From 5b295e51fe8669822ead9de3e876c4dbc4eb6c47 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@pasteur.fr>
Date: Mon, 14 Sep 2020 17:24:58 +0200
Subject: [PATCH] fix compound card page if LE-LLE or PCA data not avail.
FIX #242
---
ippisite/ippidb/templates/compound_card.html | 5 ++
ippisite/ippidb/tests/tests.py | 61 +-------------------
ippisite/ippidb/tests/tests_views.py | 32 ++++++++++
ippisite/ippidb/tests/utils.py | 61 ++++++++++++++++++++
ippisite/ippidb/views/compound_query.py | 14 ++++-
5 files changed, 110 insertions(+), 63 deletions(-)
create mode 100644 ippisite/ippidb/tests/utils.py
diff --git a/ippisite/ippidb/templates/compound_card.html b/ippisite/ippidb/templates/compound_card.html
index a2a98987..eff17990 100644
--- a/ippisite/ippidb/templates/compound_card.html
+++ b/ippisite/ippidb/templates/compound_card.html
@@ -313,6 +313,7 @@
</div>
</div>
</div>
+ {% if pca_biplot_data %}
<div class="row d-flex justify-content-center">
<div class="col-sm-12 col-md-9">
<h5 class="card_title">PCA : iPPI-DB chemical space</h5>
@@ -331,8 +332,10 @@
</div>
</div>
</div>
+ {% endif %}
</div>
<div class="tab-pane fade" id="pharmacology" role="tabpanel" aria-labelledby="pharmacology-tab">
+ {% if le_lle_biplot_data %}
<div class="row d-flex justify-content-center">
<div class="col-sm-12 col-md-9" style="margin: 10px;">
<h5 class="card_title">Efficiencies: iPPI-DB biplot LE versus LLE <span class="info_point"
@@ -371,7 +374,9 @@
</script>
</div>
</div>
+
</div>
+ {% endif %}
<div class="row d-flex justify-content-center">
<div class="col-sm-12 col-md-9" style="margin: 10px;">
<h5 class="card_title">Summary</h5>
diff --git a/ippisite/ippidb/tests/tests.py b/ippisite/ippidb/tests/tests.py
index f52e623c..77580144 100644
--- a/ippisite/ippidb/tests/tests.py
+++ b/ippisite/ippidb/tests/tests.py
@@ -10,7 +10,6 @@ from django.test import TestCase
from django.urls import reverse
import requests
-
from ippidb import models
from ippidb.ws import (
get_uniprot_info,
@@ -38,6 +37,7 @@ from ippidb.models import (
DrugBankCompound,
Protein,
)
+from .utils import create_dummy_compound, create_dummy_drugbank_compound
class MolSmiTestCase(TestCase):
@@ -94,65 +94,6 @@ class MolSmiTestCase(TestCase):
self.assertEqual(response.status_code, 400)
-def create_dummy_compound(id_, smiles):
- c = Compound()
- c.id = id_
- c.canonical_smile = smiles
- c.is_macrocycle = True
- c.aromatic_ratio = 0.0
- c.balaban_index = 0.0
- c.fsp3 = 0.0
- c.gc_molar_refractivity = 0.0
- c.log_d = 0.0
- c.a_log_p = 0.0
- c.gc_molar_refractivity = 0.0
- c.mean_atom_vol_vdw = 0.0
- c.molecular_weight = 0.0
- c.nb_acceptor_h = 0
- c.nb_aliphatic_amines = 0
- c.nb_aromatic_bonds = 0
- c.nb_aromatic_ether = 0
- c.nb_aromatic_sssr = 0
- c.nb_atom = 0
- c.nb_atom_non_h = 0
- c.nb_benzene_like_rings = 0
- c.nb_bonds = 0
- c.nb_bonds_non_h = 0
- c.nb_br = 0
- c.nb_c = 0
- c.nb_chiral_centers = 0
- c.nb_circuits = 0
- c.nb_cl = 0
- c.nb_csp2 = 0
- c.nb_csp3 = 0
- c.nb_donor_h = 0
- c.nb_double_bonds = 0
- c.nb_f = 0
- c.nb_i = 0
- c.nb_multiple_bonds = 0
- c.nb_n = 0
- c.nb_o = 0
- c.nb_rings = 0
- c.nb_rotatable_bonds = 0
- c.randic_index = 0
- c.rdf070m = 0
- c.rotatable_bond_fraction = 0
- c.sum_atom_polar = 0
- c.sum_atom_vol_vdw = 0
- c.tpsa = 0
- c.ui = 0
- c.wiener_index = 0
- c.save(autofill=True)
- return c
-
-
-def create_dummy_drugbank_compound(id_, smiles):
- dbc = DrugBankCompound()
- dbc.id = id_
- dbc.common_name = "DrugBankCompound" + str(id_)
- dbc.canonical_smiles = smiles
- dbc.save()
-
class CompoundTanimotoTestCase(TestCase):
def setUp(self):
diff --git a/ippisite/ippidb/tests/tests_views.py b/ippisite/ippidb/tests/tests_views.py
index 36099df6..81a4412d 100644
--- a/ippisite/ippidb/tests/tests_views.py
+++ b/ippisite/ippidb/tests/tests_views.py
@@ -3,8 +3,11 @@ iPPI-DB views tests
"""
from django.test import TestCase
from django.urls import reverse
+from django.core.management import call_command
from parameterized import parameterized
+from .utils import create_dummy_compound
+
tested_urlpatterns = [
"index",
"general",
@@ -37,3 +40,32 @@ class ViewTest(TestCase):
def test_url(self, url_name):
response = self.client.get(reverse(url_name))
self.assertEqual(response.status_code, 200)
+
+
+class CompoundCardViewTest(TestCase):
+ """
+ Tests for compound card
+ """
+
+ def setUp(self):
+ create_dummy_compound(1, "CC")
+
+ def test_compound_card(self):
+ """
+ basic test for compound card
+ """
+
+ call_command("lle_le")
+ call_command("pca")
+ response = self.client.get(reverse("compound_card", kwargs={"pk": 1}))
+ self.assertEqual(response.status_code, 200)
+
+
+ def test_compound_card_no_lelleplot_data(self):
+ """
+ test that compound card is ok even if LE-LLE plot
+ data are missing (which can happen during LE-LLE recomputing)
+ """
+
+ response = self.client.get(reverse("compound_card", kwargs={"pk": 1}))
+ self.assertEqual(response.status_code, 200)
diff --git a/ippisite/ippidb/tests/utils.py b/ippisite/ippidb/tests/utils.py
new file mode 100644
index 00000000..3bee4a1e
--- /dev/null
+++ b/ippisite/ippidb/tests/utils.py
@@ -0,0 +1,61 @@
+from ippidb.models import Compound, DrugBankCompound
+
+
+def create_dummy_compound(id_, smiles):
+ c = Compound()
+ c.id = id_
+ c.canonical_smile = smiles
+ c.is_macrocycle = True
+ c.aromatic_ratio = 0.0
+ c.balaban_index = 0.0
+ c.fsp3 = 0.0
+ c.gc_molar_refractivity = 0.0
+ c.log_d = 0.0
+ c.a_log_p = 0.0
+ c.gc_molar_refractivity = 0.0
+ c.mean_atom_vol_vdw = 0.0
+ c.molecular_weight = 0.0
+ c.nb_acceptor_h = 0
+ c.nb_aliphatic_amines = 0
+ c.nb_aromatic_bonds = 0
+ c.nb_aromatic_ether = 0
+ c.nb_aromatic_sssr = 0
+ c.nb_atom = 0
+ c.nb_atom_non_h = 0
+ c.nb_benzene_like_rings = 0
+ c.nb_bonds = 0
+ c.nb_bonds_non_h = 0
+ c.nb_br = 0
+ c.nb_c = 0
+ c.nb_chiral_centers = 0
+ c.nb_circuits = 0
+ c.nb_cl = 0
+ c.nb_csp2 = 0
+ c.nb_csp3 = 0
+ c.nb_donor_h = 0
+ c.nb_double_bonds = 0
+ c.nb_f = 0
+ c.nb_i = 0
+ c.nb_multiple_bonds = 0
+ c.nb_n = 0
+ c.nb_o = 0
+ c.nb_rings = 0
+ c.nb_rotatable_bonds = 0
+ c.randic_index = 0
+ c.rdf070m = 0
+ c.rotatable_bond_fraction = 0
+ c.sum_atom_polar = 0
+ c.sum_atom_vol_vdw = 0
+ c.tpsa = 0
+ c.ui = 0
+ c.wiener_index = 0
+ c.save(autofill=True)
+ return c
+
+
+def create_dummy_drugbank_compound(id_, smiles):
+ dbc = DrugBankCompound()
+ dbc.id = id_
+ dbc.common_name = "DrugBankCompound" + str(id_)
+ dbc.canonical_smiles = smiles
+ dbc.save()
diff --git a/ippisite/ippidb/views/compound_query.py b/ippisite/ippidb/views/compound_query.py
index 94ac8fe4..9d78f487 100644
--- a/ippisite/ippidb/views/compound_query.py
+++ b/ippisite/ippidb/views/compound_query.py
@@ -759,9 +759,17 @@ class CompoundDetailView(DetailView):
def get_context_data(self, **kwargs):
context = super().get_context_data(**kwargs)
- context["le_lle_biplot_data"] = LeLleBiplotData.objects.get().le_lle_biplot_data
- pca_biplot = json.loads(PcaBiplotData.objects.get().pca_biplot_data)
- context["pca_biplot_data"] = json.dumps(pca_biplot["data"])
+ try:
+ context[
+ "le_lle_biplot_data"
+ ] = LeLleBiplotData.objects.get().le_lle_biplot_data
+ except LeLleBiplotData.DoesNotExist:
+ context["le_lle_biplot_data"] = []
+ try:
+ pca_biplot = json.loads(PcaBiplotData.objects.get().pca_biplot_data)
+ except PcaBiplotData.DoesNotExist:
+ pca_biplot = {"data": [], "correlation_circle": ""}
+ context["pca_biplot_data"] = pca_biplot["data"]
context["pca_biplot_cc"] = pca_biplot["correlation_circle"]
return context
--
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