allow filter on number of publications

cf #67


Former-commit-id: 58370bc0ace2881cd3d453ec390e44cd6b0f5bcd

ippisite/ippidb/templates/compound_list.html

@@ -27,6 +27,7 @@
        {% include "slider_button.html" with label="Molecular weight" param_name="molecular_weight" %}
        {% include "slider_button.html" with label="AlogP" param_name="a_log_p" %}
        {% include "slider_button.html" with label="H donors" param_name="nb_donor_h" %}
+       {% include "slider_button.html" with label="Publications" param_name="pubs" %}
         </div>
         <div class="m-2 d-flex ">
             <span>{{ compounds.paginator.count }} compounds</span>
@@ -152,5 +153,6 @@
   {% include "slider_modal.html" with label="Molecular Weight" param_name="molecular_weight" param_min=molecular_weight_min param_max=molecular_weight_max param_value=molecular_weight step='50' param_label='Select a cutoff value for the molecular weight of the compounds to be selected'%}
   {% include "slider_modal.html" with label="AlogP" param_name="a_log_p" param_min=a_log_p_min param_max=a_log_p_max param_value=a_log_p step='1' param_label='Select a cutoff value for the AlogP of the compounds to be selected'%}
   {% include "slider_modal.html" with label="H donors" param_name="nb_donor_h" param_min=nb_donor_h_min param_max=nb_donor_h_max param_value=nb_donor_h step='1' param_label='Select a cutoff value for the number of H donors in the compounds to be selected'%}
+  {% include "slider_modal.html" with label="Publications" param_name="pubs" param_min=pubs_min param_max=pubs_max param_value=pubs step='1' param_label='Select a cutoff value for the number of publications mentioning the compounds to be selected'%}
 
 {% endblock %}

ippisite/ippidb/views.py

@@ -137,9 +137,10 @@ class IppiWizard(NamedUrlSessionWizardView):
     })
 
 
-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']))))
+def process_cutoff_value(name, context, request, annotation=None):
+    c = context['compounds']
+    context[name+'_max'] = str(int(math.ceil(float(c.aggregate(Max(name))[name + '__max']))))
+    context[name+'_min'] = str(int(math.floor(float(c.aggregate(Min(name))[name + '__min']))))
     if request.GET.get(name):
         context[name] = request.GET.get(name)
         filter_dict = {name + '__lte': context[name]}
@@ -153,22 +154,23 @@ def compound_list(request):
     Display the list of compounds
     """
     context = {}
-    compounds = Compound.objects.all()
+    # pubs is the number of publications referring to the compound
+    compounds = Compound.objects.annotate(pubs=Count('refcompoundbiblio'))
+    context['compounds'] = compounds
     if request.GET.get('family'):
-        compounds = compounds.filter(compoundaction__ppi__family__id__in=request.GET.getlist('family'))
-    # if filtering on "action on PPI"
+        context['compounds'] = context['compounds'].filter(compoundaction__ppi__family__id__in=request.GET.getlist('family'))
     if request.GET.get('ppi'):
-        compounds = compounds.filter(compoundaction__ppi__id__in=request.GET.getlist('ppi'))
+        context['compounds'] = context['compounds'].filter(compoundaction__ppi__id__in=request.GET.getlist('ppi'))
     if request.GET.get('disease'):
-        compounds = compounds.filter(compoundaction__ppi__diseases__id__in=request.GET.getlist('disease'))
+        context['compounds'] = context['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'))
+        context['compounds'] = context['compounds'].filter(compoundaction__ppi_id__ppicomplex__complex__protein__organism__id__in=request.GET.getlist('taxonomy'))
     if request.GET.get('boundcomplex'):
-        compounds = compounds.filter(compoundaction__ppi_id__ppicomplex__complex__id__in=request.GET.getlist('boundcomplex'))
-    context['compounds'] = compounds
+        context['compounds'] = context['compounds'].filter(compoundaction__ppi_id__ppicomplex__complex__id__in=request.GET.getlist('boundcomplex'))
     context = process_cutoff_value('molecular_weight', context, request)
     context = process_cutoff_value('a_log_p', context, request)
     context = process_cutoff_value('nb_donor_h', context, request)
+    context = process_cutoff_value('pubs', context, request)
     selected_families = PpiFamily.objects.filter(id__in=request.GET.getlist('family'))
     families = PpiFamily.objects.exclude(id__in=request.GET.getlist('family'))
     selected_ppis = Ppi.objects.filter(id__in=request.GET.getlist('ppi'))
@@ -181,8 +183,6 @@ def compound_list(request):
     boundcomplexes = ProteinDomainBoundComplex.objects.exclude(id__in=request.GET.getlist('boundcomplex'))
     sort_by_option_ids = ['id', 'molecular_weight', 'a_log_p', 'nb_aromatic_sssr', 'nb_chiral_centers', 'pubs']
     sort_by = request.GET.get('sort_by', 'id')
-    if sort_by in ['pubs', '-pubs']:
-        context['compounds'] = context['compounds'].annotate(pubs=Count('refcompoundbiblio'))
     context['compounds'] = context['compounds'].order_by(sort_by)
     context['compounds'] = context['compounds'].distinct()
     # handle pagination in compounds list