From c280cccc7bd810477b22ea554925aede76ebc99b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Sat, 10 Feb 2018 18:44:35 +0100
Subject: [PATCH] continue working on compound query interface (#43), WIP
- three visualization modes now
- most of the requested primary information is there
Former-commit-id: 9d5310f273011035e53643d4baf153d4769b6ca8
---
ippisite/ippidb/models.py | 10 +++++
.../ippidb/templates/compound_grid_item.html | 28 --------------
...d_table_item.html => compound_l_item.html} | 0
ippisite/ippidb/templates/compound_list.html | 37 +++++++++++++++----
.../ippidb/templates/compound_t_item.html | 10 +++++
.../ippidb/templates/compound_v_item.html | 8 ++++
ippisite/ippidb/views.py | 6 ++-
7 files changed, 62 insertions(+), 37 deletions(-)
delete mode 100644 ippisite/ippidb/templates/compound_grid_item.html
rename ippisite/ippidb/templates/{compound_table_item.html => compound_l_item.html} (100%)
create mode 100644 ippisite/ippidb/templates/compound_t_item.html
create mode 100644 ippisite/ippidb/templates/compound_v_item.html
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index eecaaf86..81350553 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -341,6 +341,16 @@ class Compound(models.Model):
pfam_ids.add(bound_complex.complex.domain.pfam_id)
return pfam_ids
+ @property
+ def compound_action_pdb_ids(self):
+ """
+ return all PDB codes of the corresponding compound actions
+ """
+ pdb_ids = set()
+ for ca in self.compoundaction_set.all():
+ pdb_ids.add(ca.pdb_id)
+ return pdb_ids
+
class MDDRActivityClass(models.Model):
name = models.CharField('Activity Class', max_length=100, unique=True)
diff --git a/ippisite/ippidb/templates/compound_grid_item.html b/ippisite/ippidb/templates/compound_grid_item.html
deleted file mode 100644
index b4e225c0..00000000
--- a/ippisite/ippidb/templates/compound_grid_item.html
+++ /dev/null
@@ -1,28 +0,0 @@
-<div class="card m-2 border border-info" style="width: 300px">
- <a href="/compound/{{ 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>
- <p>{% for pfam_id in compound.pfam_ids %}{{ pfam_id }}{% endfor %}</p>
- <p>Molecular Weight: {{ compound.molecular_weight }} g/mol</p>
- </div>
-</div>
-<!--
-<div class="col-md-4 border border-info bg-light">
- <div class="row border-info d-flex justify-content-center align-content-center">
- <a href="/compound/{{ compound.id }}">{% include "pubchem_img.html" %}</a>
- </div>
- <div class="row">
- <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>
- </div>
-</div>
--->
diff --git a/ippisite/ippidb/templates/compound_table_item.html b/ippisite/ippidb/templates/compound_l_item.html
similarity index 100%
rename from ippisite/ippidb/templates/compound_table_item.html
rename to ippisite/ippidb/templates/compound_l_item.html
diff --git a/ippisite/ippidb/templates/compound_list.html b/ippisite/ippidb/templates/compound_list.html
index accb8284..593dc1ca 100644
--- a/ippisite/ippidb/templates/compound_list.html
+++ b/ippisite/ippidb/templates/compound_list.html
@@ -67,27 +67,50 @@
{% endif %}
</span>
<span class="btn-group float-right">
- <a class="btn btn-default btn-outline-primary {% if not display_list %}active{% endif %}" href="#" {% if display_list %}onclick="modifyUrl('display_list', null)"{% endif %}>
+ <a class="btn btn-default btn-outline-primary {% if display == 'v' %}active{% endif %}" href="#" {% if display != 'v' %}onclick="modifyUrl('display', 'v')"{% endif %}>
<i class="fa fa-th" title="Vignettes"></i>
</a>
- <a class="btn btn-default btn-outline-primary {% if display_list %}active{% endif %}" href="#" {% if not display_list %}onclick="modifyUrl('display_list', true)"{% endif %}>
+ <a class="btn btn-default btn-outline-primary {% if display == 'l' %}active{% endif %}" href="#" {% if display != 'l' %}onclick="modifyUrl('display', 'l')"{% endif %}>
<i class="fa fa-bars" title="List"></i>
</a>
+ <a class="btn btn-default btn-outline-primary {% if display == 't' %}active{% endif %}" href="#" {% if display != 't' %}onclick="modifyUrl('display', 't')"{% endif %}>
+ <i class="fa fa-table" title="Table"></i>
+ </a>
</span>
</div>
</form>
{% if compounds %}
- {% if display_list %}
+ <div class="row">
+ {% if display == 'v' %}
+ {% for compound in compounds %}
+ {% include "compound_v_item.html" with compound=compound %}
+ {% endfor %}
+ {% elif display == 'l'%}
{% for compound in compounds %}
- {% include "compound_table_item.html" with compound=compound %}
+ {% include "compound_l_item.html" with compound=compound %}
{% endfor %}
{% else %}
- <div class="row">
+ <table class="table">
+ <thead>
+ <tr>
+ <th scope="col">#</th>
+ <th scope="col">Common name</th>
+ <th scope="col">Molecular weight</th>
+ <th scope="col">AlogP</th>
+ <th scope="col">PDB ligand</th>
+ <th scope="col">MDDR phase</th>
+ <th scope="col">Available tests</th>
+ <th scope="col">Available publications</th>
+ </tr>
+ </thead>
+ <tbody>
{% for compound in compounds %}
- {% include "compound_grid_item.html" with compound=compound %}
+ {% include "compound_t_item.html" with compound=compound %}
{% endfor %}
- </div>
+ </tbody>
+ </table>
{% endif %}
+ </div>
{% else %}
<p>Nothing found there!</p>
{% endif %}
diff --git a/ippisite/ippidb/templates/compound_t_item.html b/ippisite/ippidb/templates/compound_t_item.html
new file mode 100644
index 00000000..57faae85
--- /dev/null
+++ b/ippisite/ippidb/templates/compound_t_item.html
@@ -0,0 +1,10 @@
+<tr>
+ <th scope="col"><span class="badge badge-dark"><a href="/compound/{{ compound.id }}">{{ compound.id }}</a></span></th>
+ <th scope="col">{{ compound.common_name|default_if_none:"-" }}</th>
+ <th scope="col">{{ compound.molecular_weight}} g/mol</th>
+ <th scope="col">{{ compound.a_log_p }}</th>
+ <th scope="col">{% for pdb_id in compound.compound_action_pdb_ids %}{{ pdb_id }}{% endfor %}</th>
+ <th scope="col"> ? </th>
+ <th scope="col"> ? </th>
+ <th scope="col">{{ compound.biblio_refs|length }}</th>
+</tr>
diff --git a/ippisite/ippidb/templates/compound_v_item.html b/ippisite/ippidb/templates/compound_v_item.html
new file mode 100644
index 00000000..e6e54ecd
--- /dev/null
+++ b/ippisite/ippidb/templates/compound_v_item.html
@@ -0,0 +1,8 @@
+<div class="card m-2 border border-info" style="width: 300px">
+ <a href="/compound/{{ 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>
+ <p>{% for pfam_id in compound.pfam_ids %}{{ pfam_id }}{% endfor %}</p>
+ <p>Molecular Weight: {{ compound.molecular_weight }} g/mol</p>
+ </div>
+</div>
diff --git a/ippisite/ippidb/views.py b/ippisite/ippidb/views.py
index c1753120..0895e0a9 100644
--- a/ippisite/ippidb/views.py
+++ b/ippisite/ippidb/views.py
@@ -211,7 +211,9 @@ def compound_list(request):
except EmptyPage:
# If page is out of range (e.g. 9999), deliver last page of results.
compounds = paginator.page(paginator.num_pages)
- display_list = request.GET.get('display_list')
+ display = request.GET.get('display')
+ if display not in ['l', 't']:
+ display = 'v'
return render(request, 'compound_list.html', {'compounds': compounds,
'count': count,
'selected_ppis': selected_ppis,
@@ -226,7 +228,7 @@ def compound_list(request):
'selected_boundcomplexes': selected_boundcomplexes,
'boundcomplexes': boundcomplexes,
'boundcomplexes_all': boundcomplexes_all,
- 'display_list': display_list
+ 'display': display
})
def compound_card(request, compound_id):
--
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