From 7d535cf4bd665dca130e5908055257bed89ca2c0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Wed, 18 Jul 2018 18:00:09 +0200
Subject: [PATCH] spring cleaning!
removed many obsolete templates and views/urls that mapped to them
also fix #68 (access directly "query compounds" from the top menu
and remove "query pockets")
Former-commit-id: be7ecd58a5294a2717b51e57050053537d4b01de
---
ippisite/ippidb/templates/add.html | 2 +-
ippisite/ippidb/templates/base.html | 4 +-
ippisite/ippidb/templates/compound_card.html | 9 +++
.../ippidb/templates/compound_l_item.html | 4 +-
ippisite/ippidb/templates/compound_list.html | 18 +-----
.../ippidb/templates/compound_t_list.html | 2 +-
.../ippidb/templates/compound_v_item.html | 4 +-
ippisite/ippidb/templates/drug-candidate.html | 64 -------------------
ippisite/ippidb/templates/pharma.html | 60 -----------------
ippisite/ippidb/templates/pharmacology.html | 64 -------------------
ippisite/ippidb/templates/pockets.html | 60 -----------------
ippisite/ippidb/urls.py | 13 +---
ippisite/ippidb/views.py | 38 -----------
13 files changed, 21 insertions(+), 321 deletions(-)
delete mode 100644 ippisite/ippidb/templates/drug-candidate.html
delete mode 100644 ippisite/ippidb/templates/pharma.html
delete mode 100644 ippisite/ippidb/templates/pharmacology.html
delete mode 100644 ippisite/ippidb/templates/pockets.html
diff --git a/ippisite/ippidb/templates/add.html b/ippisite/ippidb/templates/add.html
index d6ee91be..e744f30f 100644
--- a/ippisite/ippidb/templates/add.html
+++ b/ippisite/ippidb/templates/add.html
@@ -9,7 +9,7 @@
<div class="inner-wrap">
<ul>
<li>
- <a href="/compound/">View Content</a>
+ <a href="/compounds/">View Content</a>
</li>
<li>
<a href="/admin-session/add/IdForm">Add New Content</a>
diff --git a/ippisite/ippidb/templates/base.html b/ippisite/ippidb/templates/base.html
index f026ddab..46b45bec 100644
--- a/ippisite/ippidb/templates/base.html
+++ b/ippisite/ippidb/templates/base.html
@@ -154,7 +154,7 @@
var datasetIndex = activePoints[0]._datasetIndex;
var selectedIndex = activePoints[0]._index;
var id = scatterChart.data.datasets[datasetIndex].data[selectedIndex].id;
- window.location = '/compound/' + id + '#' + tabHash;
+ window.location = '/compounds/' + id + '#' + tabHash;
};
};
</script>
@@ -182,7 +182,7 @@
<a href="/about">About</a>
</li>
<li>
- <a href="/queries">Queries</a>
+ <a href="/compounds">Query compounds</a>
</li>
<li>
<a href="/tutorials">Tutorials</a>
diff --git a/ippisite/ippidb/templates/compound_card.html b/ippisite/ippidb/templates/compound_card.html
index d3007bb7..001174bb 100644
--- a/ippisite/ippidb/templates/compound_card.html
+++ b/ippisite/ippidb/templates/compound_card.html
@@ -5,6 +5,15 @@
{% block content %}
{% include "kekule_display.html" %}
+<div class="inner-wrap">
+ <nav class="breadcrumb breadNav" role="navigation">
+ <div class="breadNav-label">You are here</div>
+ <div aria-labelledby="breadcrumb-label">
+ {% block breadcrumb %} <a href="/compounds/" class="breadNav-link"> > Query compounds</a> <a href="/compounds/{{ compound.id }}" class="breadNav-link"> > Compound {{ compound.id }}</a>{% endblock %}
+ </div>
+ </nav>
+</div>
+
<div class="container-fluid">
<div class="row flex-xl-nowrap">
diff --git a/ippisite/ippidb/templates/compound_l_item.html b/ippisite/ippidb/templates/compound_l_item.html
index 5fcae8ed..728ff060 100644
--- a/ippisite/ippidb/templates/compound_l_item.html
+++ b/ippisite/ippidb/templates/compound_l_item.html
@@ -1,9 +1,9 @@
<div class="row m-2 border border-info bg-light">
<div class="col-sm-3 border-info d-flex justify-content-center align-content-center">
- <a href="/compound/{{ compound.id }}">{% include "pubchem_img.html" %}</a>
+ <a href="/compounds/{{ compound.id }}">{% include "pubchem_img.html" %}</a>
</div>
<div class="col-sm-9">
- <span class="badge badge-dark"><a href="/compound/{{ compound.id }}">{{ compound.id }}</a></span>{%if compound.common_name %}<span>Common name: {{ compound.common_name }}</span>{% endif %}
+ <span class="badge badge-dark"><a href="/compounds/{{ compound.id }}">{{ compound.id }}</a></span>{%if compound.common_name %}<span>Common name: {{ compound.common_name }}</span>{% endif %}
<ul class="list-group">
{% if compound.canonical_smile %}
<li class="list-group-item">Canonical SMILES: {{ compound.canonical_smile }}</li>
diff --git a/ippisite/ippidb/templates/compound_list.html b/ippisite/ippidb/templates/compound_list.html
index 7d391871..4d4600d2 100644
--- a/ippisite/ippidb/templates/compound_list.html
+++ b/ippisite/ippidb/templates/compound_list.html
@@ -1,28 +1,14 @@
-{% extends "queries.html" %}
+{% extends "base.html" %}
{% load customtags %}
{% block title %}compounds list{% endblock %}
{% block content %}
-<div id="mainnav">
- <nav class="secondary-nav">
- <div class="inner-wrap">
- <ul>
- <li>
- <a href="/compound">By Compounds</a>
- </li>
- <li>
- <a href="/queries/pockets">By Pockets</a>
- </li>
- </ul>
- </div>
- </nav>
-</div>
<div class="inner-wrap">
<nav class="breadcrumb breadNav" role="navigation">
<div class="breadNav-label">You are here</div>
<div aria-labelledby="breadcrumb-label">
- {% block breadcrumb %} <a href="/compound/" class="breadNav-link">{{block.super}}</a> > By compounds</a>{% endblock %}
+ {% block breadcrumb %} <a href="/compounds/" class="breadNav-link"> > Query compounds</a>{% endblock %}
</div>
</nav>
</div>
diff --git a/ippisite/ippidb/templates/compound_t_list.html b/ippisite/ippidb/templates/compound_t_list.html
index a3ebaa5d..85dfaa08 100644
--- a/ippisite/ippidb/templates/compound_t_list.html
+++ b/ippisite/ippidb/templates/compound_t_list.html
@@ -22,7 +22,7 @@
<tbody>
{% for compound in compounds %}
<tr>
- <th scope="col"><span class="badge badge-dark"><a href="/compound/{{ compound.id }}">{{ compound.id }}</a></span></th>
+ <th scope="col"><span class="badge badge-dark"><a href="/compounds/{{ compound.id }}">{{ compound.id }}</a></span></th>
{% if "common_name" in fields %}
<th scope="col">{{ compound.common_name|default_if_none:"-" }}</th>
{% endif %}
diff --git a/ippisite/ippidb/templates/compound_v_item.html b/ippisite/ippidb/templates/compound_v_item.html
index dd713701..6f22bebd 100644
--- a/ippisite/ippidb/templates/compound_v_item.html
+++ b/ippisite/ippidb/templates/compound_v_item.html
@@ -1,7 +1,7 @@
<div class="card m-2 border border-info" style="width: 300px">
- <a href="/compound/{{ compound.id }}">{% include "pubchem_img.html" %}</a>
+ <a href="/compounds/{{ compound.id }}">{% include "pubchem_img.html" %}</a>
<div class="card-body" style="overflow:hidden; word-wrap:break-word;">
- <span class="badge badge-dark"><a href="/compound/{{ compound.id }}">{{ compound.id }}</a></span>
+ <span class="badge badge-dark"><a href="/compounds/{{ compound.id }}">{{ compound.id }}</a></span>
<p>{{ compound.best_pXC50_activity_ppi_family }}</p>
<p>Molecular Weight: {{ compound.molecular_weight }} g/mol</p>
</div>
diff --git a/ippisite/ippidb/templates/drug-candidate.html b/ippisite/ippidb/templates/drug-candidate.html
deleted file mode 100644
index de945b3e..00000000
--- a/ippisite/ippidb/templates/drug-candidate.html
+++ /dev/null
@@ -1,64 +0,0 @@
-{% extends "about.html" %}
-
-
-{% block title %}inhibitors of Protein-Protein Interaction Database{% endblock %}
-
-{% block content %}
-<div id="mainnav">
- <nav class="secondary-nav">
- <div class="inner-wrap">
- <ul>
- <li>
- <a href="/about/general">General informations</a>
- </li>
- <li>
- <a href="/about/pharmacology">Pharmacology</a>
- </li>
- <li>
- <a href="/about/physicochemistry">Physicochemistry</a>
- </li>
- <li>
- <a href="/about/drug-candidate">Drug candidate</a>
- </li>
- </ul>
- </div>
- </nav>
-</div>
-<div class="inner-wrap">
- <nav class="breadcrumb breadNav" role="navigation">
- <div class="breadNav-label">You are here</div>
- <div aria-labelledby="breadcrumb-label">
- {% block breadcrumb %} <a href="/compound/" class="breadNav-link">{{block.super}}</a> > Drug candidate {% endblock %}
- </div>
- </nav>
- <div id="main-wrapper" class="page">
- <div id="main">
- <div id="content" class="main-content">
- <div class="section">
- <main role="main">
- <h1 class="page-title"> DRUG CANDIDATE </h1>
- <div class="tabs"></div>
- <div class="main__inner">
- <div class="region region-content">
- <div class="page-intro">
- </div>
- <div class="color-wrap">
- <div class="region region-content">
- <div class="block block-system block-system-main">
- <div class="content">
- <div class="view-content">
-
- </div>
- </div>
- </div>
- </div>
- </div>
- </div>
- </div>
- </main><!-- .site-main -->
- </div>
- </div>
- </div><!-- div main -->
- </div>
-</div>
-{% endblock %}
diff --git a/ippisite/ippidb/templates/pharma.html b/ippisite/ippidb/templates/pharma.html
deleted file mode 100644
index 84f18529..00000000
--- a/ippisite/ippidb/templates/pharma.html
+++ /dev/null
@@ -1,60 +0,0 @@
-{% extends "base.html" %}
-
-
-{% block title %}inhibitors of Protein-Protein Interaction Database{% endblock %}
-
-{% block content %}
-<div id="mainnav">
- <nav class="secondary-nav">
- <div class="inner-wrap">
- <ul>
- <li>
- <a href="/compound">By Compounds</a>
- </li>
- <li>
- <a href="/query/pockets">By Pockets</a>
- </li>
- </ul>
- </div>
- </nav>
-</div>
-<div class="inner-wrap">
- <nav class="breadcrumb breadNav" role="navigation">
- <div class="breadNav-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">
- <div class="section">
- <main role="main">
- <h1 class="page-title"> BY PHARMACOLOGICAL CRITERIA </h1>
- <div class="tabs"></div>
- <div class="main__inner">
- <div class="region region-content">
- <div class="page-intro">
- </div>
- <div class="color-wrap">
- <div class="region region-content">
- <div class="block block-system block-system-main">
- <div class="content">
- <div class="view-content">
-
- {% block form %}{% endblock %}
-
- </div>
- </div>
- </div>
- </div>
- </div>
- </div>
- </div>
- </main><!-- .site-main -->
- </div>
- </div>
- </div><!-- div main -->
- </div>
-</div>
-{% endblock %}
diff --git a/ippisite/ippidb/templates/pharmacology.html b/ippisite/ippidb/templates/pharmacology.html
deleted file mode 100644
index 1dc9ba5f..00000000
--- a/ippisite/ippidb/templates/pharmacology.html
+++ /dev/null
@@ -1,64 +0,0 @@
-{% extends "about.html" %}
-
-
-{% block title %}inhibitors of Protein-Protein Interaction Database{% endblock %}
-
-{% block content %}
-<div id="mainnav">
- <nav class="secondary-nav">
- <div class="inner-wrap">
- <ul>
- <li>
- <a href="/about/general">General informations</a>
- </li>
- <li>
- <a href="/about/pharmacology">Pharmacology</a>
- </li>
- <li>
- <a href="/about/physicochemistry">Physicochemistry</a>
- </li>
- <li>
- <a href="/about/drug-candidate">Drug candidate</a>
- </li>
- </ul>
- </div>
- </nav>
-</div>
-<div class="inner-wrap">
- <nav class="breadcrumb breadNav" role="navigation">
- <div class="breadNav-label">You are here</div>
- <div aria-labelledby="breadcrumb-label">
- {% block breadcrumb %} <a href="/about/" class="breadNav-link">{{block.super}}</a> > Pharmacology {% endblock %}
- </div>
- </nav>
- <div id="main-wrapper" class="page">
- <div id="main">
- <div id="content" class="main-content">
- <div class="section">
- <main role="main">
- <h1 class="page-title"> PHARMACOLOGY </h1>
- <div class="tabs"></div>
- <div class="main__inner">
- <div class="region region-content">
- <div class="page-intro">
- </div>
- <div class="color-wrap">
- <div class="region region-content">
- <div class="block block-system block-system-main">
- <div class="content">
- <div class="view-content">
-
- </div>
- </div>
- </div>
- </div>
- </div>
- </div>
- </div>
- </main><!-- .site-main -->
- </div>
- </div>
- </div><!-- div main -->
- </div>
-</div>
-{% endblock %}
diff --git a/ippisite/ippidb/templates/pockets.html b/ippisite/ippidb/templates/pockets.html
deleted file mode 100644
index e9a31599..00000000
--- a/ippisite/ippidb/templates/pockets.html
+++ /dev/null
@@ -1,60 +0,0 @@
-{% extends "queries.html" %}
-
-
-{% block title %}inhibitors of Protein-Protein Interaction Database{% endblock %}
-
-{% block content %}
-<div id="mainnav">
- <nav class="secondary-nav">
- <div class="inner-wrap">
- <ul>
- <li>
- <a href="/compound">By Compounds</a>
- </li>
- <li>
- <a href="/queries/pockets">By Pockets</a>
- </li>
- </ul>
- </div>
- </nav>
-</div>
-<div class="inner-wrap">
- <nav class="breadcrumb breadNav" role="navigation">
- <div class="breadNav-label">You are here</div>
- <div aria-labelledby="breadcrumb-label">
- {% block breadcrumb %} <a href="/compound/" class="breadNav-link">{{block.super}}</a> > By Pockets{% endblock %}
- </div>
- </nav>
- <div id="main-wrapper" class="page">
- <div id="main">
- <div id="content" class="main-content">
- <div class="section">
- <main role="main">
- <h1 class="page-title"> BY POCKETS </h1>
- <div class="tabs"></div>
- <div class="main__inner">
- <div class="region region-content">
- <div class="page-intro">
- </div>
- <div class="color-wrap">
- <div class="region region-content">
- <div class="block block-system block-system-main">
- <div class="content">
- <div class="view-content">
-
- {% block form %}{% endblock %}
-
- </div>
- </div>
- </div>
- </div>
- </div>
- </div>
- </div>
- </main><!-- .site-main -->
- </div>
- </div>
- </div><!-- div main -->
- </div>
-</div>
-{% endblock %}
diff --git a/ippisite/ippidb/urls.py b/ippisite/ippidb/urls.py
index ce260fea..82df36de 100644
--- a/ippisite/ippidb/urls.py
+++ b/ippisite/ippidb/urls.py
@@ -11,17 +11,8 @@ urlpatterns = [
url(r'^$', views.index, name='index'),
url(r'^about$', views.about, name='about'),
url(r'^about/general/$', views.general, name='general'),
- url(r'^about/pharmacology/$', views.pharmacology, name='pharmacology'),
- url(r'^about/physicochemistry/$',
- views.physicochemistry, name='physicochemistry'),
- url(r'^about/drug-candidate/$',
- views.drugCandidate, name='drug-candidate'),
- url(r'^queries$', views.queries, name='queries'),
- url(r'^queries/pockets/$', views.pockets, name='pockets'),
- 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/$', views.compound_list, name='compound_list'),
- url(r'^compound/(?P<compound_id>\w+)$', views.compound_card, name='compound_card'),
+ url(r'^compounds/$', views.compound_list, name='compound_list'),
+ url(r'^compounds/(?P<compound_id>\w+)$', views.compound_card, name='compound_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 d152175e..fde5a67e 100644
--- a/ippisite/ippidb/views.py
+++ b/ippisite/ippidb/views.py
@@ -24,29 +24,6 @@ def about(request):
def general(request):
return render(request, 'general.html')
-def pharmacology(request):
- return render(request, 'pharmacology.html')
-
-
-def physicochemistry(request):
- return render(request, 'physicochemistry.html')
-
-
-def drugCandidate(request):
- return render(request, 'drug-candidate.html')
-
-
-def queries(request):
- return render(request, 'queries.html')
-
-
-def compounds(request):
- return render(request, 'compound.html')
-
-
-def pockets(request):
- return render(request, 'pockets.html')
-
def tutorials(request):
return render(request, 'tutorials.html')
@@ -160,21 +137,6 @@ class IppiWizard(NamedUrlSessionWizardView):
})
-def biblio_list(request):
- bibliographies = Bibliography.objects.all()
- return render(request, 'biblio_list.html', {'bibliographies':bibliographies})
-
-def biblio_card(request, source, id_source):
- try:
- bibliography = Bibliography.objects.get(source=source, id_source=id_source)
- except Bibliography.DoesNotExist:
- raise Http404("No bibliography data for %s:%s" % (source, id_source))
- refs = RefCompoundBiblio.objects.filter(bibliography_id = bibliography.id)
- tad_ppis = TestActivityDescription.objects.filter(biblio__source=source,biblio__id_source=id_source).select_related()
- return render(request, 'biblio_card.html', {'bibliography': bibliography,
- 'compound_biblios': refs,
- 'tad_ppis': tad_ppis})
-
def process_cutoff_value(name, context, request):
context[name+'_max'] = str(int(math.ceil(float(Compound.objects.all().aggregate(Max(name))[name + '__max']))))
context[name+'_min'] = str(int(math.floor(float(Compound.objects.all().aggregate(Min(name))[name + '__min']))))
--
GitLab