diff --git a/ippisite/ippidb/tests/__init__.py b/ippisite/ippidb/tests/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_2380_002_e-9.yaml b/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_2380_002_e-9.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..842a1db3b1005febf7a9428c0043816b08c0011d
--- /dev/null
+++ b/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_2380_002_e-9.yaml
@@ -0,0 +1,43 @@
+activity_tests:
+- cell_line_name: ''
+ compound_activity_results:
+ - activity_mol: 2380.002
+ activity_type: pIC50
+ activity_unit: 1e-9
+ compound_name: toto
+ modulation_type: I
+ is_primary: true
+ nb_active_compounds: 2
+ protein_bound_construct: F
+ protein_complex: '2'
+ test_modulation_type: I
+ test_name: test
+ test_type: BIOCH
+complex:
+- cc_nb: 1
+ complex_type: Partner
+ domain_pfam_acc: PF05053
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: ''
+ uniprot_id: O00255
+- cc_nb: 1
+ complex_type: Bound
+ domain_pfam_acc: PF05965
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: 1
+ uniprot_id: Q03164
+complexChoice: inhibited
+complexType: Inhib_Hetero2merAB
+compounds:
+- common_name: super
+ compound_name: toto
+ molecule_smiles: CCC
+diseases:
+- ;toto;1;
+- ;titi;sfddf;
+- ;tata;3232;
+family_name: Menin (PF05053)
+id_source: '15072770'
+in_silico: true
+pdb_id: 3u85
+source: PM
diff --git a/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_4_9846073_e-6.yaml b/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_4_9846073_e-6.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..0a2e61b2d45c324e1ce6c7f00592a3ce046abe87
--- /dev/null
+++ b/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_4_9846073_e-6.yaml
@@ -0,0 +1,43 @@
+activity_tests:
+- cell_line_name: ''
+ compound_activity_results:
+ - activity_mol: 4.9846073
+ activity_type: pIC50
+ activity_unit: 1e-6
+ compound_name: toto
+ modulation_type: I
+ is_primary: true
+ nb_active_compounds: 2
+ protein_bound_construct: F
+ protein_complex: '2'
+ test_modulation_type: I
+ test_name: test
+ test_type: BIOCH
+complex:
+- cc_nb: 1
+ complex_type: Partner
+ domain_pfam_acc: PF05053
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: ''
+ uniprot_id: O00255
+- cc_nb: 1
+ complex_type: Bound
+ domain_pfam_acc: PF05965
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: 1
+ uniprot_id: Q03164
+complexChoice: inhibited
+complexType: Inhib_Hetero2merAB
+compounds:
+- common_name: super
+ compound_name: toto
+ molecule_smiles: CCC
+diseases:
+- ;toto;1;
+- ;titi;sfddf;
+- ;tata;3232;
+family_name: Menin (PF05053)
+id_source: '15072770'
+in_silico: true
+pdb_id: 3u85
+source: PM
diff --git a/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_639_39406_e-3.yaml b/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_639_39406_e-3.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..459d512dd9b0f3557f5bfb3e50dcaf0140eae7a0
--- /dev/null
+++ b/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_639_39406_e-3.yaml
@@ -0,0 +1,43 @@
+activity_tests:
+- cell_line_name: ''
+ compound_activity_results:
+ - activity_mol: 639.39406
+ activity_type: pIC50
+ activity_unit: 1e-3
+ compound_name: toto
+ modulation_type: I
+ is_primary: true
+ nb_active_compounds: 2
+ protein_bound_construct: F
+ protein_complex: '2'
+ test_modulation_type: I
+ test_name: test
+ test_type: BIOCH
+complex:
+- cc_nb: 1
+ complex_type: Partner
+ domain_pfam_acc: PF05053
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: ''
+ uniprot_id: O00255
+- cc_nb: 1
+ complex_type: Bound
+ domain_pfam_acc: PF05965
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: 1
+ uniprot_id: Q03164
+complexChoice: inhibited
+complexType: Inhib_Hetero2merAB
+compounds:
+- common_name: super
+ compound_name: toto
+ molecule_smiles: CCC
+diseases:
+- ;toto;1;
+- ;titi;sfddf;
+- ;tata;3232;
+family_name: Menin (PF05053)
+id_source: '15072770'
+in_silico: true
+pdb_id: 3u85
+source: PM
diff --git a/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_6_85_e-0.yaml b/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_6_85_e-0.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..b61f094338e568128575ea14d577a93e7f9b7088
--- /dev/null
+++ b/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_6_85_e-0.yaml
@@ -0,0 +1,43 @@
+activity_tests:
+- cell_line_name: ''
+ compound_activity_results:
+ - activity_mol: 6.85
+ activity_type: pIC50
+ activity_unit: 1e-0
+ compound_name: toto
+ modulation_type: I
+ is_primary: true
+ nb_active_compounds: 2
+ protein_bound_construct: F
+ protein_complex: '2'
+ test_modulation_type: I
+ test_name: test
+ test_type: BIOCH
+complex:
+- cc_nb: 1
+ complex_type: Partner
+ domain_pfam_acc: PF05053
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: ''
+ uniprot_id: O00255
+- cc_nb: 1
+ complex_type: Bound
+ domain_pfam_acc: PF05965
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: 1
+ uniprot_id: Q03164
+complexChoice: inhibited
+complexType: Inhib_Hetero2merAB
+compounds:
+- common_name: super
+ compound_name: toto
+ molecule_smiles: CCC
+diseases:
+- ;toto;1;
+- ;titi;sfddf;
+- ;tata;3232;
+family_name: Menin (PF05053)
+id_source: '15072770'
+in_silico: true
+pdb_id: 3u85
+source: PM
diff --git a/ippisite/ippidb/tests/test_basic_entry.yaml b/ippisite/ippidb/tests/test_basic_entry.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..c1baf06500ae82f25c3fa1063b0373433336c7f8
--- /dev/null
+++ b/ippisite/ippidb/tests/test_basic_entry.yaml
@@ -0,0 +1,43 @@
+activity_tests:
+- cell_line_name: ''
+ compound_activity_results:
+ - activity_mol: 6.85
+ activity_type: pIC50
+ activity_unit: 1e-6
+ compound_name: toto
+ modulation_type: I
+ is_primary: true
+ nb_active_compounds: 2
+ protein_bound_construct: F
+ protein_complex: '2'
+ test_modulation_type: I
+ test_name: test
+ test_type: BIOCH
+complex:
+- cc_nb: 1
+ complex_type: Partner
+ domain_pfam_acc: PF05053
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: ''
+ uniprot_id: O00255
+- cc_nb: 1
+ complex_type: Bound
+ domain_pfam_acc: PF05965
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: 1
+ uniprot_id: Q03164
+complexChoice: inhibited
+complexType: Inhib_Hetero2merAB
+compounds:
+- common_name: super
+ compound_name: toto
+ molecule_smiles: CCC
+diseases:
+- ;toto;1;
+- ;titi;sfddf;
+- ;tata;3232;
+family_name: Menin (PF05053)
+id_source: '15072770'
+in_silico: true
+pdb_id: 3u85
+source: PM
diff --git a/ippisite/ippidb/tests/test_complex_no_pfam.yaml b/ippisite/ippidb/tests/test_complex_no_pfam.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..03e6c2cf616df4f93a3aefccbeb06d7a7c47b682
--- /dev/null
+++ b/ippisite/ippidb/tests/test_complex_no_pfam.yaml
@@ -0,0 +1,40 @@
+activity_tests:
+- cell_line_name: ''
+ compound_activity_results:
+ - activity_mol: 6.85
+ activity_type: pIC50
+ activity_unit: 1e-3
+ compound_name: toto
+ modulation_type: I
+ is_primary: true
+ nb_active_compounds: 2
+ protein_bound_construct: F
+ protein_complex: '1'
+ test_modulation_type: I
+ test_name: test
+ test_type: BIOCH
+complex:
+- cc_nb: 1
+ complex_type: Bound
+ domain_pfam_acc: PF00400
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: 1
+ uniprot_id: P61964
+- cc_nb: 1
+ complex_type: Partner
+ domain_pfam_acc: null
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: ''
+ uniprot_id: Q03164
+complexChoice: inhibited
+complexType: Inhib_Hetero2merAB
+compounds:
+- common_name: super
+ compound_name: toto
+ molecule_smiles: C
+diseases: []
+family_name: WD40 (PF00400)
+id_source: '26958703'
+in_silico: true
+pdb_id: 3emh
+source: PM
diff --git a/ippisite/ippidb/tests/test_entry_28.yaml b/ippisite/ippidb/tests/test_entry_28.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..d22b2cb8274900a4497432bd1b2b68df806fe256
--- /dev/null
+++ b/ippisite/ippidb/tests/test_entry_28.yaml
@@ -0,0 +1,41 @@
+activity_tests:
+- cell_line_name: ''
+ compound_activity_results:
+ - activity_mol: 3.59
+ activity_type: pKd
+ activity_unit: 1e-9
+ compound_name: '2'
+ modulation_type: I
+ is_primary: true
+ nb_active_compounds: 1
+ protein_bound_construct: F
+ protein_complex: '1'
+ test_modulation_type: B
+ test_name: biolayer interferometry assay
+ test_type: BIOCH
+complex:
+- cc_nb: 1
+ complex_type: Partner
+ domain_pfam_acc: null
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: 1
+ uniprot_id: Q60795
+- cc_nb: 1
+ complex_type: Bound
+ domain_pfam_acc: PF01344
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: 1
+ uniprot_id: Q9Z2X8
+complexChoice: inhibited
+complexType: Inhib_Hetero2merAB
+compounds:
+- common_name: ''
+ compound_name: '2'
+ molecule_smiles: c1cc2c(cc1)c(ccc2N(S(=O)(=O)c1ccc(cc1)OC)CC(=O)O)N(S(=O)(=O)c1ccc(cc1)OC)CC(=O)O
+diseases:
+- ;cancer;MONDO:0004992;
+family_name: KEAP1 / NRF2
+id_source: '24512214 '
+in_vitro: true
+pdb_id: 3wn7
+source: PM
diff --git a/ippisite/ippidb/tests/test_simple_heterodimer.yaml b/ippisite/ippidb/tests/test_simple_heterodimer.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..c3c5f7c7e926a4ff22dea3dc30fe61645921323b
--- /dev/null
+++ b/ippisite/ippidb/tests/test_simple_heterodimer.yaml
@@ -0,0 +1,51 @@
+activity_tests:
+- cell_line_name: ''
+ compound_activity_results:
+ - activity_mol: 6.85
+ activity_type: pIC50
+ activity_unit: 1e-3
+ compound_name: 16d
+ modulation_type: I
+ is_primary: true
+ nb_active_compounds: 2
+ protein_bound_construct: F
+ protein_complex: '1'
+ test_modulation_type: I
+ test_name: test
+ test_type: BIOCH
+complex:
+- cc_nb: 1
+ complex_type: Bound
+ domain_pfam_acc: PF00400
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: 1
+ uniprot_id: P61964
+- cc_nb: 1
+ complex_type: Partner
+ domain_pfam_acc: null
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: ''
+ uniprot_id: Q03164
+complexChoice: inhibited
+complexType: Inhib_Hetero2merAB
+compounds:
+- common_name: officially 16d
+ compound_name: 16d
+ ligand_id: ABC
+ molecule_smiles: CN1CCN(CC1)C1=C(C=C(C=C1)C1=CC(=CC=C1)CN1CCOCC1)NC(=O)C1=CNC(C=C1C(F)(F)F)=O
+- common_name: officially 14a
+ compound_name: 14a
+ is_macrocycle: false
+ molecule_iupac: N-(2-(4-Methylpiperazin-1-yl)-5-nitrophenyl)-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide
+- common_name: stuck
+ compound_name: lili
+ is_macrocycle: false
+ molecule_smiles: C1CCC1
+diseases: []
+family_name: WD40 (PF00400)
+id_source: '26958703'
+in_silico: true
+in_vitro: true
+pdb_id: 3emh
+source: PM
+xray: true
diff --git a/ippisite/ippidb/tests/test_simple_stabilized_heterodimer.yaml b/ippisite/ippidb/tests/test_simple_stabilized_heterodimer.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..1d79dd1e8f4868957a4919195a9feecb6eae92fd
--- /dev/null
+++ b/ippisite/ippidb/tests/test_simple_stabilized_heterodimer.yaml
@@ -0,0 +1,44 @@
+activity_tests:
+- cell_line_name: ''
+ compound_activity_results:
+ - activity_mol: 0.25
+ activity_type: pIC50
+ activity_unit: 1e-6
+ compound_name: FC
+ modulation_type: S
+ is_primary: true
+ nb_active_compounds: 2
+ protein_bound_construct: F
+ protein_complex: '1'
+ test_modulation_type: I
+ test_name: pull down
+ test_type: BIOCH
+complex:
+- cc_nb: 1
+ complex_type: Bound
+ domain_pfam_acc: PF00244
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: 1
+ uniprot_id: P31947
+- cc_nb: 1
+ complex_type: Bound
+ domain_pfam_acc: null
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: 1
+ uniprot_id: P03372
+complexChoice: stabilized
+complexType: Stab_Hetero2merAB
+compounds:
+- common_name: fusicoccin
+ compound_name: FC
+ ligand_id: FSC
+ molecule_smiles: COC[C@H]1CC[C@H]2[C@@H](C)[C@@H](O)[C@H](O[C@H]3O[C@H](COC(C)(C)C=C)[C@@H](O)[C@H](OC(C)=O)[C@H]3O)C3=C(C[C@H](O)[C@]3(C)\C=C1/2)[C@H](C)COC(C)=O
+diseases:
+- ;breast cancer;MONDO:0007254;
+family_name: 14-3-3 / ER
+id_source: '23676274'
+in_cellulo: true
+in_vitro: true
+pdb_id: 4jc3
+source: PM
+xray: true
diff --git a/ippisite/ippidb/tests/test_stabilizer_204.yaml b/ippisite/ippidb/tests/test_stabilizer_204.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..59cd362476b8f5d6fe7f041faa8fec36b90a23c2
--- /dev/null
+++ b/ippisite/ippidb/tests/test_stabilizer_204.yaml
@@ -0,0 +1,40 @@
+source: PM
+id_source: '23808890'
+in_vitro: true
+xray: true
+pdb_id: 4ihl
+complexChoice: stabilized
+complexType: Stab_Hetero2merAB
+complex:
+ - cc_nb: 1
+ complex_type: Bound
+ domain_pfam_acc: PF00244
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: 1
+ uniprot_id: P63104
+ - cc_nb: 1
+ complex_type: Bound
+ domain_pfam_acc: null
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: 1
+ uniprot_id: P04049
+family_name: 14-3-3 / C-RAF
+diseases:
+ - ;melanoma;(MONDO_0005105);
+compounds:
+ - common_name: Cotylenin A
+ compound_name: Cotylenin A
+ molecule_smiles: COC[C@H]1O[C@H](O[C@H]2[C@H](O)[C@H](C)[C@@H]3CC[C@](O)(COC)C3=C[C@@]3(C)CCC(C(C)C)=C23)[C@H](O)[C@H]2O[C@H]3O[C@@]12O[C@@]3(C)[C@@H]1CO1
+activity_tests:
+- test_type: BIOCH
+ test_name: Fluorescence Polarization
+ protein_bound_construct: F
+ test_modulation_type: B
+ nb_active_compounds: 1
+ protein_complex: '1'
+ compound_activity_results:
+ - activity_mol: 20
+ activity_type: pKd
+ activity_unit: 1e-10
+ compound_name: Cotylenin A
+ modulation_type: S
\ No newline at end of file
diff --git a/ippisite/ippidb/tests/test_with_all_tests.yaml b/ippisite/ippidb/tests/test_with_all_tests.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..3b8fefd311af4176a2e92deb7d9f5cef535b9cd5
--- /dev/null
+++ b/ippisite/ippidb/tests/test_with_all_tests.yaml
@@ -0,0 +1,72 @@
+activity_tests:
+- cell_line_name: ''
+ compound_activity_results:
+ - activity_mol: 6.85
+ activity_type: pIC50
+ activity_unit: 1e-3
+ compound_name: toto
+ modulation_type: I
+ is_primary: true
+ nb_active_compounds: 2
+ protein_bound_construct: F
+ protein_complex: '2'
+ test_modulation_type: I
+ test_name: test
+ test_type: BIOCH
+complex:
+- cc_nb: 1
+ complex_type: Partner
+ domain_pfam_acc: PF05053
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: ''
+ uniprot_id: O00255
+- cc_nb: 1
+ complex_type: Bound
+ domain_pfam_acc: PF05965
+ ppc_copy_nb: 1
+ ppp_copy_nb_per_p: 1
+ uniprot_id: Q03164
+complexChoice: inhibited
+complexType: Inhib_Hetero2merAB
+compounds:
+- common_name: super
+ compound_name: toto
+ molecule_smiles: CCC
+cytotox: true
+cytotox_tests:
+- cell_line_name: '1043SK '
+ compound_concentration: '2'
+ compound_cytotox_results:
+ - compound_name: toto
+ toxicity: 'True'
+ test_name: test
+diseases:
+- ''
+- ;titi;sfddf;
+- ;tutu;5456456;
+- ;tutu;5456456;
+- ''
+family_name: Menin (PF05053)
+id_source: '15072770'
+in_silico: true
+pdb_id: 3u85
+pharmacokinetic: true
+pharmacokinetic_tests:
+- administration_mode: IV
+ cell_line_name: '1043SK '
+ compound_pk_results:
+ - auc: '1'
+ c_max: '5.2'
+ clearance: '1.2'
+ compound_name: toto
+ oral_bioavailability: '22'
+ t_demi: '5'
+ t_max: '5'
+ tolerated: 'True'
+ voldistribution: '5.5'
+ concentration: '1.2'
+ dose: '3.5'
+ dose_interval: '2'
+ organism: 1
+ test_name: test
+source: PM
diff --git a/ippisite/ippidb/tests/tests_contribute.py b/ippisite/ippidb/tests/tests_contribute.py
index cd123dda54d8d512d8a3e4838a42199bdc60101d..5ecf48a3b84c3d319a703bbc6b52bce956c8bc9a 100644
--- a/ippisite/ippidb/tests/tests_contribute.py
+++ b/ippisite/ippidb/tests/tests_contribute.py
@@ -1,23 +1,15 @@
"""
iPPI-DB contribution module tests
"""
-import math
-from decimal import Decimal
-from tempfile import NamedTemporaryFile
-
from django.contrib.auth import get_user_model
from django.contrib.auth.models import Permission
from django.contrib.contenttypes.models import ContentType
-from django.db.models import Value
-from django.db.models.functions import Concat
from django.test import TestCase
from django.urls import reverse
from ippidb import models
-from ippidb.admin import grant_contribution_permission
from ippidb.forms import PDBForm
-from ippidb.ws import convert_iupac_to_smiles, get_uniprot_info
from live_settings import live_settings
import requests_cache
@@ -125,1046 +117,10 @@ class PDBFormTestCase(TestCase):
def test_invalid_nouniprot(self):
form = PDBForm({"pdb_id": "3wn8"})
self.assertFalse(
- form.is_valid(), "PDB code with no Uniprot mapping (3wn8) should be rejected"
+ form.is_valid(),
+ "PDB code with no Uniprot mapping (3wn8) should be rejected",
)
self.assertTrue(
form.has_error("pdb_id", code="no_mapping"),
"PDB code with no Uniprot mapping (3wn8) should be rejected with no_mappping error code",
)
-
-
-class ContributionViewsTestCase(TestCase):
- """
- This class tests the Contribution Wizard by interacting with it
- in the same way a user would do.
- """
-
- def setUp(self):
- login = "contributor"
- password = "12345"
- User = get_user_model()
- User.objects.create_user(username=login, password=password)
- self.client.login(username=login, password=password)
- grant_contribution_permission(None, None, User.objects.all())
- symmetry = models.Symmetry()
- symmetry.code = "AS"
- symmetry.description = "asymmetric"
- symmetry.save()
- models.Taxonomy.objects.create(taxonomy_id=9606, name="Homo sapiens")
-
- @staticmethod
- def get_step_url(step_id):
- step_url = reverse("admin-session-add")
- if step_id is not None:
- step_url += step_id + "/"
- return step_url
-
- def _process_contribution_wizard(self, entry_data):
- def compute_ppi_name(entry_data):
- bound_uniprots = [
- item["uniprot_id"]
- for item in entry_data["complex"]
- if item["complex_type"] == "Bound"
- ]
- partner_uniprots = [
- item["uniprot_id"]
- for item in entry_data["complex"]
- if item["complex_type"] == "Partner"
- ]
- bound_protein_names = [
- get_uniprot_info(uniprot_id)["short_name"]
- for uniprot_id in bound_uniprots
- ]
- partner_protein_names = [
- get_uniprot_info(uniprot_id)["short_name"]
- for uniprot_id in partner_uniprots
- ]
- bound_protein_names.sort()
- partner_protein_names.sort()
- bound_str = ",".join(bound_protein_names)
- partner_str = ",".join(partner_protein_names)
- name = bound_str
- if partner_str != "":
- name += " / " + partner_str
- return name
-
- future_expected_equals = [
- (
- models.Bibliography.objects.count,
- models.Bibliography.objects.count() + 1,
- "Bibliography count",
- ),
- (
- models.Contribution.objects.count,
- models.Contribution.objects.count() + 1,
- "Contribution count",
- ),
- (
- models.Compound.objects.count,
- models.Compound.objects.count() + len(entry_data["compounds"]),
- "Compounds count",
- ),
- (
- models.Compound.objects.validated().count,
- models.Compound.objects.validated().count(),
- "Validated Compounds count should remains the same",
- ),
- (
- models.CompoundAction.objects.count,
- models.CompoundAction.objects.count() + len(entry_data["compounds"]),
- "Compound Actions count",
- ),
- (
- models.TestActivityDescription.objects.count,
- models.TestActivityDescription.objects.count()
- + len(entry_data.get("activity_tests", [])),
- "Activity tests count",
- ),
- (
- models.TestCytotoxDescription.objects.count,
- models.TestCytotoxDescription.objects.count()
- + len(entry_data.get("cytotox_tests", [])),
- "Cytotox tests count",
- ),
- (
- models.TestPKDescription.objects.count,
- models.TestPKDescription.objects.count()
- + len(entry_data.get("pharmacokinetic_tests", [])),
- "Pharmacokinetic tests count",
- ),
- (
- lambda: models.PpiFamily.objects.get().name,
- entry_data.get("family_name"),
- "Ppi family name",
- ),
- (
- lambda: models.Ppi.objects.get().family.name,
- entry_data.get("family_name"),
- "Ppi family name from PPI",
- ),
- (
- lambda: models.Ppi.objects.get().name,
- compute_ppi_name(entry_data),
- "Ppi name",
- ),
- ]
- for activity_tests in entry_data["activity_tests"]:
- for compound_activity_results in activity_tests[
- "compound_activity_results"
- ]:
- if (
- "activity_mol" in compound_activity_results
- and compound_activity_results["activity_mol"] != ""
- ):
- compound_activity_results["activity"] = -math.log10(
- Decimal(str(compound_activity_results["activity_mol"]))
- * Decimal(str(compound_activity_results["activity_unit"]))
- )
-
- self._process_contribution_wizard_without_sanity_check(entry_data)
-
- for fcn, results, msg in future_expected_equals:
- self.assertEqual(fcn(), results, msg=msg)
- post_validation_expected_equals = [
- (
- models.Compound.objects.validated().count,
- models.Compound.objects.count(),
- "Validated Compounds count should have increased",
- )
- ]
- contribution_to_be_validated = models.Contribution.objects.get(validated=False)
- contribution_to_be_validated.validated = True
- contribution_to_be_validated.save()
- for fcn, results, msg in post_validation_expected_equals:
- self.assertEqual(fcn(), results, msg=msg)
-
- def _process_contribution_wizard_without_sanity_check(
- self, entry_data, error_expected_in_step=None
- ):
- """
- The contribution add "wizard"
- returns a 200
- """
- wizard_data = self._generate_wizard_data(entry_data)
- for step in wizard_data:
- # import json
- # print(json.dumps(step, indent=4))
- 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 "
- 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"]
- response = self.client.post(step_url, form_data)
- error_is_now = (
- error_expected_in_step == step.get("step-id")
- and response.status_code != 302
- )
- if (
- response.status_code != 302
- and step.get("step-id") != "done"
- or error_is_now
- ):
- 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}"
- )
- if error_is_now:
- self.assertEqual(response.status_code, 200, err_msg)
- return
- 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"))
- self.assertEqual(
- response.url,
- redirect_url,
- f"wrong redirection URL after step {step['step-id']}",
- )
- self.assertEqual(
- response.url,
- reverse("contribution-detail", kwargs={"contribution_pk": 1}),
- f"wrong final URL, should be the contribution permanent URL",
- )
-
- 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"],
- }
-
- def get_bibliography_form():
- ret = {
- "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",
- }
- for k in [
- "cytotox",
- "xray",
- "in_silico",
- "in_vitro",
- "in_cellulo",
- "in_vivo",
- "pharmacokinetic",
- ]:
- if entry_data.get(k, False):
- ret[k] = "on"
- return ret
-
- def get_pdb_form():
- return {"pdb_id": entry_data["pdb_id"]}
-
- def get_complex_type_form():
- return {
- "complexType": entry_data["complexType"],
- "complexChoice": entry_data["complexChoice"],
- }
-
- 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,
- }
- 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
- except models.Domain.DoesNotExist as dne:
- 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"
- ]
- 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
- "selected_diseases": "\n".join(entry_data["diseases"]),
- }
-
- def get_compound_form():
- data = {
- "TOTAL_FORMS": len(entry_data["compounds"]),
- # FIXME there should be a way to list more than one compound
- "INITIAL_FORMS": len(entry_data["compounds"]),
- "MIN_NUM_FORMS": 1,
- "MAX_NUM_FORMS": 1000,
- }
- for idx, compound_data_item in enumerate(entry_data["compounds"]):
- data[f"{idx}-common_name"] = (compound_data_item["common_name"],)
- data[f"{idx}-compound_name"] = (compound_data_item["compound_name"],)
- if "molecule_smiles" in compound_data_item:
- data[f"{idx}-molecule_smiles"] = (
- compound_data_item["molecule_smiles"],
- )
- elif "molecule_iupac" in compound_data_item:
- # if a IUPAC is provided for tests assume convert it to SMILES
- molecule_smiles = convert_iupac_to_smiles(
- compound_data_item["molecule_iupac"]
- )
- data[f"{idx}-molecule_smiles"] = molecule_smiles
- data[f"{idx}-is_macrocycle"] = compound_data_item.get(
- "is_macrocycle", False
- )
- return data
-
- def get_activity_description_form():
- data = {
- "TOTAL_FORMS": len(entry_data.get("activity_tests", [])),
- "INITIAL_FORMS": 0,
- "MIN_NUM_FORMS": 0,
- "MAX_NUM_FORMS": 1000,
- }
- for idx, activity_test in enumerate(entry_data.get("activity_tests", [])):
- data[f"{idx}-ppi"] = ""
- data[f"{idx}-test_name"] = activity_test["test_name"]
- data[f"{idx}-is_primary"] = activity_test["is_primary"]
- data[f"{idx}-protein_bound_construct"] = activity_test[
- "protein_bound_construct"
- ]
- data[f"{idx}-test_type"] = activity_test["test_type"]
- data[f"{idx}-test_modulation_type"] = activity_test[
- "test_modulation_type"
- ]
- data[f"{idx}-nb_active_compounds"] = activity_test[
- "nb_active_compounds"
- ]
- data[f"{idx}-cell_line_name"] = activity_test["cell_line_name"]
- data[f"{idx}-protein_complex"] = activity_test["protein_complex"]
- data[
- f"{idx}-compoundactivityresult_set-activity-results-TOTAL_FORMS"
- ] = 1 # len(activity_test.get("compound_activity_results",[]))
- data[
- f"{idx}-compoundactivityresult_set-activity-results-INITIAL_FORMS"
- ] = 0
- data[
- f"{idx}-compoundactivityresult_set-activity-results-MIN_NUM_FORMS"
- ] = 0
- data[
- f"{idx}-compoundactivityresult_set-activity-results-MAX_NUM_FORMS"
- ] = 1000
- for nidx, compound_activity_result in enumerate(
- activity_test["compound_activity_results"]
- ):
- data[
- f"{idx}-compoundactivityresult_set-activity-results-{nidx}-compound_name"
- ] = compound_activity_result["compound_name"]
- data[
- f"{idx}-compoundactivityresult_set-activity-results-{nidx}-activity_type"
- ] = compound_activity_result["activity_type"]
- try:
- data[
- f"{idx}-compoundactivityresult_set-activity-results-{nidx}-activity_mol"
- ] = compound_activity_result["activity_mol"]
- data[
- f"{idx}-compoundactivityresult_set-activity-results-{nidx}-activity_unit"
- ] = compound_activity_result["activity_unit"]
- except KeyError:
- pass
- data[
- f"{idx}-compoundactivityresult_set-activity-results-{nidx}-modulation_type"
- ] = compound_activity_result["modulation_type"]
- # "id": "",
- # "test_activity_description": "",
- return data
-
- def get_cytotox_description_form():
- data = {
- "TOTAL_FORMS": len(entry_data.get("cytotox_tests", [])),
- "INITIAL_FORMS": 0,
- "MIN_NUM_FORMS": 1,
- "MAX_NUM_FORMS": 1000,
- }
- for idx, cytotox_test in enumerate(entry_data.get("cytotox_tests", [])):
- data[f"{idx}-test_name"] = cytotox_test["test_name"]
- data[f"{idx}-compound_concentration"] = cytotox_test[
- "compound_concentration"
- ]
- data[f"{idx}-cell_line_name"] = cytotox_test["cell_line_name"]
-
- data[
- f"{idx}-compoundcytotoxicityresult_set-cytotox-results-TOTAL_FORMS"
- ] = len(cytotox_test.get("compound_cytotox_results", []))
- data[
- f"{idx}-compoundcytotoxicityresult_set-cytotox-results-INITIAL_FORMS"
- ] = 0
- data[
- f"{idx}-compoundcytotoxicityresult_set-cytotox-results-MIN_NUM_FORMS"
- ] = 0
- data[
- f"{idx}-compoundcytotoxicityresult_set-cytotox-results-MAX_NUM_FORMS"
- ] = 1000
- for nidx, result in enumerate(cytotox_test["compound_cytotox_results"]):
- data[
- f"{idx}-compoundcytotoxicityresult_set-cytotox-results-{nidx}-compound_name"
- ] = result["compound_name"]
- data[
- f"{idx}-compoundcytotoxicityresult_set-cytotox-results-{nidx}-toxicity"
- ] = result["toxicity"]
- return data
-
- def get_pk_description_form():
- data = {
- "TOTAL_FORMS": len(entry_data.get("pharmacokinetic_tests", [])),
- "INITIAL_FORMS": 0,
- "MIN_NUM_FORMS": 1,
- "MAX_NUM_FORMS": 1000,
- }
- for idx, pk_test in enumerate(entry_data.get("pharmacokinetic_tests", [])):
- data[f"{idx}-test_name"] = pk_test["test_name"]
- data[f"{idx}-organism"] = pk_test["organism"]
- data[f"{idx}-administration_mode"] = pk_test["administration_mode"]
- data[f"{idx}-concentration"] = pk_test["concentration"]
- data[f"{idx}-dose"] = pk_test["dose"]
- data[f"{idx}-dose_interval"] = pk_test["dose_interval"]
- data[f"{idx}-cell_line_name"] = pk_test["cell_line_name"]
-
- data[f"{idx}-compoundpkresult_set-pk-results-TOTAL_FORMS"] = len(
- pk_test.get("compound_pk_results", [])
- )
- data[f"{idx}-compoundpkresult_set-pk-results-INITIAL_FORMS"] = 0
- data[f"{idx}-compoundpkresult_set-pk-results-MIN_NUM_FORMS"] = 0
- data[f"{idx}-compoundpkresult_set-pk-results-MAX_NUM_FORMS"] = 1000
- for nidx, result in enumerate(pk_test["compound_pk_results"]):
- data[
- f"{idx}-compoundpkresult_set-pk-results-{nidx}-tolerated"
- ] = result["tolerated"]
- data[f"{idx}-compoundpkresult_set-pk-results-{nidx}-auc"] = result[
- "auc"
- ]
- data[
- f"{idx}-compoundpkresult_set-pk-results-{nidx}-clearance"
- ] = result["clearance"]
- data[
- f"{idx}-compoundpkresult_set-pk-results-{nidx}-c_max"
- ] = result["c_max"]
- data[
- f"{idx}-compoundpkresult_set-pk-results-{nidx}-oral_bioavailability"
- ] = result["oral_bioavailability"]
- data[
- f"{idx}-compoundpkresult_set-pk-results-{nidx}-t_demi"
- ] = result["t_demi"]
- data[
- f"{idx}-compoundpkresult_set-pk-results-{nidx}-t_max"
- ] = result["t_max"]
- data[
- f"{idx}-compoundpkresult_set-pk-results-{nidx}-voldistribution"
- ] = result["voldistribution"]
- data[
- f"{idx}-compoundpkresult_set-pk-results-{nidx}-compound_name"
- ] = result["compound_name"]
- return data
-
- form_callables = {
- 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,
- "ActivityDescriptionFormSet": get_activity_description_form,
- }
- if entry_data.get("cytotox", False):
- form_callables[
- "TestCytotoxDescriptionFormSet"
- ] = get_cytotox_description_form
- if entry_data.get("pharmacokinetic", False):
- form_callables["TestPKDescriptionFormSet"] = get_pk_description_form
-
- # Adding a step for "done" in order to also save the data in the db
- form_callables["done"] = lambda: None
-
- form_ids = iter(list(form_callables.keys())[1:])
- for step in form_callables.keys():
- item = {
- "step-id": step,
- "form-data": form_callables[step](),
- "next": next(form_ids, None),
- }
- yield item
-
- def get_basic_entry(self):
- """
- Basic entry test
- """
- return {
- "source": "PM",
- "id_source": "15072770",
- "in_silico": True,
- "pdb_id": "3u85",
- "diseases": [";toto;1;", ";titi;sfddf;", ";tata;3232;"],
- "complexChoice": "inhibited",
- "complexType": "Inhib_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": "Q03164",
- "complex_type": "Bound",
- "domain_pfam_acc": "PF05965",
- "ppc_copy_nb": 1,
- "cc_nb": 1,
- "ppp_copy_nb_per_p": 1,
- },
- ],
- "family_name": "Menin (PF05053)",
- "compounds": [
- {
- "molecule_smiles": "CCC",
- "compound_name": "toto",
- "common_name": "super",
- }
- ],
- "activity_tests": [
- {
- "test_name": "test",
- "is_primary": True,
- "protein_bound_construct": "F",
- "test_type": "BIOCH",
- "test_modulation_type": "I",
- "nb_active_compounds": 2,
- "cell_line_name": "",
- # means first in the list above
- "protein_complex": "2",
- "compound_activity_results": [
- {
- "compound_name": "toto",
- "activity_type": "pIC50",
- "activity_mol": 6.85,
- "activity_unit": "1e-6",
- "modulation_type": "I",
- }
- ],
- }
- ],
- }
-
- def test_basic_entry(self):
- self._process_contribution_wizard(self.get_basic_entry())
-
- def get_entry_28(self):
- """
- Test for the "contribution #28"
- """
- return {
- "source": "PM",
- "id_source": "24512214 ",
- "in_vitro": True,
- "pdb_id": "3wn7",
- "diseases": ["cancer (MONDO:0004992)"],
- # FIXME continue here
- "complexChoice": "inhibited",
- "complexType": "Inhib_Hetero2merAB",
- "complex": [
- {
- "uniprot_id": "Q60795",
- "complex_type": "Partner",
- "domain_pfam_acc": None,
- "ppc_copy_nb": 1,
- "cc_nb": 1,
- "ppp_copy_nb_per_p": 1,
- },
- {
- "uniprot_id": "Q9Z2X8",
- "complex_type": "Bound",
- "domain_pfam_acc": "PF01344",
- "ppc_copy_nb": 1,
- "cc_nb": 1,
- "ppp_copy_nb_per_p": 1,
- },
- ],
- "family_name": "KEAP1 / NRF2",
- "compounds": [
- {
- "molecule_smiles": "c1cc2c(cc1)c(ccc2N(S(=O)(=O)c1ccc(cc1)"
- "OC)CC(=O)O)N(S(=O)(=O)c1ccc(cc1)OC)CC(=O)O",
- "compound_name": "2",
- "common_name": "",
- }
- ],
- "activity_tests": [
- {
- "test_name": "biolayer interferometry assay",
- "is_primary": True,
- "protein_bound_construct": "F",
- "test_type": "BIOCH",
- "test_modulation_type": "B",
- "nb_active_compounds": 1,
- "cell_line_name": "",
- # means first in the list above
- "protein_complex": "1",
- "compound_activity_results": [
- {
- "compound_name": "2",
- "activity_type": "pKd",
- "activity_mol": 3.59,
- "activity_unit": "1e-9",
- "modulation_type": "I",
- }
- ],
- }
- ],
- }
-
- def test_entry_28(self):
- self._process_contribution_wizard(self.get_entry_28())
-
- def _test_activity_computation_and_storage(self, value, power):
- basic_entry = self.get_basic_entry()
- for activity_tests in basic_entry["activity_tests"]:
- for compound_activity_results in activity_tests[
- "compound_activity_results"
- ]:
- compound_activity_results["activity_unit"] = "1e-%i" % power
- try:
- del compound_activity_results["activity"]
- except KeyError:
- pass
- self._process_contribution_wizard(basic_entry)
- bibliography = models.Bibliography.objects.get(
- id_source=basic_entry["id_source"]
- )
- for activity_tests in basic_entry["activity_tests"]:
- for compound_activity_results in activity_tests[
- "compound_activity_results"
- ]:
- compound = models.RefCompoundBiblio.objects.get(
- bibliography=bibliography,
- compound_name=compound_activity_results["compound_name"],
- ).compound
- results = models.CompoundActivityResult.objects.get(
- activity_type=compound_activity_results["activity_type"],
- modulation_type=compound_activity_results["modulation_type"],
- compound=compound,
- )
- self.assertEqual(
- Decimal(compound_activity_results["activity"]).quantize(
- Decimal(10)
- ** -models.CompoundActivityResult._meta.get_field(
- "activity"
- ).decimal_places
- ),
- results.activity,
- )
-
- def test_activity_computation_and_storage(self):
- self._test_activity_computation_and_storage(0.685, 0)
-
- def test_activity_computation_and_storage_3(self):
- self._test_activity_computation_and_storage(639.39406, 3)
-
- def test_activity_computation_and_storage_6(self):
- self._test_activity_computation_and_storage(4.9846073, 6)
-
- def test_activity_computation_and_storage_9(self):
- self._test_activity_computation_and_storage(2380.002, 9)
-
- def test_activity_computation_and_storage_12(self):
- self._test_activity_computation_and_storage(1.018, 12)
-
- def test_no_activity_fails(self):
- basic_entry = self.get_basic_entry()
- for activity_tests in basic_entry["activity_tests"]:
- for compound_activity_results in activity_tests[
- "compound_activity_results"
- ]:
- compound_activity_results["activity_unit"] = ""
- compound_activity_results["activity_mol"] = ""
- try:
- del compound_activity_results["activity"]
- except KeyError:
- pass
- self._process_contribution_wizard_without_sanity_check(
- basic_entry, error_expected_in_step="ActivityDescriptionFormSet",
- )
-
- def test_with_all_tests(self):
- """
- Basic entry test
- """
- entry_data = {
- "source": "PM",
- "id_source": "15072770",
- "in_silico": True,
- "pharmacokinetic": True,
- "cytotox": True,
- "pdb_id": "3u85",
- "diseases": ["", ";titi;sfddf;", ";tutu;5456456;", ";tutu;5456456;", ""],
- "complexChoice": "inhibited",
- "complexType": "Inhib_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": "Q03164",
- "complex_type": "Bound",
- "domain_pfam_acc": "PF05965",
- "ppc_copy_nb": 1,
- "cc_nb": 1,
- "ppp_copy_nb_per_p": 1,
- },
- ],
- "family_name": "Menin (PF05053)",
- "compounds": [
- {
- "molecule_smiles": "CCC",
- "compound_name": "toto",
- "common_name": "super",
- }
- ],
- "activity_tests": [
- {
- "test_name": "test",
- "is_primary": True,
- "protein_bound_construct": "F",
- "test_type": "BIOCH",
- "test_modulation_type": "I",
- "nb_active_compounds": 2,
- "cell_line_name": "",
- # means first in the list above
- "protein_complex": "2",
- "compound_activity_results": [
- {
- "compound_name": "toto",
- "activity_type": "pIC50",
- "activity_mol": 6.85,
- "activity_unit": "1e-3",
- "modulation_type": "I",
- }
- ],
- }
- ],
- "pharmacokinetic_tests": [
- {
- "test_name": "test",
- "organism": 1,
- "administration_mode": "IV",
- "concentration": "1.2",
- "dose": "3.5",
- "dose_interval": "2",
- "cell_line_name": "1043SK ",
- # means position in the list above
- "compound_pk_results": [
- {
- "tolerated": "True",
- "auc": "1",
- "clearance": "1.2",
- "c_max": "5.2",
- "oral_bioavailability": "22",
- "t_demi": "5",
- "t_max": "5",
- "voldistribution": "5.5",
- "compound_name": "toto",
- }
- ],
- }
- ],
- "cytotox_tests": [
- {
- "test_name": "test",
- "compound_concentration": "2",
- "cell_line_name": "1043SK ",
- "compound_cytotox_results": [
- {"compound_name": "toto", "toxicity": "True"}
- ],
- }
- ],
- }
- self._process_contribution_wizard(entry_data)
- input_diseases = set(entry_data["diseases"])
- input_diseases.remove("")
- self.assertSetEqual(
- input_diseases,
- set(
- models.Ppi.objects.get(pdb_id=entry_data["pdb_id"])
- .diseases.annotate(
- raw=Concat(Value(";"), "name", Value(";"), "identifier", Value(";"))
- )
- .values_list("raw", flat=True)
- ),
- )
-
- def test_complex_no_pfam(self):
- """
- Test that it is possible to not select any domain
- for one of the partners in the complex
- (see #77)
- """
- entry_data = {
- "source": "PM",
- "id_source": "26958703",
- "in_silico": True,
- "pdb_id": "3emh",
- "diseases": [],
- "complexChoice": "inhibited",
- "complexType": "Inhib_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": "Q03164",
- "complex_type": "Partner",
- "domain_pfam_acc": None,
- "ppc_copy_nb": 1,
- "cc_nb": 1,
- "ppp_copy_nb_per_p": "",
- },
- ],
- "family_name": "WD40 (PF00400)",
- "compounds": [
- {
- "molecule_smiles": "C",
- "compound_name": "toto",
- "common_name": "super",
- }
- ],
- "activity_tests": [
- {
- "test_name": "test",
- "is_primary": True,
- "protein_bound_construct": "F",
- "test_type": "BIOCH",
- "test_modulation_type": "I",
- "nb_active_compounds": 2,
- "cell_line_name": "",
- # means position in the list above
- "protein_complex": "1",
- "compound_activity_results": [
- {
- "compound_name": "toto",
- "activity_type": "pIC50",
- "activity_mol": 6.85,
- "activity_unit": "1e-3",
- "modulation_type": "I",
- }
- ],
- }
- ],
- }
- self._process_contribution_wizard(entry_data)
-
- def test_simple_heterodimer(self):
- """
- Test provided for simple heterodimer
- """
- entry_data = {
- "source": "PM",
- "id_source": "26958703",
- "in_silico": True,
- "in_vitro": True,
- "xray": True,
- "pdb_id": "3emh",
- "diseases": [],
- "complexChoice": "inhibited",
- "complexType": "Inhib_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": "Q03164",
- "complex_type": "Partner",
- "domain_pfam_acc": None,
- "ppc_copy_nb": 1,
- "cc_nb": 1,
- "ppp_copy_nb_per_p": "",
- },
- ],
- "family_name": "WD40 (PF00400)",
- "compounds": [
- {
- "molecule_smiles": r"CN1CCN(CC1)C1=C(C=C(C=C1)C1=CC(=CC=C1)"
- r"CN1CCOCC1)NC(=O)C1=CNC(C=C1C(F)(F)F)=O",
- "compound_name": "16d",
- "common_name": "officially 16d",
- "ligand_id": "ABC",
- },
- {
- "molecule_iupac": "N-(2-(4-Methylpiperazin-1-yl)-5-nitrophenyl)"
- "-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide",
- "compound_name": "14a",
- "common_name": "officially 14a",
- "is_macrocycle": False,
- },
- {
- "molecule_smiles": "C1CCC1",
- "compound_name": "lili",
- "common_name": "stuck",
- "is_macrocycle": False,
- },
- ],
- "activity_tests": [
- {
- "test_name": "test",
- "is_primary": True,
- "protein_bound_construct": "F",
- "test_type": "BIOCH",
- "test_modulation_type": "I",
- "nb_active_compounds": 2,
- "cell_line_name": "",
- # means position in the list above
- "protein_complex": "1",
- "compound_activity_results": [
- {
- "compound_name": "16d",
- "activity_type": "pIC50",
- "activity_mol": 6.85,
- "activity_unit": "1e-3",
- "modulation_type": "I",
- }
- ],
- }
- ],
- }
-
- self._process_contribution_wizard(entry_data)
-
- def test_simple_stabilized_heterodimer(self):
- """
- Test provided for stabilized heterodimer
- """
- entry_data = {
- "source": "PM",
- "id_source": "23676274",
- "in_cellulo": True,
- "in_vitro": True,
- "xray": True,
- "pdb_id": "4jc3",
- "complexChoice": "stabilized",
- "complexType": "Stab_Hetero2merAB",
- "complex": [
- {
- "uniprot_id": "P31947",
- "complex_type": "Bound",
- "domain_pfam_acc": "PF00244",
- "ppc_copy_nb": 1,
- "cc_nb": 1,
- "ppp_copy_nb_per_p": 1,
- },
- {
- "uniprot_id": "P03372",
- "complex_type": "Bound",
- "domain_pfam_acc": None,
- "ppc_copy_nb": 1,
- "cc_nb": 1,
- "ppp_copy_nb_per_p": 1,
- },
- ],
- "family_name": "14-3-3 / ER",
- "diseases": ["breast cancer, MONDO:0007254"],
- "compounds": [
- {
- "molecule_smiles": r"COC[C@H]1CC[C@H]2[C@@H](C)[C@@H](O)"
- r"[C@H](O[C@H]3O[C@H](COC(C)(C)C=C)[C@@H](O)[C@H](OC(C)=O)"
- r"[C@H]3O)C3=C(C[C@H](O)[C@]3(C)\C=C1/2)[C@H](C)COC(C)=O",
- "compound_name": "FC",
- "common_name": "fusicoccin",
- "ligand_id": "FSC",
- }
- ],
- "activity_tests": [
- {
- "test_name": "pull down",
- "is_primary": True,
- "protein_bound_construct": "F",
- "test_type": "BIOCH",
- "test_modulation_type": "I",
- "nb_active_compounds": 2,
- "cell_line_name": "",
- # means position in the list above
- "protein_complex": "1",
- "compound_activity_results": [
- {
- "compound_name": "FC",
- "activity_type": "pIC50",
- "activity_mol": 0.25,
- "activity_unit": "1e-6",
- "modulation_type": "S",
- }
- ],
- }
- ],
- }
-
- self._process_contribution_wizard(entry_data)
-
- def write_in_tmp_file(self, response):
- """
- Write an HTTP response contents into a temporary file for debug
-
- :param response: response that will be saved
- :type respons: django.http.HttpResponse
- :return: path to the temporary file created
- :rtype: str
- """
- with NamedTemporaryFile(delete=False, suffix=".html") as f:
- f.write(response.content)
- return f.name
diff --git a/ippisite/ippidb/tests/tests_contribute_e2e.py b/ippisite/ippidb/tests/tests_contribute_e2e.py
new file mode 100644
index 0000000000000000000000000000000000000000..373fc4a9cf9f9f40efbbeba3335388fc58aa414e
--- /dev/null
+++ b/ippisite/ippidb/tests/tests_contribute_e2e.py
@@ -0,0 +1,600 @@
+"""
+iPPI-DB contribution module "end to end" tests
+"""
+import math
+import os
+from decimal import Decimal
+from tempfile import NamedTemporaryFile
+import yaml
+import glob
+
+from django.contrib.auth import get_user_model
+from django.db.models import Value
+from django.db.models.functions import Concat
+from django.test import TestCase
+from django.urls import reverse
+from parameterized import parameterized
+import requests_cache
+
+from ippidb import models
+from ippidb.admin import grant_contribution_permission
+from ippidb.ws import get_uniprot_info
+
+
+requests_cache.install_cache("tests_contribute_cache", backend="sqlite")
+
+
+def compute_ppi_name(entry_data):
+ """
+ return the expected PPI name from a given contribution entry_data
+ """
+ bound_uniprots = [
+ item["uniprot_id"]
+ for item in entry_data["complex"]
+ if item["complex_type"] == "Bound"
+ ]
+ partner_uniprots = [
+ item["uniprot_id"]
+ for item in entry_data["complex"]
+ if item["complex_type"] == "Partner"
+ ]
+ bound_protein_names = [
+ get_uniprot_info(uniprot_id)["short_name"]
+ for uniprot_id in bound_uniprots
+ ]
+ partner_protein_names = [
+ get_uniprot_info(uniprot_id)["short_name"]
+ for uniprot_id in partner_uniprots
+ ]
+ bound_protein_names.sort()
+ partner_protein_names.sort()
+ bound_str = ",".join(bound_protein_names)
+ partner_str = ",".join(partner_protein_names)
+ name = bound_str
+ if partner_str != "":
+ name += " / " + partner_str
+ return name
+
+
+class ContributionE2ETestCase(TestCase):
+ """
+ This class tests the Contribution Wizard by interacting with it
+ in the same way a user would do.
+ """
+
+ def setUp(self):
+ login = "contributor"
+ password = "12345"
+ User = get_user_model()
+ User.objects.create_user(username=login, password=password)
+ self.client.login(username=login, password=password)
+ grant_contribution_permission(None, None, User.objects.all())
+ symmetry = models.Symmetry()
+ symmetry.code = "AS"
+ symmetry.description = "asymmetric"
+ symmetry.save()
+ models.Taxonomy.objects.create(taxonomy_id=9606, name="Homo sapiens")
+
+ @staticmethod
+ def get_step_url(step_id):
+ step_url = reverse("admin-session-add")
+ if step_id is not None:
+ step_url += step_id + "/"
+ return step_url
+
+ def _process_contribution_wizard(self, entry_data):
+ future_expected_equals = [
+ (
+ models.Bibliography.objects.count,
+ models.Bibliography.objects.count() + 1,
+ "Bibliography count",
+ ),
+ (
+ models.Contribution.objects.count,
+ models.Contribution.objects.count() + 1,
+ "Contribution count",
+ ),
+ (
+ models.Compound.objects.count,
+ models.Compound.objects.count() + len(entry_data["compounds"]),
+ "Compounds count",
+ ),
+ (
+ models.Compound.objects.validated().count,
+ models.Compound.objects.validated().count(),
+ "Validated Compounds count should remains the same",
+ ),
+ (
+ models.CompoundAction.objects.count,
+ models.CompoundAction.objects.count() + len(entry_data["compounds"]),
+ "Compound Actions count",
+ ),
+ (
+ models.TestActivityDescription.objects.count,
+ models.TestActivityDescription.objects.count()
+ + len(entry_data.get("activity_tests", [])),
+ "Activity tests count",
+ ),
+ (
+ models.TestCytotoxDescription.objects.count,
+ models.TestCytotoxDescription.objects.count()
+ + len(entry_data.get("cytotox_tests", [])),
+ "Cytotox tests count",
+ ),
+ (
+ models.TestPKDescription.objects.count,
+ models.TestPKDescription.objects.count()
+ + len(entry_data.get("pharmacokinetic_tests", [])),
+ "Pharmacokinetic tests count",
+ ),
+ (
+ lambda: models.PpiFamily.objects.get().name,
+ entry_data.get("family_name"),
+ "Ppi family name",
+ ),
+ (
+ lambda: models.Ppi.objects.get().family.name,
+ entry_data.get("family_name"),
+ "Ppi family name from PPI",
+ ),
+ (
+ lambda: models.Ppi.objects.get().name,
+ compute_ppi_name(entry_data),
+ "Ppi name",
+ ),
+ ]
+ for activity_tests in entry_data["activity_tests"]:
+ for compound_activity_results in activity_tests[
+ "compound_activity_results"
+ ]:
+ if (
+ "activity_mol" in compound_activity_results
+ and compound_activity_results["activity_mol"] != ""
+ ):
+ compound_activity_results["activity"] = -math.log10(
+ Decimal(str(compound_activity_results["activity_mol"]))
+ * Decimal(str(compound_activity_results["activity_unit"]))
+ )
+
+ self._process_contribution_wizard_without_sanity_check(entry_data)
+
+ for fcn, results, msg in future_expected_equals:
+ self.assertEqual(fcn(), results, msg=msg)
+ post_validation_expected_equals = [
+ (
+ models.Compound.objects.validated().count,
+ models.Compound.objects.count(),
+ "Validated Compounds count should have increased",
+ )
+ ]
+ contribution_to_be_validated = models.Contribution.objects.get(validated=False)
+ contribution_to_be_validated.validated = True
+ contribution_to_be_validated.save()
+ for fcn, results, msg in post_validation_expected_equals:
+ self.assertEqual(fcn(), results, msg=msg)
+
+ def _process_contribution_wizard_without_sanity_check(
+ self, entry_data, error_expected_in_step=None
+ ):
+ """
+ The contribution add "wizard"
+ returns a 200
+ """
+ wizard_data = self._generate_wizard_data(entry_data)
+ for step in wizard_data:
+ 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 "
+ 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"]
+ response = self.client.post(step_url, form_data)
+ error_is_now = (
+ error_expected_in_step == step.get("step-id")
+ and response.status_code != 302
+ )
+ if (
+ response.status_code != 302
+ and step.get("step-id") != "done"
+ or error_is_now
+ ):
+ 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}"
+ )
+ if error_is_now:
+ self.assertEqual(response.status_code, 200, err_msg)
+ return
+ 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"))
+ self.assertEqual(
+ response.url,
+ redirect_url,
+ f"wrong redirection URL after step {step['step-id']}",
+ )
+ self.assertEqual(
+ response.url,
+ reverse("contribution-detail", kwargs={"contribution_pk": 1}),
+ f"wrong final URL, should be the contribution permanent URL",
+ )
+
+ 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"],
+ }
+
+ def get_bibliography_form():
+ ret = {
+ "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",
+ }
+ for k in [
+ "cytotox",
+ "xray",
+ "in_silico",
+ "in_vitro",
+ "in_cellulo",
+ "in_vivo",
+ "pharmacokinetic",
+ ]:
+ if entry_data.get(k, False):
+ ret[k] = "on"
+ return ret
+
+ def get_pdb_form():
+ return {"pdb_id": entry_data["pdb_id"]}
+
+ def get_complex_type_form():
+ return {
+ "complexType": entry_data["complexType"],
+ "complexChoice": entry_data["complexChoice"],
+ }
+
+ 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,
+ }
+ 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
+ except models.Domain.DoesNotExist as dne:
+ 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"
+ ]
+ 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
+ "selected_diseases": "\n".join(entry_data["diseases"]),
+ }
+
+ def get_compound_form():
+ data = {
+ "TOTAL_FORMS": len(entry_data["compounds"]),
+ # FIXME there should be a way to list more than one compound
+ "INITIAL_FORMS": len(entry_data["compounds"]),
+ "MIN_NUM_FORMS": 1,
+ "MAX_NUM_FORMS": 1000,
+ }
+ for idx, compound_data_item in enumerate(entry_data["compounds"]):
+ data[f"{idx}-common_name"] = (compound_data_item["common_name"],)
+ data[f"{idx}-compound_name"] = (compound_data_item["compound_name"],)
+ if "molecule_smiles" in compound_data_item:
+ data[f"{idx}-molecule_smiles"] = (
+ compound_data_item["molecule_smiles"],
+ )
+ elif "molecule_iupac" in compound_data_item:
+ # if a IUPAC is provided for tests assume convert it to SMILES
+ # molecule_smiles = convert_iupac_to_smiles(
+ # compound_data_item["molecule_iupac"]
+ # )
+ data[f"{idx}-molecule_iupac"] = compound_data_item["molecule_iupac"]
+ data[f"{idx}-is_macrocycle"] = compound_data_item.get(
+ "is_macrocycle", False
+ )
+ if "ligand_id" in compound_data_item:
+ data[f"{idx}-ligand_id"] = compound_data_item["ligand_id"]
+ return data
+
+ def get_activity_description_form():
+ data = {
+ "TOTAL_FORMS": len(entry_data.get("activity_tests", [])),
+ "INITIAL_FORMS": 0,
+ "MIN_NUM_FORMS": 0,
+ "MAX_NUM_FORMS": 1000,
+ }
+ for idx, activity_test in enumerate(entry_data.get("activity_tests", [])):
+ data[f"{idx}-ppi"] = ""
+ data[f"{idx}-test_name"] = activity_test["test_name"]
+ data[f"{idx}-is_primary"] = activity_test.get("is_primary", False)
+ data[f"{idx}-protein_bound_construct"] = activity_test[
+ "protein_bound_construct"
+ ]
+ data[f"{idx}-test_type"] = activity_test["test_type"]
+ data[f"{idx}-test_modulation_type"] = activity_test[
+ "test_modulation_type"
+ ]
+ data[f"{idx}-nb_active_compounds"] = activity_test[
+ "nb_active_compounds"
+ ]
+ if "cell_line_name" in activity_test:
+ data[f"{idx}-cell_line_name"] = activity_test["cell_line_name"]
+ data[f"{idx}-protein_complex"] = activity_test["protein_complex"]
+ data[
+ f"{idx}-compoundactivityresult_set-activity-results-TOTAL_FORMS"
+ ] = 1 # len(activity_test.get("compound_activity_results",[]))
+ data[
+ f"{idx}-compoundactivityresult_set-activity-results-INITIAL_FORMS"
+ ] = 0
+ data[
+ f"{idx}-compoundactivityresult_set-activity-results-MIN_NUM_FORMS"
+ ] = 0
+ data[
+ f"{idx}-compoundactivityresult_set-activity-results-MAX_NUM_FORMS"
+ ] = 1000
+ for nidx, compound_activity_result in enumerate(
+ activity_test["compound_activity_results"]
+ ):
+ data[
+ f"{idx}-compoundactivityresult_set-activity-results-{nidx}-compound_name"
+ ] = compound_activity_result["compound_name"]
+ data[
+ f"{idx}-compoundactivityresult_set-activity-results-{nidx}-activity_type"
+ ] = compound_activity_result["activity_type"]
+ try:
+ data[
+ f"{idx}-compoundactivityresult_set-activity-results-{nidx}-activity_mol"
+ ] = compound_activity_result["activity_mol"]
+ data[
+ f"{idx}-compoundactivityresult_set-activity-results-{nidx}-activity_unit"
+ ] = compound_activity_result["activity_unit"]
+ except KeyError:
+ pass
+ data[
+ f"{idx}-compoundactivityresult_set-activity-results-{nidx}-modulation_type"
+ ] = compound_activity_result["modulation_type"]
+ # "id": "",
+ # "test_activity_description": "",
+ return data
+
+ def get_cytotox_description_form():
+ data = {
+ "TOTAL_FORMS": len(entry_data.get("cytotox_tests", [])),
+ "INITIAL_FORMS": 0,
+ "MIN_NUM_FORMS": 1,
+ "MAX_NUM_FORMS": 1000,
+ }
+ for idx, cytotox_test in enumerate(entry_data.get("cytotox_tests", [])):
+ data[f"{idx}-test_name"] = cytotox_test["test_name"]
+ data[f"{idx}-compound_concentration"] = cytotox_test[
+ "compound_concentration"
+ ]
+ data[f"{idx}-cell_line_name"] = cytotox_test["cell_line_name"]
+
+ data[
+ f"{idx}-compoundcytotoxicityresult_set-cytotox-results-TOTAL_FORMS"
+ ] = len(cytotox_test.get("compound_cytotox_results", []))
+ data[
+ f"{idx}-compoundcytotoxicityresult_set-cytotox-results-INITIAL_FORMS"
+ ] = 0
+ data[
+ f"{idx}-compoundcytotoxicityresult_set-cytotox-results-MIN_NUM_FORMS"
+ ] = 0
+ data[
+ f"{idx}-compoundcytotoxicityresult_set-cytotox-results-MAX_NUM_FORMS"
+ ] = 1000
+ for nidx, result in enumerate(cytotox_test["compound_cytotox_results"]):
+ data[
+ f"{idx}-compoundcytotoxicityresult_set-cytotox-results-{nidx}-compound_name"
+ ] = result["compound_name"]
+ data[
+ f"{idx}-compoundcytotoxicityresult_set-cytotox-results-{nidx}-toxicity"
+ ] = result["toxicity"]
+ return data
+
+ def get_pk_description_form():
+ data = {
+ "TOTAL_FORMS": len(entry_data.get("pharmacokinetic_tests", [])),
+ "INITIAL_FORMS": 0,
+ "MIN_NUM_FORMS": 1,
+ "MAX_NUM_FORMS": 1000,
+ }
+ for idx, pk_test in enumerate(entry_data.get("pharmacokinetic_tests", [])):
+ data[f"{idx}-test_name"] = pk_test["test_name"]
+ data[f"{idx}-organism"] = pk_test["organism"]
+ data[f"{idx}-administration_mode"] = pk_test["administration_mode"]
+ data[f"{idx}-concentration"] = pk_test["concentration"]
+ data[f"{idx}-dose"] = pk_test["dose"]
+ data[f"{idx}-dose_interval"] = pk_test["dose_interval"]
+ data[f"{idx}-cell_line_name"] = pk_test["cell_line_name"]
+
+ data[f"{idx}-compoundpkresult_set-pk-results-TOTAL_FORMS"] = len(
+ pk_test.get("compound_pk_results", [])
+ )
+ data[f"{idx}-compoundpkresult_set-pk-results-INITIAL_FORMS"] = 0
+ data[f"{idx}-compoundpkresult_set-pk-results-MIN_NUM_FORMS"] = 0
+ data[f"{idx}-compoundpkresult_set-pk-results-MAX_NUM_FORMS"] = 1000
+ for nidx, result in enumerate(pk_test["compound_pk_results"]):
+ data[
+ f"{idx}-compoundpkresult_set-pk-results-{nidx}-tolerated"
+ ] = result["tolerated"]
+ data[f"{idx}-compoundpkresult_set-pk-results-{nidx}-auc"] = result[
+ "auc"
+ ]
+ data[
+ f"{idx}-compoundpkresult_set-pk-results-{nidx}-clearance"
+ ] = result["clearance"]
+ data[
+ f"{idx}-compoundpkresult_set-pk-results-{nidx}-c_max"
+ ] = result["c_max"]
+ data[
+ f"{idx}-compoundpkresult_set-pk-results-{nidx}-oral_bioavailability"
+ ] = result["oral_bioavailability"]
+ data[
+ f"{idx}-compoundpkresult_set-pk-results-{nidx}-t_demi"
+ ] = result["t_demi"]
+ data[
+ f"{idx}-compoundpkresult_set-pk-results-{nidx}-t_max"
+ ] = result["t_max"]
+ data[
+ f"{idx}-compoundpkresult_set-pk-results-{nidx}-voldistribution"
+ ] = result["voldistribution"]
+ data[
+ f"{idx}-compoundpkresult_set-pk-results-{nidx}-compound_name"
+ ] = result["compound_name"]
+ return data
+
+ form_callables = {
+ 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,
+ "ActivityDescriptionFormSet": get_activity_description_form,
+ }
+ if entry_data.get("cytotox", False):
+ form_callables[
+ "TestCytotoxDescriptionFormSet"
+ ] = get_cytotox_description_form
+ if entry_data.get("pharmacokinetic", False):
+ form_callables["TestPKDescriptionFormSet"] = get_pk_description_form
+
+ # Adding a step for "done" in order to also save the data in the db
+ form_callables["done"] = lambda: None
+
+ form_ids = iter(list(form_callables.keys())[1:])
+ for step in form_callables.keys():
+ item = {
+ "step-id": step,
+ "form-data": form_callables[step](),
+ "next": next(form_ids, None),
+ }
+ yield item
+
+ @parameterized.expand(
+ [
+ entry_path
+ for entry_path in glob.glob(
+ os.path.join(os.path.dirname(__file__), "*.yaml")
+ )
+ ]
+ )
+ def test_entry(self, entry_path):
+ # load the test data
+ entry_data = yaml.load(open(entry_path, "r"), Loader=yaml.FullLoader)
+ # process the wizard
+ self._process_contribution_wizard(entry_data)
+ # test diseases
+ input_diseases = set(entry_data["diseases"])
+ input_diseases.discard("")
+ self.assertSetEqual(
+ input_diseases,
+ set(
+ models.Ppi.objects.get(pdb_id=entry_data["pdb_id"])
+ .diseases.annotate(
+ raw=Concat(Value(";"), "name", Value(";"), "identifier", Value(";"))
+ )
+ .values_list("raw", flat=True)
+ ),
+ )
+ # test compounds
+ for c in entry_data["compounds"]:
+ if "molecule_smiles" in c:
+ comp = models.Compound.objects.get(canonical_smile=c["molecule_smiles"])
+ elif "molecule_iupac" in c:
+ comp = models.Compound.objects.get(iupac_name=c["molecule_iupac"])
+ # test ligand ID has been stored if the X ray data option is checked
+ if entry_data.get("xray", False) is True:
+ self.assertEqual(comp.ligand_id, c.get("ligand_id", None))
+ # test activity
+ bibliography = models.Bibliography.objects.get(
+ id_source=entry_data["id_source"].strip()
+ )
+ for activity_tests in entry_data["activity_tests"]:
+ for compound_activity_results in activity_tests[
+ "compound_activity_results"
+ ]:
+ compound = models.RefCompoundBiblio.objects.get(
+ bibliography=bibliography,
+ compound_name=compound_activity_results["compound_name"],
+ ).compound
+ results = models.CompoundActivityResult.objects.get(
+ activity_type=compound_activity_results["activity_type"],
+ modulation_type=compound_activity_results["modulation_type"],
+ compound=compound,
+ )
+ self.assertEqual(
+ Decimal(compound_activity_results["activity"]).quantize(
+ Decimal(10)
+ ** -models.CompoundActivityResult._meta.get_field(
+ "activity"
+ ).decimal_places
+ ),
+ results.activity,
+ )
+
+ def write_in_tmp_file(self, response):
+ """
+ Write an HTTP response contents into a temporary file for debug
+
+ :param response: response that will be saved
+ :type respons: django.http.HttpResponse
+ :return: path to the temporary file created
+ :rtype: str
+ """
+ with NamedTemporaryFile(delete=False, suffix=".html") as f:
+ f.write(response.content)
+ return f.name
diff --git a/ippisite/ippidb/tests/tests_utils.py b/ippisite/ippidb/tests/tests_utils.py
index bf59015d9be616de248045867607c9bda862589a..5c73f34e75dc2ebeb17c8b63d4eb9470b7da2a0b 100644
--- a/ippisite/ippidb/tests/tests_utils.py
+++ b/ippisite/ippidb/tests/tests_utils.py
@@ -6,7 +6,7 @@ import re
from django.test import TestCase
from openbabel import vectorUnsignedInt, OBFingerprint
-from .utils import FingerPrinter, mol2smi, smi2mol, smi2inchi, smi2inchikey, smi2sdf
+from ippidb.utils import FingerPrinter, mol2smi, smi2mol, smi2inchi, smi2inchikey, smi2sdf
class MolSmiTestCase(TestCase):