletions.
36 changes: 34 additions & 2 deletions tests/test_api_methods.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ def test_chem_shifts_by_residue_all():
assert repr(test_chem_shifts2) == repr(model_chem_shifts2)


def test_chem_shifts_by_residue_specific_amino_acid():
def test_chem_shifts_by_residue_amino_acids_list():
starfile_generator = nmrstarlib.read_files("tests/example_data/NMRSTAR3/bmr18569.str",
"tests/example_data/NMRSTAR2/bmr18569.str")
starfile1 = next(starfile_generator)
Expand All @@ -36,8 +36,24 @@ def test_chem_shifts_by_residue_specific_amino_acid():
assert repr(test_chem_shifts1) == repr(model_chem_shifts1)
assert repr(test_chem_shifts2) == repr(model_chem_shifts2)

def test_chem_shifts_by_residue_atoms_list():
starfile_generator = nmrstarlib.read_files("tests/example_data/NMRSTAR3/bmr18569.str",
"tests/example_data/NMRSTAR2/bmr18569.str")
starfile1 = next(starfile_generator)
starfile2 = next(starfile_generator)
test_chem_shifts1 = starfile1.chem_shifts_by_residue(atoms=("CA", "CB"), nmrstar_version="3")
test_chem_shifts2 = starfile2.chem_shifts_by_residue(atoms=("CA", "CB"), nmrstar_version="2")

with open("tests/example_data/NMRSTAR3/chem_shifts_by_residue_CA_CB.json", "r") as infile:
model_chem_shifts1 = json.load(infile, object_pairs_hook=OrderedDict)
with open("tests/example_data/NMRSTAR2/chem_shifts_by_residue_CA_CB.json", "r") as infile:
model_chem_shifts2 = json.load(infile, object_pairs_hook=OrderedDict)

assert repr(test_chem_shifts1) == repr(model_chem_shifts1)
assert repr(test_chem_shifts2) == repr(model_chem_shifts2)


def test_chem_shifts_by_residue_specific_amino_acid_specific_atoms():
def test_chem_shifts_by_residue_amino_acids_list_atoms_list():
starfile_generator = nmrstarlib.read_files("tests/example_data/NMRSTAR3/bmr18569.str",
"tests/example_data/NMRSTAR2/bmr18569.str")
starfile1 = next(starfile_generator)
Expand All @@ -50,5 +66,21 @@ def test_chem_shifts_by_residue_specific_amino_acid_specific_atoms():
with open("tests/example_data/NMRSTAR2/chem_shifts_by_residue_SER_CA_CB.json", "r") as infile:
model_chem_shifts2 = json.load(infile, object_pairs_hook=OrderedDict)

assert repr(test_chem_shifts1) == repr(model_chem_shifts1)
assert repr(test_chem_shifts2) == repr(model_chem_shifts2)

def test_chem_shifts_by_residue_amino_acids_and_atoms_dict():
starfile_generator = nmrstarlib.read_files("tests/example_data/NMRSTAR3/bmr18569.str",
"tests/example_data/NMRSTAR2/bmr18569.str")
starfile1 = next(starfile_generator)
starfile2 = next(starfile_generator)
test_chem_shifts1 = starfile1.chem_shifts_by_residue(amino_acids_and_atoms={"SER":("HA", "CA"), "MET":("CA", "CB")}, nmrstar_version="3")
test_chem_shifts2 = starfile2.chem_shifts_by_residue(amino_acids_and_atoms={"SER":("HA", "CA"), "MET":("CA", "CB")}, nmrstar_version="2")

with open("tests/example_data/NMRSTAR3/chem_shifts_by_residue_SER_HA_CA_MET_CA_CB.json", "r") as infile:
model_chem_shifts1 = json.load(infile, object_pairs_hook=OrderedDict)
with open("tests/example_data/NMRSTAR2/chem_shifts_by_residue_SER_HA_CA_MET_CA_CB.json", "r") as infile:
model_chem_shifts2 = json.load(infile, object_pairs_hook=OrderedDict)

assert repr(test_chem_shifts1) == repr(model_chem_shifts1)
assert repr(test_chem_shifts2) == repr(model_chem_shifts2)
82 changes: 50 additions & 32 deletions tests/test_converter.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
import shutil
from nmrstarlib import nmrstarlib
from nmrstarlib.converter import Converter
from nmrstarlib.translator import StarFileToStarFile


def teardown_module(module):
Expand All @@ -9,16 +10,20 @@ def teardown_module(module):


def test_from_nmrstar_to_json_single_file():
converter = Converter(from_path="tests/example_data/NMRSTAR3/bmr18569.str",
to_path="tests/example_data/NMRSTAR3/tmp/bmr18569.json",
from_format="nmrstar",
to_format="json")
nmrstar_file_translator = StarFileToStarFile(from_path="tests/example_data/NMRSTAR3/bmr18569.str",
to_path="tests/example_data/NMRSTAR3/tmp/bmr18569.json",
from_format="nmrstar",
to_format="json")
converter = Converter(file_generator=nmrstar_file_translator)
converter.convert()
converter = Converter(from_path="tests/example_data/NMRSTAR2/bmr18569.str",
to_path="tests/example_data/NMRSTAR2/tmp/bmr18569.json",
from_format="nmrstar",
to_format="json")

nmrstar_file_translator = StarFileToStarFile(from_path="tests/example_data/NMRSTAR2/bmr18569.str",
to_path="tests/example_data/NMRSTAR2/tmp/bmr18569.json",
from_format="nmrstar",
to_format="json")
converter = Converter(file_generator=nmrstar_file_translator)
converter.convert()

starfile_generator = nmrstarlib.read_files("tests/example_data/NMRSTAR3/tmp/bmr18569.json",
"tests/example_data/NMRSTAR2/tmp/bmr18569.json")
starfile1 = next(starfile_generator)
Expand All @@ -27,16 +32,20 @@ def test_from_nmrstar_to_json_single_file():


def test_from_json_to_nmrstar_single_file():
converter = Converter(from_path="tests/example_data/NMRSTAR3/tmp/bmr18569.json",
to_path="tests/example_data/NMRSTAR3/tmp/bmr18569.str",
from_format="json",
to_format="nmrstar")
nmrstar_file_translator = StarFileToStarFile(from_path="tests/example_data/NMRSTAR3/tmp/bmr18569.json",
to_path="tests/example_data/NMRSTAR3/tmp/bmr18569.str",
from_format="json",
to_format="nmrstar")
converter = Converter(file_generator=nmrstar_file_translator)
converter.convert()
converter = Converter(from_path="tests/example_data/NMRSTAR2/tmp/bmr18569.json",
to_path="tests/example_data/NMRSTAR2/tmp/bmr18569.str",
from_format="json",
to_format="nmrstar")

nmrstar_file_translator = StarFileToStarFile(from_path="tests/example_data/NMRSTAR2/tmp/bmr18569.json",
to_path="tests/example_data/NMRSTAR2/tmp/bmr18569.str",
from_format="json",
to_format="nmrstar")
converter = Converter(file_generator=nmrstar_file_translator)
converter.convert()

starfile_generator = nmrstarlib.read_files("tests/example_data/NMRSTAR3/tmp/bmr18569.str",
"tests/example_data/NMRSTAR2/tmp/bmr18569.str")
starfile1 = next(starfile_generator)
Expand All @@ -45,16 +54,21 @@ def test_from_json_to_nmrstar_single_file():


def test_from_nmrstar_to_json_directory():
converter = Converter(from_path="tests/example_data/NMRSTAR3/starfiles_directory",
to_path="tests/example_data/NMRSTAR3/tmp/starfiles_directory_json",
from_format="nmrstar",
to_format="json")
nmrstar_file_translator = StarFileToStarFile(from_path="tests/example_data/NMRSTAR3/starfiles_directory",
to_path="tests/example_data/NMRSTAR3/tmp/starfiles_directory_json",
from_format="nmrstar",
to_format="json")

converter = Converter(file_generator=nmrstar_file_translator)
converter.convert()
converter = Converter(from_path="tests/example_data/NMRSTAR2/starfiles_directory",
to_path="tests/example_data/NMRSTAR2/tmp/starfiles_directory_json",
from_format="nmrstar",
to_format="json")

nmrstar_file_translator = StarFileToStarFile(from_path="tests/example_data/NMRSTAR2/starfiles_directory",
to_path="tests/example_data/NMRSTAR2/tmp/starfiles_directory_json",
from_format="nmrstar",
to_format="json")
converter = Converter(file_generator=nmrstar_file_translator)
converter.convert()

starfile_generator = nmrstarlib.read_files("tests/example_data/NMRSTAR3/tmp/starfiles_directory_json",
"tests/example_data/NMRSTAR2/tmp/starfiles_directory_json")
starfiles_list = list(starfile_generator)
Expand All @@ -63,16 +77,20 @@ def test_from_nmrstar_to_json_directory():


def test_from_json_to_nmrstar_directory():
converter = Converter(from_path="tests/example_data/NMRSTAR3/tmp/starfiles_directory_json",
to_path="tests/example_data/NMRSTAR3/tmp/starfiles_directory_nmrstar",
from_format="json",
to_format="nmrstar")
nmrstar_file_translator = StarFileToStarFile(from_path="tests/example_data/NMRSTAR3/tmp/starfiles_directory_json",
to_path="tests/example_data/NMRSTAR3/tmp/starfiles_directory_nmrstar",
from_format="json",
to_format="nmrstar")
converter = Converter(file_generator=nmrstar_file_translator)
converter.convert()
converter = Converter(from_path="tests/example_data/NMRSTAR2/tmp/starfiles_directory_json",
to_path="tests/example_data/NMRSTAR2/tmp/starfiles_directory_nmrstar",
from_format="json",
to_format="nmrstar")

nmrstar_file_translator = StarFileToStarFile(from_path="tests/example_data/NMRSTAR2/tmp/starfiles_directory_json",
to_path="tests/example_data/NMRSTAR2/tmp/starfiles_directory_nmrstar",
from_format="json",
to_format="nmrstar")
converter = Converter(file_generator=nmrstar_file_translator)
converter.convert()

starfile_generator = nmrstarlib.read_files("tests/example_data/NMRSTAR3/tmp/starfiles_directory_nmrstar",
"tests/example_data/NMRSTAR2/tmp/starfiles_directory_nmrstar")
starfiles_list = list(starfile_generator)
Expand Down
7 changes: 5 additions & 2 deletions tests/test_csviewer.py
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Original file line number Diff line number Diff line change
@@ -1,10 +1,13 @@
import shutil
import os
from nmrstarlib.csviewer import CSViewer


def teardown_module(module):
shutil.rmtree("tests/example_data/NMRSTAR3/tmp")
shutil.rmtree("tests/example_data/NMRSTAR2/tmp")
if os.path.exists("tests/example_data/NMRSTAR3/tmp"):
shutil.rmtree("tests/example_data/NMRSTAR3/tmp")
if os.path.exists("tests/example_data/NMRSTAR2/tmp"):
shutil.rmtree("tests/example_data/NMRSTAR2/tmp")


def test_csviewer_all():
Expand Down

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