From adb7bfb9151336ed567ef07d55dc5efb7026de19 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Wed, 6 Dec 2017 17:15:20 +0100
Subject: [PATCH] add select on bound complex to compounds list
Former-commit-id: 4519106f57e981f615014827ca5f2f841cc2f477
---
ippisite/ippidb/models.py | 3 ++-
ippisite/ippidb/templates/compound_list.html | 1 +
ippisite/ippidb/views.py | 18 ++++++++++++++++--
3 files changed, 19 insertions(+), 3 deletions(-)
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 0dbfdb63..72b96de6 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -163,6 +163,8 @@ class ProteinDomainComplex(models.Model):
def __str__(self):
return '{}-{}'.format(self.protein_id, self.domain_id)
+ def name(self):
+ return self.protein.short_name
class ProteinDomainBoundComplex(ProteinDomainComplex):
ppp_copy_nb_per_p = models.IntegerField(
@@ -244,7 +246,6 @@ class PpiComplex(models.Model):
def __str__(self):
return 'PPI {}, Complex {} ({})'.format(self.ppi, self.complex, self.cc_nb)
-
class Compound(models.Model):
canonical_smile = models.CharField(
'Canonical Smile', unique=True, max_length=500)
diff --git a/ippisite/ippidb/templates/compound_list.html b/ippisite/ippidb/templates/compound_list.html
index e852b03a..8b7a7e10 100644
--- a/ippisite/ippidb/templates/compound_list.html
+++ b/ippisite/ippidb/templates/compound_list.html
@@ -37,6 +37,7 @@
{% include "multiselection_list_menu.html" with label="PPI" selected_list=selected_ppis unselected_list=ppis param_name="ppi" limit_param_name="ppis_limit" limit_param_value=ppis_limit %}
{% include "multiselection_list_menu.html" with label="Disease" selected_list=selected_diseases unselected_list=diseases param_name="disease" limit_param_name="diseases_limit" limit_param_value=diseases_limit %}
{% include "multiselection_list_menu.html" with label="Organism" selected_list=selected_taxonomies unselected_list=taxonomies param_name="taxonomy" limit_param_name="taxonomies_limit" limit_param_value=taxonomies_limit %}
+ {% include "multiselection_list_menu.html" with label="Bound complex" selected_list=selected_boundcomplexes unselected_list=boundcomplexes param_name="boundcomplex" limit_param_name="boundcomplexes_limit" limit_param_value=boundcomplexes_limit %}
</form>
</div>
<main class="col-12 col-md-9 col-xl-10 pl-md-5 bd-content" role="main">
diff --git a/ippisite/ippidb/views.py b/ippisite/ippidb/views.py
index 8e746a22..e66b2e4a 100644
--- a/ippisite/ippidb/views.py
+++ b/ippisite/ippidb/views.py
@@ -5,7 +5,7 @@ from django.http import HttpResponseRedirect, Http404
from django.core.paginator import Paginator, EmptyPage, PageNotAnInteger
from formtools.wizard.views import SessionWizardView, NamedUrlSessionWizardView
from .forms import IdForm, BibliographyForm, PDBForm, ProteinForm, ProteinDomainComplexTypeForm, ProteinDomainComplexForm, PpiForm, PpiComplexForm, ProteinFormSet,ActivityForm, CompoundForm, CompoundFormSet
-from .models import Protein, Bibliography, ProteinDomainComplex, RefCompoundBiblio, TestActivityDescription, Compound, Ppi, Disease, Taxonomy
+from .models import Protein, Bibliography, ProteinDomainComplex, ProteinDomainBoundComplex, RefCompoundBiblio, TestActivityDescription, Compound, Ppi, Disease, Taxonomy
from .ws import get_pdb_uniprot_mapping
@@ -197,6 +197,8 @@ def compound_list(request):
compounds = compounds.filter(compoundaction__ppi__diseases__id__in=request.GET.getlist('disease'))
if request.GET.get('taxonomy'):
compounds = compounds.filter(compoundaction__ppi_id__ppicomplex__complex__protein__organism__id__in=request.GET.getlist('taxonomy'))
+ if request.GET.get('boundcomplexes'):
+ compounds = compounds.filter(compoundaction__ppi_id__ppicomplex__complex__id__in=request.GET.getlist('boundcomplex'))
try:
ppis_limit = int(request.GET.get('ppis_limit'))
except:
@@ -209,6 +211,10 @@ def compound_list(request):
taxonomies_limit = int(request.GET.get('taxonomies_limit'))
except:
taxonomies_limit = None
+ try:
+ boundcomplexes_limit = int(request.GET.get('boundcomplexes_limit'))
+ except:
+ boundcomplexes_limit = None
selected_ppis = Ppi.objects.filter(id__in=request.GET.getlist('ppi'))
ppis = Ppi.objects.exclude(id__in=request.GET.getlist('ppi'))
if ppis_limit is not None:
@@ -221,6 +227,10 @@ def compound_list(request):
taxonomies = Taxonomy.objects.exclude(id__in=request.GET.getlist('taxonomy'))
if taxonomies_limit is not None:
taxonomies = taxonomies[:taxonomies_limit]
+ selected_boundcomplexes = ProteinDomainBoundComplex.objects.filter(id__in=request.GET.getlist('boundcomplex'))
+ boundcomplexes = ProteinDomainBoundComplex.objects.exclude(id__in=request.GET.getlist('boundcomplex'))
+ if boundcomplexes_limit is not None:
+ boundcomplexes = boundcomplexes[:boundcomplexes_limit]
# handle pagination in compounds list
paginator = Paginator(compounds, 5)
page = request.GET.get('page')
@@ -241,7 +251,11 @@ def compound_list(request):
'diseases_limit': ppis_limit,
'selected_taxonomies': selected_taxonomies,
'taxonomies': taxonomies,
- 'taxonomies_limit': taxonomies_limit})
+ 'taxonomies_limit': taxonomies_limit,
+ 'selected_boundcomplexes': selected_boundcomplexes,
+ 'boundcomplexes': boundcomplexes,
+ 'boundcomplexes_limit': boundcomplexes_limit
+ })
def compound_card(request, compound_id):
try:
--
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