From 88ce1e7de4c91cea9e04f79ba917c8c99737a4fc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Fri, 13 Oct 2017 17:04:28 +0200
Subject: [PATCH] create first "bibliography access" to the DB
Former-commit-id: 4fe2403ad50929281eddcd6202b7c96cb72a3a5e
---
ippisite/ippidb/templates/ppi_card.html | 80 +++++++++++++++++++++++++
ippisite/ippidb/urls.py | 1 +
ippisite/ippidb/views.py | 14 ++++-
3 files changed, 92 insertions(+), 3 deletions(-)
create mode 100644 ippisite/ippidb/templates/ppi_card.html
diff --git a/ippisite/ippidb/templates/ppi_card.html b/ippisite/ippidb/templates/ppi_card.html
new file mode 100644
index 00000000..64fb070d
--- /dev/null
+++ b/ippisite/ippidb/templates/ppi_card.html
@@ -0,0 +1,80 @@
+{% extends "base.html" %}
+
+
+{% block title %}inhibitors of Protein-Protein Interaction Database{% endblock %}
+
+{% block content %}
+<div id="mainnav">
+</div>
+<div class="inner-wrap">
+ <nav class="breadcrumb" role="navigation">
+ <div id="breadcrumb-label" class="breadcrumb-label">You are here</div>
+ <div aria-labelledby="breadcrumb-label">
+ Fonction Fil d'Arianne
+ </div>
+ </nav>
+ <div id="main-wrapper" class="page">
+ <div id="main">
+ <div id="content" class="main-content">
+ <main role="main">
+ <div class="row">
+ <div class="col-3">
+ <div class="nav flex-column nav-pills" id="v-pills-tab" role="tablist">
+ <a class="nav-link active" id="v-pills-bib-tab" data-toggle="pill" href="#v-pills-bib" role="tab" aria-controls="v-pills-bib" aria-expanded="true">Bibliography</a>
+ <a class="nav-link" id="v-pills-comp-tab" data-toggle="pill" href="#v-pills-comp" role="tab" aria-controls="v-pills-comp" aria-expanded="true">Compounds</a>
+ <a class="nav-link" id="v-pills-target-tab" data-toggle="pill" href="#v-pills-target" role="tab" aria-controls="v-pills-target" aria-expanded="true">Targets</a>
+ <a class="nav-link" id="v-pills-test-tab" data-toggle="pill" href="#v-pills-test" role="tab" aria-controls="v-pills-test" aria-expanded="true">Tests</a>
+ </div>
+ </div>
+ <div class="col-9">
+ <div class="tab-content" id="v-pills-tabContent">
+ <div class="tab-pane fade show active" id="v-pills-bib" role="tabpanel" aria-labelledby="v-pills-bib-tab">
+ <div class="card">
+ <div class="card-body">
+ <p><a target="_blank" class="card-link" href="https://www.ncbi.nlm.nih.gov/pubmed/{{ bibliography.id_source }}">{{ bibliography.authors_list }}. {{ authors.biblio_year }}. {{ bibliography.title }} {{ bibliography.journal_name }}. </a></p>
+ </div>
+ </div>
+ <div class="card">
+ <div class="card-body">
+ <ul class="list-group">
+ <li class="list-group-item">Cytotoxicity data: {% if bibliography.cytotox %}✓{% else %}✗{% endif %}</li>
+ <li class="list-group-item"><i>in silico</i> study: {% if bibliography.in_silico %}✓{% else %}✗{% endif %}</li>
+ <li class="list-group-item"><i>in vitro</i> study: {% if bibliography.in_vitro %}✓{% else %}✗{% endif %}</li>
+ <li class="list-group-item"><i>in vivo</i> study: {% if bibliography.in_vivo %}✓{% else %}✗{% endif %}</li>
+ <li class="list-group-item"><i>in cellulo</i> study: {% if bibliography.in_cellulo %}✓{% else %}✗{% endif %}</li>
+ <li class="list-group-item">pharmacokinetic study: {% if bibliography.pharmacokinetic %}✓{% else %}✗{% endif %}</li>
+ <li class="list-group-item">X-ray study: {% if bibliography.x_ray %}✓{% else %}✗{% endif %}</li>
+ </ul>
+ </div>
+ </div>
+ </div>
+ <div class="tab-pane fade" id="v-pills-comp" role="tabpanel" aria-labelledby="v-pills-comp-tab">
+ {% for compound_biblio in compound_biblios %}
+ <div class="card">
+ <div class="card-body">
+ <ul class="list-group">
+ <li class="list-group-item">Common name: {{ compound_biblio.compound.common_name }}</li>
+ <li class="list-group-item">MDDR: <i>TODO</i></li>
+ <li class="list-group-item">Canonical SMILES: {{ compound_biblio.compound.canonical_smile }}</li>
+ <li class="list-group-item">IUPAC name: {{ compound_biblio.compound.iupac_name }}</li>
+ <li class="list-group-item">mentionned as {{ compound_biblio.compound_name }}</li>
+ </ul>
+ </div>
+ </div>
+ {% endfor %}
+ </div>
+ <div class="tab-pane fade" id="v-pills-target" role="tabpanel" aria-labelledby="v-pills-target-tab">
+ Target info
+ </div>
+ <div class="tab-pane fade" id="v-pills-test" role="tabpanel" aria-labelledby="v-pills-test-tab">
+ Tests info
+ </div>
+ </div>
+ </div>
+ </div>
+ </main><!-- .site-main -->
+ </div>
+ </div><!-- div main -->
+ </div>
+</div>
+{% endblock %}
diff --git a/ippisite/ippidb/urls.py b/ippisite/ippidb/urls.py
index 3cfaacf9..dd5ce175 100644
--- a/ippisite/ippidb/urls.py
+++ b/ippisite/ippidb/urls.py
@@ -19,6 +19,7 @@ urlpatterns = [
url(r'^query$', views.query, name='query'),
url(r'^query/pharma/$', views.pharma, name='pharma'),
url(r'^query/chemical/$', views.chemical, name='chemical'),
+ url(r'^biblio_ppi/(?P<biblio_id>\d+)$', views.ppi_card, name='biblio_ppi_card'),
url(r'^tutorials$', views.tutorials, name='tutorials'),
url(r'^admin-session$', views.adminSession, name='admin-session'),
url(r'^admin-session/add/(?P<step>.+)/$',
diff --git a/ippisite/ippidb/views.py b/ippisite/ippidb/views.py
index ec5c4ac8..de3a327a 100644
--- a/ippisite/ippidb/views.py
+++ b/ippisite/ippidb/views.py
@@ -1,11 +1,11 @@
import ippidb
from django.shortcuts import render
-from django.http import HttpResponseRedirect
+from django.http import HttpResponseRedirect, Http404
from formtools.wizard.views import SessionWizardView, NamedUrlSessionWizardView
from .forms import IdForm, BibliographyForm, PDBForm, ProteinForm, ProteinDomainComplexTypeForm, ProteinDomainComplexForm, PpiForm, ProteinFormSet, PDBFormSet
-from .models import Protein, Bibliography, ProteinDomainComplex
+from .models import Protein, Bibliography, ProteinDomainComplex, RefCompoundBiblio
from .ws import get_pdb_uniprot_mapping
@@ -20,7 +20,6 @@ def about(request):
def general(request):
return render(request, 'general.html')
-
def pharmacology(request):
return render(request, 'pharmacology.html')
@@ -130,3 +129,12 @@ class IppiWizard(NamedUrlSessionWizardView):
return render(self.request, '/admin-session/add.html', {
'form_data': [form.cleaned_data for form in form_list],
})
+
+def ppi_card(request, biblio_id):
+ try:
+ bibliography = Bibliography.objects.get(pk=biblio_id)
+ except Bibliography.DoesNotExist:
+ raise Http404("No bibliography data for %s" % biblio_id)
+ refs = RefCompoundBiblio.objects.filter(bibliography_id = bibliography.id)
+ return render(request, 'ppi_card.html', {'bibliography': bibliography,
+ 'compound_biblios': refs})
--
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