diff --git a/ippisite/ippidb/tests.py b/ippisite/ippidb/tests.py
index ed1a17904e24745f18af1a925a7b71991ffd8fa4..ea26a69d260f2bf50664f5eb1efe1a5ad42ad574 100644
--- a/ippisite/ippidb/tests.py
+++ b/ippisite/ippidb/tests.py
@@ -13,8 +13,13 @@ from openbabel import vectorUnsignedInt, OBFingerprint
from ippidb import ws, models
from ippidb.ws import get_uniprot_info
-from .models import Compound, CompoundTanimoto, create_tanimoto, \
- update_compound_cached_properties, Symmetry
+from .models import (
+ Compound,
+ CompoundTanimoto,
+ create_tanimoto,
+ update_compound_cached_properties,
+ Symmetry,
+)
from .models import DrugBankCompound
from .utils import FingerPrinter, mol2smi, smi2mol, smi2inchi, smi2inchikey
@@ -28,9 +33,11 @@ class MolSmiTestCase(TestCase):
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 " \
+ 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)
@@ -45,11 +52,14 @@ class SmiInchi(TestCase):
"""
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-" \
+ 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):
@@ -67,21 +77,19 @@ class FingerPrinterTestCase(TestCase):
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.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])}
+ 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'))
+ 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))
@@ -95,33 +103,35 @@ class FingerPrinterTestCase(TestCase):
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)
+ 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)
+ 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)
+ 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.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)
+ self.assertEqual(
+ self.fingerprinter.tanimoto_smiles(self.smiles, self.smiles_dict),
+ self.tanimoto_dict,
+ )
def create_dummy_compound(id_, smiles):
@@ -179,13 +189,12 @@ def create_dummy_compound(id_, smiles):
def create_dummy_drugbank_compound(id_, smiles):
dbc = DrugBankCompound()
dbc.id = id_
- dbc.common_name = 'DrugBankCompound' + str(id_)
+ dbc.common_name = "DrugBankCompound" + str(id_)
dbc.canonical_smiles = smiles
dbc.save()
class CompoundTanimotoTestCase(TestCase):
-
def setUp(self):
self.smiles_dict = {1: "CC", 2: "CCC"}
self.query = "CC"
@@ -201,12 +210,12 @@ class CompoundTanimotoTestCase(TestCase):
class CompoundTanimotoTestCaseCompound1ECFP4(TestCase):
-
def setUp(self):
self.smiles_dict = {
1: "CC(C)C(=O)c1cc(C(=O)c2ccc(Oc3ccccc3)cc2)c(O)c(O)c1O",
2: "NC(=N)N[C@H](C1CCCCC1)C(=O)NCC(=O)N1CCC(CC1)c1cc(n[nH]1)"
- "-c1ccc(Cl)cc1Cl"}
+ "-c1ccc(Cl)cc1Cl",
+ }
self.query = "CC(C)C(=O)c1cc(C(=O)c2ccc(Oc3ccccc3)cc2)c(O)c(O)c1O"
for id_, smiles in self.smiles_dict.items():
create_dummy_compound(id_, smiles)
@@ -220,7 +229,6 @@ class CompoundTanimotoTestCaseCompound1ECFP4(TestCase):
class CompoundAnnotationsTestCase(TestCase):
-
def test_lipinsky_ok(self):
# c is ok for Lipinsky
c = create_dummy_compound(1, "CC")
@@ -327,20 +335,19 @@ class CompoundAnnotationsTestCase(TestCase):
class QueryCompoundViewsTestCase(TestCase):
-
@classmethod
def setUpTestData(cls):
c = create_dummy_compound(1, "CC")
c = create_dummy_compound(2, "CCC")
- call_command('lle_le')
- call_command('pca')
+ call_command("lle_le")
+ call_command("pca")
def test_existing_compound(self):
"""
The detail view of an existing compound
returns a 200
"""
- url = reverse('compound_card', kwargs={'pk': 1})
+ url = reverse("compound_card", kwargs={"pk": 1})
response = self.client.get(url)
self.assertEqual(response.status_code, 200)
@@ -349,7 +356,7 @@ class QueryCompoundViewsTestCase(TestCase):
The detail view of a non-existing compound
returns a 404 not found.
"""
- url = reverse('compound_card', kwargs={'pk': 9})
+ url = reverse("compound_card", kwargs={"pk": 9})
response = self.client.get(url)
self.assertEqual(response.status_code, 404)
@@ -358,7 +365,7 @@ class QueryCompoundViewsTestCase(TestCase):
The compounds list view
returns a 200
"""
- url = reverse('compound_list')
+ url = reverse("compound_list")
response = self.client.get(url)
self.assertEqual(response.status_code, 200)
@@ -369,50 +376,60 @@ class TestGetDoiInfo(TestCase):
"""
def test_get_doi_info(self):
- resp = ws.get_doi_info('10.1073/pnas.0805139105')
- self.assertEqual(resp['title'], 'A quantitative atlas of mitotic'
- ' phosphorylation')
- self.assertEqual(resp['journal_name'], 'Proceedings of the National'
- ' Academy of Sciences')
- self.assertEqual(resp['biblio_year'], 2008)
- self.assertEqual(resp['authors_list'],
- 'Dephoure N., Zhou C., Villen J., Beausoleil S. A., '
- 'Bakalarski C. E., Elledge S. J., Gygi S. P.')
+ resp = ws.get_doi_info("10.1073/pnas.0805139105")
+ self.assertEqual(
+ resp["title"], "A quantitative atlas of mitotic" " phosphorylation"
+ )
+ self.assertEqual(
+ resp["journal_name"], "Proceedings of the National" " Academy of Sciences"
+ )
+ self.assertEqual(resp["biblio_year"], 2008)
+ self.assertEqual(
+ resp["authors_list"],
+ "Dephoure N., Zhou C., Villen J., Beausoleil S. A., "
+ "Bakalarski C. E., Elledge S. J., Gygi S. P.",
+ )
class TestGetPfamInfo(TestCase):
def test_create_protein(self):
- target = {'id': 'bZIP_1', 'description': 'bZIP transcription factor'}
- resp = ws.get_pfam_info('PF00170')
+ target = {"id": "bZIP_1", "description": "bZIP transcription factor"}
+ resp = ws.get_pfam_info("PF00170")
self.assertEqual(resp, target)
class TestGetGooglePatentInfo(TestCase):
def test_it(self):
- target = {'title': 'Secure virtual machine bootstrap in untrusted'
- ' cloud infrastructures',
- 'journal_name': None,
- 'biblio_year': '2010',
- 'authors_list': 'Fabio R. Maino, Pere Monclus, David A.'
- ' McGrew, Robert T. Bell, '
- 'Steven Joseph Rich, Cisco Technology Inc'}
- resp = ws.get_google_patent_info('US8856504')
+ target = {
+ "title": "Secure virtual machine bootstrap in untrusted"
+ " cloud infrastructures",
+ "journal_name": None,
+ "biblio_year": "2010",
+ "authors_list": "Fabio R. Maino, Pere Monclus, David A."
+ " McGrew, Robert T. Bell, "
+ "Steven Joseph Rich, Cisco Technology Inc",
+ }
+ resp = ws.get_google_patent_info("US8856504")
self.assertEqual(resp, target)
def test_entry_not_found(self):
- self.assertRaises(ws.PatentNotFound, ws.get_google_patent_info,
- 'US8856504US8856504US885US8856504US8856504')
+ self.assertRaises(
+ ws.PatentNotFound,
+ ws.get_google_patent_info,
+ "US8856504US8856504US885US8856504US8856504",
+ )
class TestGetPubMEDIdInfo(TestCase):
def test_create_protein(self):
- target = {'title': 'Gene List significance at-a-glance with'
- ' GeneValorization.',
- 'journal_name': 'Bioinformatics (Oxford, England)',
- 'biblio_year': '2011',
- 'authors_list': 'Brancotte B, Biton A, Bernard-Pierrot I, '
- 'Radvanyi F, Reyal F, Cohen-Boulakia S'}
- resp = ws.get_pubmed_info('21349868')
+ target = {
+ "title": "Gene List significance at-a-glance with" " GeneValorization.",
+ "journal_name": "Bioinformatics (Oxford, England)",
+ "biblio_year": "2011",
+ "authors_list": "Brancotte B, Biton A, Bernard-Pierrot I, "
+ "Radvanyi F, Reyal F, Cohen-Boulakia S",
+ }
+ resp = ws.get_pubmed_info("21349868")
self.assertEqual(resp, target)
@@ -422,66 +439,99 @@ class TestGetUniprotInfo(TestCase):
"""
def test_get_uniprot_info(self):
- resp = get_uniprot_info('Q15286')
- self.assertEqual(resp['recommended_name'],
- 'Ras-related protein Rab-35')
- self.assertEqual(resp['organism'], 9606)
- self.assertEqual(resp['gene_id'], 11021)
- exp_gene_names = [{'name': 'RAB35', 'type': 'primary'},
- {'name': 'RAB1C', 'type': 'synonym'},
- {'name': 'RAY', 'type': 'synonym'}]
- self.assertEqual(sorted(resp['gene_names'], key=lambda k: k['name']),
- sorted(exp_gene_names, key=lambda k: k['name']))
- self.assertEqual(resp['entry_name'], 'RAB35_HUMAN')
- self.assertEqual(resp['short_name'], 'RAB35')
- exp_molecular_functions = ['GO_0003924', 'GO_0005525', 'GO_0005546',
- 'GO_0019003']
- self.assertEqual(sorted(resp['molecular_functions']),
- sorted(exp_molecular_functions))
- exp_cellular_localisations = ['GO_0000139', 'GO_0005829', 'GO_0005886',
- 'GO_0005905', 'GO_0010008', 'GO_0030665',
- 'GO_0031253', 'GO_0042470', 'GO_0045171',
- 'GO_0045334', 'GO_0055038', 'GO_0070062',
- 'GO_0098993']
- self.assertEqual(sorted(resp['cellular_localisations']),
- sorted(exp_cellular_localisations))
- exp_biological_processes = ['GO_0000281', 'GO_0006886', 'GO_0008104',
- 'GO_0016197', 'GO_0019882', 'GO_0031175',
- 'GO_0032456', 'GO_0032482', 'GO_0036010',
- 'GO_0048227', 'GO_1990090']
- self.assertEqual(sorted(resp['biological_processes']),
- sorted(exp_biological_processes))
- exp_accessions = ['Q15286', 'B2R6E0', 'B4E390']
- self.assertEqual(sorted(resp['accessions']),
- sorted(exp_accessions))
+ resp = get_uniprot_info("Q15286")
+ self.assertEqual(resp["recommended_name"], "Ras-related protein Rab-35")
+ self.assertEqual(resp["organism"], 9606)
+ self.assertEqual(resp["gene_id"], 11021)
+ exp_gene_names = [
+ {"name": "RAB35", "type": "primary"},
+ {"name": "RAB1C", "type": "synonym"},
+ {"name": "RAY", "type": "synonym"},
+ ]
+ self.assertEqual(
+ sorted(resp["gene_names"], key=lambda k: k["name"]),
+ sorted(exp_gene_names, key=lambda k: k["name"]),
+ )
+ self.assertEqual(resp["entry_name"], "RAB35_HUMAN")
+ self.assertEqual(resp["short_name"], "RAB35")
+ exp_molecular_functions = [
+ "GO_0003924",
+ "GO_0005525",
+ "GO_0005546",
+ "GO_0019003",
+ ]
+ self.assertEqual(
+ sorted(resp["molecular_functions"]), sorted(exp_molecular_functions)
+ )
+ exp_cellular_localisations = [
+ "GO_0000139",
+ "GO_0005829",
+ "GO_0005886",
+ "GO_0005905",
+ "GO_0010008",
+ "GO_0030665",
+ "GO_0031253",
+ "GO_0042470",
+ "GO_0045171",
+ "GO_0045334",
+ "GO_0055038",
+ "GO_0070062",
+ "GO_0098993",
+ ]
+ self.assertEqual(
+ sorted(resp["cellular_localisations"]), sorted(exp_cellular_localisations)
+ )
+ exp_biological_processes = [
+ "GO_0000281",
+ "GO_0006886",
+ "GO_0008104",
+ "GO_0016197",
+ "GO_0019882",
+ "GO_0031175",
+ "GO_0032456",
+ "GO_0032482",
+ "GO_0036010",
+ "GO_0048227",
+ "GO_1990090",
+ ]
+ self.assertEqual(
+ sorted(resp["biological_processes"]), sorted(exp_biological_processes)
+ )
+ exp_accessions = ["Q15286", "B2R6E0", "B4E390"]
+ self.assertEqual(sorted(resp["accessions"]), sorted(exp_accessions))
exp_citations = [
- {'doi': '10.1006/bbrc.1994.2889', 'pmid': '7811277'},
- {'doi': '10.1038/ng1285', 'pmid': '14702039'},
- {'doi': '10.1038/nature04569', 'pmid': '16541075'},
- {'doi': '10.1101/gr.2596504', 'pmid': '15489334'},
- {'doi': '10.1016/j.cub.2006.07.020', 'pmid': '16950109'},
- {'doi': '10.1021/pr060363j', 'pmid': '17081065'},
- {'doi': '10.1074/jbc.M109.050930', 'pmid': '20154091'},
- {'doi': '10.1186/1752-0509-5-17', 'pmid': '21269460'},
- {'doi': '10.1038/nature10335', 'pmid': '21822290'},
- {'doi': '10.1038/emboj.2012.16', 'pmid': '22307087'},
- {'doi': '10.1111/j.1600-0854.2011.01294.x', 'pmid': '21951725'},
- {'doi': '10.1021/pr300630k', 'pmid': '23186163'},
- {'doi': '10.1002/pmic.201400617', 'pmid': '25944712'},
- {'doi': '10.1073/pnas.1110415108', 'pmid': '22065758'}
+ {"doi": "10.1006/bbrc.1994.2889", "pmid": "7811277"},
+ {"doi": "10.1038/ng1285", "pmid": "14702039"},
+ {"doi": "10.1038/nature04569", "pmid": "16541075"},
+ {"doi": "10.1101/gr.2596504", "pmid": "15489334"},
+ {"doi": "10.1016/j.cub.2006.07.020", "pmid": "16950109"},
+ {"doi": "10.1021/pr060363j", "pmid": "17081065"},
+ {"doi": "10.1074/jbc.M109.050930", "pmid": "20154091"},
+ {"doi": "10.1186/1752-0509-5-17", "pmid": "21269460"},
+ {"doi": "10.1038/nature10335", "pmid": "21822290"},
+ {"doi": "10.1038/emboj.2012.16", "pmid": "22307087"},
+ {"doi": "10.1111/j.1600-0854.2011.01294.x", "pmid": "21951725"},
+ {"doi": "10.1021/pr300630k", "pmid": "23186163"},
+ {"doi": "10.1002/pmic.201400617", "pmid": "25944712"},
+ {"doi": "10.1073/pnas.1110415108", "pmid": "22065758"},
+ ]
+ self.assertEqual(
+ sorted(exp_citations, key=lambda k: k["pmid"]),
+ sorted(resp["citations"], key=lambda k: k["pmid"]),
+ )
+ exp_alternative_names = [
+ {"full": "GTP-binding protein RAY"},
+ {"full": "Ras-related protein Rab-1C"},
]
- self.assertEqual(sorted(exp_citations, key=lambda k: k['pmid']),
- sorted(resp['citations'], key=lambda k: k['pmid']))
- exp_alternative_names = [{'full': 'GTP-binding protein RAY'},
- {'full': 'Ras-related protein Rab-1C'}]
self.assertEqual(
- sorted(exp_alternative_names, key=lambda k: k['full']),
- sorted(resp['alternative_names'], key=lambda k: k['full']))
+ sorted(exp_alternative_names, key=lambda k: k["full"]),
+ sorted(resp["alternative_names"], key=lambda k: k["full"]),
+ )
def test_get_uniprot_info_domains(self):
- resp = get_uniprot_info('O00255')
- exp_domains = ['PF05053']
- self.assertEqual(sorted(resp['domains']), sorted(exp_domains))
+ resp = get_uniprot_info("O00255")
+ exp_domains = ["PF05053"]
+ self.assertEqual(sorted(resp["domains"]), sorted(exp_domains))
class TestGetPDBUniProtMapping(TestCase):
@@ -490,15 +540,14 @@ class TestGetPDBUniProtMapping(TestCase):
"""
def test_find_info(self):
- target = sorted(['Q03164', 'O00255'])
- resp = ws.get_pdb_uniprot_mapping('3u85')
+ target = sorted(["Q03164", "O00255"])
+ resp = ws.get_pdb_uniprot_mapping("3u85")
resp = sorted(resp)
self.assertEqual(resp, target)
self.assertEqual(len(resp), len(set(resp)))
def test_entry_not_found(self):
- self.assertRaises(ws.EntryNotFoundError, ws.get_pdb_uniprot_mapping,
- 'Xu85')
+ self.assertRaises(ws.EntryNotFoundError, ws.get_pdb_uniprot_mapping, "Xu85")
class TestConvertIUPACToSMILESAndMore(TestCase):
@@ -509,54 +558,53 @@ class TestConvertIUPACToSMILESAndMore(TestCase):
def test_valid(self):
pairs = [
(
- '2,4,6-trinitrotoluene',
+ "2,4,6-trinitrotoluene",
{
"inchi": "InChI=1/C7H5N3O6/c1-4-6(9(13)14)2-5(8(11)12)"
- "3-7(4)10(15)16/h2-3H,1H3",
+ "3-7(4)10(15)16/h2-3H,1H3",
"stdinchi": "InChI=1S/C7H5N3O6/c1-4-6(9(13)14)2-5(8(11)"
- "12)3-7(4)10(15)16/h2-3H,1H3",
+ "12)3-7(4)10(15)16/h2-3H,1H3",
"stdinchikey": "SPSSULHKWOKEEL-UHFFFAOYSA-N",
"smiles": "[N+](=O)([O-])C1=C(C)C(=CC(=C1)[N+](=O)[O-])"
- "[N+](=O)[O-]",
- }
+ "[N+](=O)[O-]",
+ },
),
(
- '3-{1-oxo-6-[4-(piperidin-4-yl)butanamido]-2,3-dihydro-1H-'
- 'isoindol-2-yl}propanoic acid',
+ "3-{1-oxo-6-[4-(piperidin-4-yl)butanamido]-2,3-dihydro-1H-"
+ "isoindol-2-yl}propanoic acid",
{
"inchi": "InChI=1/C20H27N3O4/c24-18(3-1-2-14-6-9-21-10-"
- "7-14)22-16-5-4-15-13-23(11-8-19(25)26)20(27)17"
- "(15)12-16/h4-5,12,14,21H,1-3,6-11,13H2,(H,22,"
- "24)(H,25,26)/f/h22,25H",
+ "7-14)22-16-5-4-15-13-23(11-8-19(25)26)20(27)17"
+ "(15)12-16/h4-5,12,14,21H,1-3,6-11,13H2,(H,22,"
+ "24)(H,25,26)/f/h22,25H",
"stdinchi": "InChI=1S/C20H27N3O4/c24-18(3-1-2-14-6-9-21"
- "-10-7-14)22-16-5-4-15-13-23(11-8-19(25)26)"
- "20(27)17(15)12-16/h4-5,12,14,21H,1-3,6-11,"
- "13H2,(H,22,24)(H,25,26)",
+ "-10-7-14)22-16-5-4-15-13-23(11-8-19(25)26)"
+ "20(27)17(15)12-16/h4-5,12,14,21H,1-3,6-11,"
+ "13H2,(H,22,24)(H,25,26)",
"stdinchikey": "HWRXVANHVCXVHA-UHFFFAOYSA-N",
- "smiles": "O=C1N(CC2=CC=C(C=C12)NC(CCCC1CCNCC1)=O)CCC(=O)O"
- }
-
- )
+ "smiles": "O=C1N(CC2=CC=C(C=C12)NC(CCCC1CCNCC1)=O)CCC(=O)O",
+ },
+ ),
]
for iupac, dict_expected in pairs:
dict_returned = ws.convert_iupac_to_smiles_and_inchi(iupac)
self.assertEqual(dict_expected["smiles"], dict_returned["smiles"])
self.assertEqual(dict_expected["inchi"], dict_returned["inchi"])
- self.assertEqual(dict_expected["stdinchi"],
- dict_returned["stdinchi"])
- self.assertEqual(dict_expected["stdinchikey"],
- dict_returned["stdinchikey"])
+ self.assertEqual(dict_expected["stdinchi"], dict_returned["stdinchi"])
+ self.assertEqual(dict_expected["stdinchikey"], dict_returned["stdinchikey"])
def test_invalid_entry(self):
- self.assertRaises(ws.EntryNotFoundError,
- ws.convert_iupac_to_smiles_and_inchi,
- '3-{1-oxo-6-[4-(piperid')
- self.assertRaises(ws.EntryNotFoundError,
- ws.convert_iupac_to_smiles_and_inchi, None)
+ self.assertRaises(
+ ws.EntryNotFoundError,
+ ws.convert_iupac_to_smiles_and_inchi,
+ "3-{1-oxo-6-[4-(piperid",
+ )
+ self.assertRaises(
+ ws.EntryNotFoundError, ws.convert_iupac_to_smiles_and_inchi, None
+ )
class DuplicateGeneNameTestCase(TestCase):
-
def test_works(self):
- models.Protein.objects.get_or_create(uniprot_id='P12497')
- models.Protein.objects.get_or_create(uniprot_id='P0C6F2')
+ models.Protein.objects.get_or_create(uniprot_id="P12497")
+ models.Protein.objects.get_or_create(uniprot_id="P0C6F2")
diff --git a/ippisite/ippidb/tests_contribute.py b/ippisite/ippidb/tests_contribute.py
index 8a2bc3529db134cef0dc5b37b80a81ac4337816b..cab5e273c6fb3cfcc2750e6f03ca61fbcccecac8 100644
--- a/ippisite/ippidb/tests_contribute.py
+++ b/ippisite/ippidb/tests_contribute.py
@@ -20,21 +20,21 @@ class ContributionViewsTestCase(TestCase):
"""
def setUp(self):
- login = 'contributor'
- password = '12345'
+ login = "contributor"
+ password = "12345"
User = get_user_model()
User.objects.create_user(username=login, password=password)
self.client.login(username=login, password=password)
symmetry = models.Symmetry()
- symmetry.code = 'AS'
- symmetry.description = 'asymmetric'
+ symmetry.code = "AS"
+ symmetry.description = "asymmetric"
symmetry.save()
@staticmethod
def get_step_url(step_id):
- step_url = reverse('admin-session-add')
+ step_url = reverse("admin-session-add")
if step_id is not None:
- step_url += step_id+'/'
+ step_url += step_id + "/"
return step_url
def _process_contribution_wizard(self, wizard_data):
@@ -43,162 +43,164 @@ class ContributionViewsTestCase(TestCase):
returns a 200
"""
for step in wizard_data:
- step_url = self.get_step_url(step.get('step-id'))
+ step_url = self.get_step_url(step.get("step-id"))
response = self.client.get(step_url)
# post form data
- if step.get('form-data') is not None:
- err_msg = f"Response code not ok when getting form " \
+ if step.get("form-data") is not None:
+ err_msg = (
+ f"Response code not ok when getting form "
f"for {step.get('step-id')} at {step_url}"
+ )
self.assertEqual(response.status_code, 200, err_msg)
form_data = {
- step['step-id'] + '-' + param_name: value
- for param_name, value in step.get('form-data').items()
- }
- form_data['ippi_wizard-current_step'] = step['step-id']
+ step["step-id"] + "-" + param_name: value
+ for param_name, value in step.get("form-data").items()
+ }
+ form_data["ippi_wizard-current_step"] = step["step-id"]
response = self.client.post(step_url, form_data)
if response.status_code != 302:
file_path = self.write_in_tmp_file(response)
- err_msg = f"Response code not ok when getting form for " \
- f"{step.get('step-id')} at {step_url}. Server" \
- f" response is stored in {file_path}"
+ err_msg = (
+ f"Response code not ok when getting form for "
+ f"{step.get('step-id')} at {step_url}. Server"
+ f" response is stored in {file_path}"
+ )
self.assertEqual(response.status_code, 302, err_msg)
# check redirect to next step (if there is one)
- if step.get('next') is not None:
- redirect_url = self.get_step_url(step.get('next'))
+ if step.get("next") is not None:
+ redirect_url = self.get_step_url(step.get("next"))
self.assertEqual(response.url, redirect_url, step)
def _generate_wizard_data(self, entry_data):
"""
Generate the wizard form data dynamically based on iPPI-DB entry data
"""
+
def get_id_form():
return {
- 'source': entry_data['source'],
- 'id_source': entry_data['id_source']
+ "source": entry_data["source"],
+ "id_source": entry_data["id_source"],
}
def get_bibliography_form():
return {
- 'source': entry_data['source'],
- 'id_source': entry_data['id_source'],
- 'title':
- 'Opportunistic+amoebae:+challenges'
- '+in+prophylaxis+and+treatment.',
- 'journal_name': 'Drug+resistance+updates+:+reviews+and+'
- 'commentaries+in+antimicrobial+and+anticancer'
- '+chemotherapy',
- 'authors_list': 'Schuster+FL,+Visvesvara+GS',
- 'biblio_year': '2004',
- 'in_silico': 'on'
+ "source": entry_data["source"],
+ "id_source": entry_data["id_source"],
+ "title": "Opportunistic+amoebae:+challenges"
+ "+in+prophylaxis+and+treatment.",
+ "journal_name": "Drug+resistance+updates+:+reviews+and+"
+ "commentaries+in+antimicrobial+and+anticancer"
+ "+chemotherapy",
+ "authors_list": "Schuster+FL,+Visvesvara+GS",
+ "biblio_year": "2004",
+ "in_silico": "on",
}
def get_pdb_form():
- return {
- 'pdb_id': entry_data['pdb_id']
- }
+ return {"pdb_id": entry_data["pdb_id"]}
def get_complex_type_form():
- return {
- 'complexType': 'Hetero2MerAB',
- 'complexChoice': 'inhibited'
- }
+ return {"complexType": "Hetero2MerAB", "complexChoice": "inhibited"}
def get_complex_form():
data = {
- 'TOTAL_FORMS': len(entry_data['complex']),
- 'INITIAL_FORMS': len(entry_data['complex']),
- 'MIN_NUM_FORMS': 0,
- 'MAX_NUM_FORMS': 1000,
+ "TOTAL_FORMS": len(entry_data["complex"]),
+ "INITIAL_FORMS": len(entry_data["complex"]),
+ "MIN_NUM_FORMS": 0,
+ "MAX_NUM_FORMS": 1000,
}
- for idx, entry_complex in enumerate(entry_data['complex']):
- data['{}-protein'.format(idx)] = models.Protein.objects.get(
- uniprot_id=entry_complex['uniprot_id']).id
- data['{}-complex_type'.format(idx)] = \
- entry_complex['complex_type']
- if entry_complex['domain_pfam_acc'] is not None:
+ for idx, entry_complex in enumerate(entry_data["complex"]):
+ data["{}-protein".format(idx)] = models.Protein.objects.get(
+ uniprot_id=entry_complex["uniprot_id"]
+ ).id
+ data["{}-complex_type".format(idx)] = entry_complex["complex_type"]
+ if entry_complex["domain_pfam_acc"] is not None:
try:
- data['{}-domain'.format(idx)] = \
- models.Domain.objects.get(
- pfam_acc=entry_complex['domain_pfam_acc']).id
+ data["{}-domain".format(idx)] = models.Domain.objects.get(
+ pfam_acc=entry_complex["domain_pfam_acc"]
+ ).id
except models.Domain.DoesNotExist as dne:
- print('No domain in DB for PFAM ACC {}'.format(
- entry_complex['domain_pfam_acc']))
+ print(
+ "No domain in DB for PFAM ACC {}".format(
+ entry_complex["domain_pfam_acc"]
+ )
+ )
raise dne
else:
- data['{}-domain'.format(idx)] = ''
- data['{}-ppc_copy_nb'.format(idx)] = \
- entry_complex['ppc_copy_nb']
- data['{}-cc_nb'.format(idx)] = entry_complex['cc_nb']
- data['{}-ppp_copy_nb_per_p'.format(idx)] = \
- entry_complex['ppp_copy_nb_per_p']
+ data["{}-domain".format(idx)] = ""
+ data["{}-ppc_copy_nb".format(idx)] = entry_complex["ppc_copy_nb"]
+ data["{}-cc_nb".format(idx)] = entry_complex["cc_nb"]
+ data["{}-ppp_copy_nb_per_p".format(idx)] = entry_complex[
+ "ppp_copy_nb_per_p"
+ ]
return data
def get_ppi_form():
return {
- 'family': '',
- 'pdb_id': entry_data['pdb_id'],
- 'family_name': entry_data['family_name'],
- 'symmetry': 1, # FIXME
- 'pockets_nb': 1, # FIXME
- 'other_diseases': 'test', # FIXME
+ "family": "",
+ "pdb_id": entry_data["pdb_id"],
+ "family_name": entry_data["family_name"],
+ "symmetry": 1, # FIXME
+ "pockets_nb": 1, # FIXME
+ "other_diseases": "test", # FIXME
}
def get_compound_form():
return {
- 'TOTAL_FORMS': 1,
+ "TOTAL_FORMS": 1,
# FIXME there should be a way to list more than one compound
- 'INITIAL_FORMS': 0,
- 'MIN_NUM_FORMS': 1,
- 'MAX_NUM_FORMS': 1000,
- '0-common_name': entry_data['common_name'],
- '0-compound_name': entry_data['compound_name'],
- '0-molecule_smiles': entry_data['molecule_smiles'],
+ "INITIAL_FORMS": 0,
+ "MIN_NUM_FORMS": 1,
+ "MAX_NUM_FORMS": 1000,
+ "0-common_name": entry_data["common_name"],
+ "0-compound_name": entry_data["compound_name"],
+ "0-molecule_smiles": entry_data["molecule_smiles"],
}
def get_activity_description_form():
return {
- 'TOTAL_FORMS': 0,
- 'INITIAL_FORMS': 0,
- 'MIN_NUM_FORMS': 0,
- 'MAX_NUM_FORMS': 1000,
+ "TOTAL_FORMS": 0,
+ "INITIAL_FORMS": 0,
+ "MIN_NUM_FORMS": 0,
+ "MAX_NUM_FORMS": 1000,
}
def get_cytotox_description_form():
return {
- 'TOTAL_FORMS': 0,
- 'INITIAL_FORMS': 0,
- 'MIN_NUM_FORMS': 0,
- 'MAX_NUM_FORMS': 1000,
+ "TOTAL_FORMS": 0,
+ "INITIAL_FORMS": 0,
+ "MIN_NUM_FORMS": 0,
+ "MAX_NUM_FORMS": 1000,
}
def get_pk_description_form():
return {
- 'TOTAL_FORMS': 0,
- 'INITIAL_FORMS': 0,
- 'MIN_NUM_FORMS': 0,
- 'MAX_NUM_FORMS': 1000,
+ "TOTAL_FORMS": 0,
+ "INITIAL_FORMS": 0,
+ "MIN_NUM_FORMS": 0,
+ "MAX_NUM_FORMS": 1000,
}
form_callable = {
None: lambda: None,
- 'IdForm': get_id_form,
- 'BibliographyForm': get_bibliography_form,
- 'PDBForm': get_pdb_form,
- 'ProteinDomainComplexTypeForm': get_complex_type_form,
- 'ProteinDomainComplexForm': get_complex_form,
- 'PpiForm': get_ppi_form,
- 'CompoundForm': get_compound_form,
- 'TestActivityDescriptionFormSet': get_activity_description_form,
- 'TestCytotoxDescriptionFormSet': get_cytotox_description_form,
- 'TestPKDescriptionFormSet': get_pk_description_form
+ "IdForm": get_id_form,
+ "BibliographyForm": get_bibliography_form,
+ "PDBForm": get_pdb_form,
+ "ProteinDomainComplexTypeForm": get_complex_type_form,
+ "ProteinDomainComplexForm": get_complex_form,
+ "PpiForm": get_ppi_form,
+ "CompoundForm": get_compound_form,
+ "TestActivityDescriptionFormSet": get_activity_description_form,
+ "TestCytotoxDescriptionFormSet": get_cytotox_description_form,
+ "TestPKDescriptionFormSet": get_pk_description_form,
}
form_ids = iter(list(form_callable.keys())[1:])
for step in form_callable.keys():
item = {
- 'step-id': step,
- 'form-data': form_callable[step](),
- 'next': next(form_ids, None)
- }
+ "step-id": step,
+ "form-data": form_callable[step](),
+ "next": next(form_ids, None),
+ }
yield item
def test_basic_entry(self):
@@ -206,34 +208,34 @@ class ContributionViewsTestCase(TestCase):
Basic entry test
"""
entry_data = {
- 'source': 'PM',
- 'id_source': '15072770',
- 'in_silico': 'on',
- 'pdb_id': '3u85',
- 'complexChoice': 'inhibited',
- 'complexType': 'Hetero2MerAB',
- 'complex': [
+ "source": "PM",
+ "id_source": "15072770",
+ "in_silico": "on",
+ "pdb_id": "3u85",
+ "complexChoice": "inhibited",
+ "complexType": "Hetero2MerAB",
+ "complex": [
{
- 'uniprot_id': 'O00255',
- 'complex_type': 'Partner',
- 'domain_pfam_acc': 'PF05053',
- 'ppc_copy_nb': 1,
- 'cc_nb': 1,
- 'ppp_copy_nb_per_p': '',
+ "uniprot_id": "O00255",
+ "complex_type": "Partner",
+ "domain_pfam_acc": "PF05053",
+ "ppc_copy_nb": 1,
+ "cc_nb": 1,
+ "ppp_copy_nb_per_p": "",
},
{
- 'uniprot_id': 'Q03164',
- 'complex_type': 'Bound',
- 'domain_pfam_acc': 'PF05965',
- 'ppc_copy_nb': 1,
- 'cc_nb': 1,
- 'ppp_copy_nb_per_p': 1,
+ "uniprot_id": "Q03164",
+ "complex_type": "Bound",
+ "domain_pfam_acc": "PF05965",
+ "ppc_copy_nb": 1,
+ "cc_nb": 1,
+ "ppp_copy_nb_per_p": 1,
},
],
- 'family_name': 'BCL2-Like+/+BAX',
- 'molecule_smiles': 'CCC',
- 'compound_name': 'toto',
- 'common_name': 'super'
+ "family_name": "BCL2-Like+/+BAX",
+ "molecule_smiles": "CCC",
+ "compound_name": "toto",
+ "common_name": "super",
}
wizard_data = self._generate_wizard_data(entry_data)
self._process_contribution_wizard(wizard_data)
@@ -245,34 +247,34 @@ class ContributionViewsTestCase(TestCase):
(see #77)
"""
entry_data = {
- 'source': 'PM',
- 'id_source': '26958703',
- 'in_silico': 'on',
- 'pdb_id': '3emh',
- 'complexChoice': 'inhibited',
- 'complexType': 'Hetero2MerAB',
- 'complex': [
+ "source": "PM",
+ "id_source": "26958703",
+ "in_silico": "on",
+ "pdb_id": "3emh",
+ "complexChoice": "inhibited",
+ "complexType": "Hetero2MerAB",
+ "complex": [
{
- 'uniprot_id': 'P61964',
- 'complex_type': 'Bound',
- 'domain_pfam_acc': 'PF00400',
- 'ppc_copy_nb': 1,
- 'cc_nb': 1,
- 'ppp_copy_nb_per_p': 1,
+ "uniprot_id": "P61964",
+ "complex_type": "Bound",
+ "domain_pfam_acc": "PF00400",
+ "ppc_copy_nb": 1,
+ "cc_nb": 1,
+ "ppp_copy_nb_per_p": 1,
},
{
- 'uniprot_id': 'Q03164',
- 'complex_type': 'Partner',
- 'domain_pfam_acc': None,
- 'ppc_copy_nb': 1,
- 'cc_nb': 1,
- 'ppp_copy_nb_per_p': '',
+ "uniprot_id": "Q03164",
+ "complex_type": "Partner",
+ "domain_pfam_acc": None,
+ "ppc_copy_nb": 1,
+ "cc_nb": 1,
+ "ppp_copy_nb_per_p": "",
},
],
- 'family_name': 'family',
- 'molecule_smiles': 'C',
- 'compound_name': 'toto',
- 'common_name': 'super'
+ "family_name": "family",
+ "molecule_smiles": "C",
+ "compound_name": "toto",
+ "common_name": "super",
}
wizard_data = self._generate_wizard_data(entry_data)
self._process_contribution_wizard(wizard_data)