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Commit 2c5f7202 authored by Hervé MENAGER's avatar Hervé MENAGER
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extract all utils tests to a separate test module

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ippisite/ippidb/tests.py
+ 0
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View file @ 2c5f7202
...@@ -8,7 +8,6 @@ from django.contrib.auth import get_user_model ...@@ -8,7 +8,6 @@ from django.contrib.auth import get_user_model
from django.core.management import call_command from django.core.management import call_command
from django.test import TestCase from django.test import TestCase
from django.urls import reverse from django.urls import reverse
from openbabel import vectorUnsignedInt, OBFingerprint
import requests import requests
...@@ -26,7 +25,6 @@ from .models import ( ...@@ -26,7 +25,6 @@ from .models import (
PcaBiplotData, PcaBiplotData,
) )
from .models import DrugBankCompound, Protein from .models import DrugBankCompound, Protein
from .utils import FingerPrinter, mol2smi, smi2mol, smi2inchi, smi2inchikey, smi2sdf
class MolSmiTestCase(TestCase): class MolSmiTestCase(TestCase):
...@@ -44,12 +42,6 @@ class MolSmiTestCase(TestCase): ...@@ -44,12 +42,6 @@ class MolSmiTestCase(TestCase):
" 0 0 0 0 0 0 0 0\nM END\n" " 0 0 0 0 0 0 0 0\nM END\n"
) )
def test_mol2smi(self):
self.assertEqual(mol2smi(self.mol), self.smiles)
def test_smi2mol2smi(self):
self.assertTrue(re.compile(self.mol).match(smi2mol(self.smiles)))
def test_view_smi2mol_valid(self): def test_view_smi2mol_valid(self):
url = reverse("smi2mol") url = reverse("smi2mol")
response = self.client.get(url, {"smiString": self.smiles}) response = self.client.get(url, {"smiString": self.smiles})
...@@ -89,94 +81,6 @@ class MolSmiTestCase(TestCase): ...@@ -89,94 +81,6 @@ class MolSmiTestCase(TestCase):
self.assertEqual(response.status_code, 400) self.assertEqual(response.status_code, 400)
class SmiInchi(TestCase):
"""
Test INCHI and INCHIKEY generation functions
"""
def setUp(self):
self.smiles_str = (
"CC(C)C(=O)C1=C(C(=C(C(=C1)C(=O)C2=CC=C(C=C2)" "OC3=CC=CC=C3)O)O)O"
)
self.inchi_str = (
"InChI=1S/C23H20O6/c1-13(2)19(24)17-12-18(22"
"(27)23(28)21(17)26)20(25)14-8-10-16(11-9-14)29-15-6-4-3-"
"5-7-15/h3-13,26-28H,1-2H3"
)
self.inchikey_str = "CVVQMBDTMYUWTR-UHFFFAOYSA-N"
def test_smi2inchi(self):
self.assertEqual(smi2inchi(self.smiles_str), self.inchi_str)
def test_smi2inchikey(self):
self.assertEqual(smi2inchikey(self.smiles_str), self.inchikey_str)
class FingerPrinterTestCase(TestCase):
"""
Test FingerPrinter class
"""
def setUp(self):
self.fingerprinter = FingerPrinter("FP4")
self.smiles = "CC"
self.fp = vectorUnsignedInt([1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
self.smiles_dict = {1: "CC", 2: "CCC"}
self.fp_dict = {
1: vectorUnsignedInt([1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]),
2: vectorUnsignedInt([3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]),
}
self.tanimoto_dict = {1: 1.0, 2: 0.5}
def test_fingerprints_available(self):
# test that all necessary fingerprints are available
self.assertIsNotNone(OBFingerprint.FindFingerprint("FP2"))
self.assertIsNotNone(OBFingerprint.FindFingerprint("FP4"))
self.assertIsNotNone(OBFingerprint.FindFingerprint("ECFP4"))
def assertEqualVUI(self, vui_one, vui_two):
return self.assertEqual(list(vui_one), list(vui_two))
def assertEqualVUIdict(self, vuidict_one, vuidict_two):
vuidict_one = {id_: list(vui) for id_, vui in vuidict_one.items()}
vuidict_two = {id_: list(vui) for id_, vui in vuidict_two.items()}
return self.assertEqual(vuidict_one, vuidict_two)
def test_fp(self):
self.assertEqualVUI(self.fingerprinter.fp(self.smiles), self.fp)
def test_fp_dict(self):
self.assertEqualVUIdict(
self.fingerprinter.fp_dict(self.smiles_dict), self.fp_dict
)
def test_tanimoto_fps(self):
self.assertEqual(
self.fingerprinter.tanimoto_fps(self.smiles, self.fp_dict),
self.tanimoto_dict,
)
def test_tanimoto_smiles(self):
self.assertEqual(
self.fingerprinter.tanimoto_smiles(self.smiles, self.smiles_dict),
self.tanimoto_dict,
)
class FingerPrinterTestCaseCompound1ECFP4(TestCase):
def setUp(self):
self.fingerprinter = FingerPrinter("ECFP4")
self.smiles = "CC(C)C(=O)c1cc(C(=O)c2ccc(Oc3ccccc3)cc2)c(O)c(O)c1O"
self.smiles_dict = {1: "CC(C)C(=O)c1cc(C(=O)c2ccc(Oc3ccccc3)cc2)c(O)" "c(O)c1O"}
self.tanimoto_dict = {1: 1.0}
def test_tanimoto_smiles(self):
self.assertEqual(
self.fingerprinter.tanimoto_smiles(self.smiles, self.smiles_dict),
self.tanimoto_dict,
)
def create_dummy_compound(id_, smiles): def create_dummy_compound(id_, smiles):
c = Compound() c = Compound()
c.id = id_ c.id = id_
...@@ -918,30 +822,6 @@ class TestConvertSMILESToIUPAC(TestCase): ...@@ -918,30 +822,6 @@ class TestConvertSMILESToIUPAC(TestCase):
) )
class TestConvertSMILESToSDF(TestCase):
"""
Test converting a smiles to SDF using openbabel
"""
def test_valid(self):
smiles_to_sdfs = {
"C": [
"1",
" OpenBabel04142011372D",
"",
" 1 0 0 0 0 0 0 0 0 0999 V2000",
" 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0",
"M END",
"$$$$",
]
}
for smiles, expected_lines in smiles_to_sdfs.items():
result = smi2sdf({1: smiles})
result_lines = result.split("\n")
for line_idx in [0, 2, 3, 4, 5, 6]:
self.assertEqual(result_lines[line_idx], expected_lines[line_idx])
class DuplicateGeneNameTestCase(TestCase): class DuplicateGeneNameTestCase(TestCase):
def test_works(self): def test_works(self):
models.Protein.objects.get_or_create(uniprot_id="P12497") models.Protein.objects.get_or_create(uniprot_id="P12497")
......
ippisite/ippidb/tests_utils.py 0 → 100644
+ 143
− 0
View file @ 2c5f7202
"""
iPPI-DB unit tests
"""
import re
from django.test import TestCase
from openbabel import vectorUnsignedInt, OBFingerprint
from .utils import FingerPrinter, mol2smi, smi2mol, smi2inchi, smi2inchikey, smi2sdf
class MolSmiTestCase(TestCase):
"""
Test MOL to SMILES and SMILES to MOL format conversion functions
"""
def setUp(self):
self.smiles = "C"
# the MOL version is also a valid regexp to validate arbitrary name in
# the openbabel-generated version
self.mol = (
"\n OpenBabel[0-9]{11}D\n\n 1 0 0 0 0 0 0 0 "
" 0 0999 V2000\n 1.0000 0.0000 0.0000 C 0 0 0 0 "
" 0 0 0 0 0 0 0 0\nM END\n"
)
def test_mol2smi(self):
self.assertEqual(mol2smi(self.mol), self.smiles)
def test_smi2mol2smi(self):
self.assertTrue(re.compile(self.mol).match(smi2mol(self.smiles)))
class SmiInchiTestCase(TestCase):
"""
Test INCHI and INCHIKEY generation functions
"""
def setUp(self):
self.smiles_str = (
"CC(C)C(=O)C1=C(C(=C(C(=C1)C(=O)C2=CC=C(C=C2)" "OC3=CC=CC=C3)O)O)O"
)
self.inchi_str = (
"InChI=1S/C23H20O6/c1-13(2)19(24)17-12-18(22"
"(27)23(28)21(17)26)20(25)14-8-10-16(11-9-14)29-15-6-4-3-"
"5-7-15/h3-13,26-28H,1-2H3"
)
self.inchikey_str = "CVVQMBDTMYUWTR-UHFFFAOYSA-N"
def test_smi2inchi(self):
self.assertEqual(smi2inchi(self.smiles_str), self.inchi_str)
def test_smi2inchikey(self):
self.assertEqual(smi2inchikey(self.smiles_str), self.inchikey_str)
class FingerPrinterTestCase(TestCase):
"""
Test FingerPrinter class
"""
def setUp(self):
self.fingerprinter = FingerPrinter("FP4")
self.smiles = "CC"
self.fp = vectorUnsignedInt([1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
self.smiles_dict = {1: "CC", 2: "CCC"}
self.fp_dict = {
1: vectorUnsignedInt([1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]),
2: vectorUnsignedInt([3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]),
}
self.tanimoto_dict = {1: 1.0, 2: 0.5}
def test_fingerprints_available(self):
# test that all necessary fingerprints are available
self.assertIsNotNone(OBFingerprint.FindFingerprint("FP2"))
self.assertIsNotNone(OBFingerprint.FindFingerprint("FP4"))
self.assertIsNotNone(OBFingerprint.FindFingerprint("ECFP4"))
def assertEqualVUI(self, vui_one, vui_two):
return self.assertEqual(list(vui_one), list(vui_two))
def assertEqualVUIdict(self, vuidict_one, vuidict_two):
vuidict_one = {id_: list(vui) for id_, vui in vuidict_one.items()}
vuidict_two = {id_: list(vui) for id_, vui in vuidict_two.items()}
return self.assertEqual(vuidict_one, vuidict_two)
def test_fp(self):
self.assertEqualVUI(self.fingerprinter.fp(self.smiles), self.fp)
def test_fp_dict(self):
self.assertEqualVUIdict(
self.fingerprinter.fp_dict(self.smiles_dict), self.fp_dict
)
def test_tanimoto_fps(self):
self.assertEqual(
self.fingerprinter.tanimoto_fps(self.smiles, self.fp_dict),
self.tanimoto_dict,
)
def test_tanimoto_smiles(self):
self.assertEqual(
self.fingerprinter.tanimoto_smiles(self.smiles, self.smiles_dict),
self.tanimoto_dict,
)
class FingerPrinterTestCaseCompound1ECFP4(TestCase):
def setUp(self):
self.fingerprinter = FingerPrinter("ECFP4")
self.smiles = "CC(C)C(=O)c1cc(C(=O)c2ccc(Oc3ccccc3)cc2)c(O)c(O)c1O"
self.smiles_dict = {1: "CC(C)C(=O)c1cc(C(=O)c2ccc(Oc3ccccc3)cc2)c(O)" "c(O)c1O"}
self.tanimoto_dict = {1: 1.0}
def test_tanimoto_smiles(self):
self.assertEqual(
self.fingerprinter.tanimoto_smiles(self.smiles, self.smiles_dict),
self.tanimoto_dict,
)
class ConvertSMILESToSDFTestCase(TestCase):
"""
Test converting a smiles to SDF using openbabel
"""
def setUp(self):
self.smiles = "C"
# the MOL version is also a valid regexp to validate arbitrary name in
# the openbabel-generated version
self.sdf = (
"1\n"
" OpenBabel[0-9]{11}D\n"
"\n"
" 1 0 0 0 0 0 0 0 0 0999 V2000\n"
" 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
"M END\n"
"\$\$\$\$\n"
)
def test_valid(self):
result = smi2sdf({1: self.smiles})
self.assertTrue(re.compile(self.sdf).search(result))
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