From 0f39aeceff2a3c500b5a6ffd54c35f63415d742c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Wed, 8 Nov 2017 16:48:24 +0100
Subject: [PATCH] compounds list, WIP
Former-commit-id: adeba92bffdb7d35210e3ac43a7247352d04dd47
---
ippisite/ippidb/models.py | 6 ++
.../ippidb/templates/biblio_citation.html | 1 +
.../ippidb/templates/compound_abstract.html | 47 ++++++++++++++++
ippisite/ippidb/templates/compound_list.html | 56 +++++++++++++++++++
ippisite/ippidb/templates/kekule_display.html | 13 +++++
ippisite/ippidb/urls.py | 1 +
ippisite/ippidb/views.py | 19 ++++++-
7 files changed, 142 insertions(+), 1 deletion(-)
create mode 100644 ippisite/ippidb/templates/biblio_citation.html
create mode 100644 ippisite/ippidb/templates/compound_abstract.html
create mode 100644 ippisite/ippidb/templates/compound_list.html
create mode 100644 ippisite/ippidb/templates/kekule_display.html
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index ad07f70a..232e595e 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -320,6 +320,12 @@ class Compound(models.Model):
mddr_compound = models.ForeignKey(
'MDDRCompoundImport', blank=True, null=True)
+ @property
+ def biblio_refs(self):
+ """
+ return all RefCompoundBiblio related to this complex
+ """
+ return RefCompoundBiblio.objects.filter(compound=self)
class MDDRActivityClass(models.Model):
name = models.CharField('Activity Class', max_length=100, unique=True)
diff --git a/ippisite/ippidb/templates/biblio_citation.html b/ippisite/ippidb/templates/biblio_citation.html
new file mode 100644
index 00000000..a7cc6b8f
--- /dev/null
+++ b/ippisite/ippidb/templates/biblio_citation.html
@@ -0,0 +1 @@
+<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>
diff --git a/ippisite/ippidb/templates/compound_abstract.html b/ippisite/ippidb/templates/compound_abstract.html
new file mode 100644
index 00000000..99b7e740
--- /dev/null
+++ b/ippisite/ippidb/templates/compound_abstract.html
@@ -0,0 +1,47 @@
+<div class="row m-2 border border-info bg-light">
+ <div class="col-5 bg-info">
+ <div id="{{ compound.id }}_smilesdisplay"
+ data-widget="Kekule.ChemWidget.Viewer2D" data-auto-fit="true"
+ data-toolbar-evoke-modes="[0]" style="width: 200px; height: 200px;">
+ </div>
+ <textarea rows="10" cols="50" id="{{ compound.id }}_smilesvalue" style="display:none;">{{ compound.canonical_smile }}</textarea>
+ <script>
+ $(window).on('load', function(){
+ kekule_display('{{ compound.id }}_smilesvalue','{{ compound.id }}_smilesdisplay')
+ });
+ </script>
+ </div>
+ <div class="col-7">
+ <ul class="list-group">
+ {% if compound.common_name %}
+ <li class="list-group-item">Common name: {{ compound.common_name }}</li>
+ {% endif %}
+ {% if compound.canonical_smile %}
+ <li class="list-group-item">Canonical SMILES: {{ compound.canonical_smile }}</li>
+ {% endif %}
+ {% if compound.iupac_name %}
+ <li class="list-group-item">IUPAC name: {{ compound.iupac_name }}</li>
+ {% endif %}
+ </ul>
+ <p>in bibliography</p>
+ <ul class="list-group">
+ {% for biblio_ref in compound.biblio_refs %}
+ <li class="list-group-item">Mentionned in {% include "biblio_citation.html" with bibliography=biblio_ref.bibliography%} as <i>{{ biblio_ref.compound_name }}</i></li>
+ {% endfor %}
+ </ul>
+ {%if compound.pubchem_id or compound.chembl_id or compound.chemspider_id %}
+ <p>in other databases</p>
+ <ul class="list-group">
+ {% if compound.pubchem_id %}
+ <li class="list-group-item">PubChem: <a href="https://pubchem.ncbi.nlm.nih.gov/compound/{{ compound.pubchem_id }}" target="_blank">{{ compound.pubchem_id }}</a></li>
+ {% endif %}
+ {% if compound.chembl_id %}
+ <li class="list-group-item">ChEMBL: <a href="https://www.ebi.ac.uk/chembldb/compound/inspect/{{ compound.chembl_id}}" target="_blank">{{ compound.chembl_id}}</a></li>
+ {% endif %}
+ {% if compound.chemspider_id %}
+ <li class="list-group-item">ChemSpider: <a href="http://www.chemspider.com/Chemical-Structure.{{ compound.chemspider_id}}.html" target="_blank">{{ compound.chemspider_id}}</a></li>
+ {% endif %}
+ </ul>
+ {% endif %}
+ </div>
+</div>
diff --git a/ippisite/ippidb/templates/compound_list.html b/ippisite/ippidb/templates/compound_list.html
new file mode 100644
index 00000000..f0286625
--- /dev/null
+++ b/ippisite/ippidb/templates/compound_list.html
@@ -0,0 +1,56 @@
+{% extends "base.html" %}
+
+
+{% block title %}compound{% endblock %}
+
+{% block content %}
+
+{% include "kekule_display.html" %}
+<div class="container-fluid">
+<div class="row flex-xl-nowrap">
+ <div class="col-12 col-md-3 col-xl-2 bd-sidebar">
+<form>
+ <div class="form-group row">
+ <div class="form-check">
+ {% for ppi in ppis|slice:":5" %}
+ <label class="form-check-label">
+ {{ ppi.name }}
+ <input class="form-check-input" type="checkbox" value="{{ ppi.id }}" onchange="this.form.submit()" name="ppi">
+ </label>
+ {% endfor %}
+ </div>
+ </div>
+</form>
+</div>
+<main class="col-12 col-md-9 col-xl-10 py-md-3 pl-md-5 bd-content" role="main">
+{% if compounds %}
+ {% for compound in compounds %}
+ {% include "compound_abstract.html" with compound=compound %}
+ {% endfor %}
+{% else %}
+ <p>No bibliographies available.</p>
+{% endif %}
+ </main>
+</div>
+</div>
+
+<nav>
+ <ul class="pagination justify-content-end">
+ {% if compounds.has_previous %}
+ <li class="page-item">
+ <a class="page-link" href="?page={{ compounds.previous_page_number }}" tabindex="-1">Previous</a>
+ </li>
+ {% endif %}
+
+ <li class="page-item disabled">
+ <span class="page-link">Page {{ compounds.number }} of {{ compounds.paginator.num_pages }}.</span>
+ </li>
+
+ {% if compounds.has_next %}
+ <li class="page-item">
+ <a class="page-link" href="?page={{ compounds.next_page_number }}" tabindex="-1">Next</a>
+ </li>
+ {% endif %}
+ </ul>
+</nav>
+{% endblock %}
diff --git a/ippisite/ippidb/templates/kekule_display.html b/ippisite/ippidb/templates/kekule_display.html
new file mode 100644
index 00000000..c6184e1e
--- /dev/null
+++ b/ippisite/ippidb/templates/kekule_display.html
@@ -0,0 +1,13 @@
+<script>
+ Kekule.Indigo.enable();
+ function kekule_display(smiles_id, viewer_id) {
+ var smi = document.getElementById(smiles_id).value;
+ var chemViewer = new Kekule.ChemWidget.Viewer(document.getElementById(viewer_id));
+ chemViewer.setEnableToolbar(false)
+ .setEnableDirectInteraction(false)
+ .setEnableEdit(false)
+ .setToolButtons([]);
+ var mol = Kekule.IO.loadFormatData(smi, "smi");
+ chemViewer.setChemObj(mol);
+ }
+</script>
diff --git a/ippisite/ippidb/urls.py b/ippisite/ippidb/urls.py
index 45047aee..0a738f11 100644
--- a/ippisite/ippidb/urls.py
+++ b/ippisite/ippidb/urls.py
@@ -21,6 +21,7 @@ urlpatterns = [
url(r'^query/chemical/$', views.chemical, name='chemical'),
url(r'^biblio/(?P<source>\w{2})(?P<id_source>\w+)$', views.biblio_card, name='biblio_card'),
url(r'^biblio/$', views.biblio_list, name='biblio_list'),
+ url(r'^compound/$', views.compound_list, name='compound_list'),
url(r'^tutorials$', 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 b8243ab0..a9c644b4 100644
--- a/ippisite/ippidb/views.py
+++ b/ippisite/ippidb/views.py
@@ -2,9 +2,11 @@ import ippidb
from django.shortcuts import render
from django.http import HttpResponseRedirect, Http404
+from django.core.paginator import Paginator, EmptyPage, PageNotAnInteger
from formtools.wizard.views import SessionWizardView, NamedUrlSessionWizardView
+
from .forms import BibliographyForm, PDBForm, ProteinForm, ProteinDomainComplexTypeForm, ProteinDomainComplexForm, PpiForm, ProteinFormSet
-from .models import Protein, Bibliography, ProteinDomainComplex, RefCompoundBiblio, TestActivityDescription
+from .models import Protein, Bibliography, ProteinDomainComplex, RefCompoundBiblio, TestActivityDescription, Compound, Ppi
from .ws import get_pdb_uniprot_mapping
@@ -152,3 +154,18 @@ def biblio_card(request, source, id_source):
return render(request, 'biblio_card.html', {'bibliography': bibliography,
'compound_biblios': refs,
'tad_ppis': tad_ppis})
+
+def compound_list(request):
+ compounds = Compound.objects.all()
+ paginator = Paginator(compounds, 5)
+ ppis = Ppi.objects.all()
+ page = request.GET.get('page')
+ try:
+ compounds = paginator.page(page)
+ except PageNotAnInteger:
+ # If page is not an integer, deliver first page.
+ compounds = paginator.page(1)
+ except EmptyPage:
+ # If page is out of range (e.g. 9999), deliver last page of results.
+ compounds = paginator.page(paginator.num_pages)
+ return render(request, 'compound_list.html', {'compounds': compounds, 'ppis': ppis})
--
GitLab