From 6f5a4bb9516a25b374f1ec919f063221066cdd1c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Tue, 31 Jul 2018 11:41:24 +0200
Subject: [PATCH] restructure the compounds list view
* this view is now class based and a lot more structured
* filters are handled supposedly in a clever manner
Former-commit-id: 510e9b5282b06d28fb839ba20ff44d76ab41f584
---
ippisite/ippidb/templates/compound_list.html | 54 ++---
ippisite/ippidb/urls.py | 2 +-
ippisite/ippidb/views.py | 233 ++++++++++++-------
3 files changed, 171 insertions(+), 118 deletions(-)
diff --git a/ippisite/ippidb/templates/compound_list.html b/ippisite/ippidb/templates/compound_list.html
index 8e1cd2cf..adc3a788 100644
--- a/ippisite/ippidb/templates/compound_list.html
+++ b/ippisite/ippidb/templates/compound_list.html
@@ -30,32 +30,32 @@
{% include "slider_button.html" with label="Publications" param_name="pubs" %}
</div>
<div class="m-2 d-flex ">
- <span>{{ compounds.paginator.count }} compounds</span>
- {% if selected_families or selected_ppis or selected_diseases or selected_taxonomies or selected_boundcomplexes or molecular_weight != molecular_weight_max or a_log_p != a_log_p_max or nb_donor_h != nb_donor_h_max or pubs != pubs_min %}
+ <span>{{ paginator.count }} compounds</span>
+ {% if selected_family or selected_ppi or selected_disease or selected_taxonomy or selected_boundcomplex or molecular_weight != molecular_weight_max or a_log_p != a_log_p_max or nb_donor_h != nb_donor_h_max or pubs != pubs_min %}
<span>
- filters:
- {% if selected_families %}
- {% for selected in selected_families %}
+ {% if selected_family %}
+ {% for selected in selected_family %}
{% include "selected_badge.html" with param_name="family" selected=selected %}
{% endfor %}
{% endif %}
- {% if selected_ppis %}
- {% for selected in selected_ppis %}
+ {% if selected_ppi %}
+ {% for selected in selected_ppi %}
{% include "selected_badge.html" with param_name="ppi" selected=selected %}
{% endfor %}
{% endif %}
- {% if selected_diseases %}
- {% for selected in selected_diseases %}
+ {% if selected_disease %}
+ {% for selected in selected_disease %}
{% include "selected_badge.html" with param_name="disease" selected=selected %}
{% endfor %}
{% endif %}
- {% if selected_taxonomies %}
- {% for selected in selected_taxonomies %}
+ {% if selected_taxonomy %}
+ {% for selected in selected_taxonomy %}
{% include "selected_badge.html" with param_name="taxonomy" selected=selected %}
{% endfor %}
{% endif %}
- {% if selected_boundcomplexes %}
- {% for selected in selected_boundcomplexes %}
+ {% if selected_boundcomplex %}
+ {% for selected in selected_boundcomplex %}
{% include "selected_badge.html" with param_name="boundcomplex" selected=selected %}
{% endfor %}
{% endif %}
@@ -96,20 +96,20 @@
</span>
</div>
</form>
-{% if compounds %}
+{% if page_obj %}
<div class="container-fluid">
{% if display == 'v' %}
<div class="d-flex flex-wrap m-2 justify-content-around">
- {% for compound in compounds %}
+ {% for compound in page_obj %}
{% include "compound_v_item.html" with compound=compound %}
{% endfor %}
</div>
{% elif display == 'l'%}
- {% for compound in compounds %}
+ {% for compound in page_obj %}
{% include "compound_l_item.html" with compound=compound %}
{% endfor %}
{% else %}
- {% include "compound_t_list.html" with compounds=compounds %}
+ {% include "compound_t_list.html" with compounds=page_obj %}
{% endif %}
</div>
{% else %}
@@ -121,9 +121,9 @@
<nav class="d-flex">
<ul class="pagination pagination-sm ml-auto">
- {% if compounds.has_previous %}
+ {% if page_obj.has_previous %}
<li class="page-item">
- <a class="page-link" href="?{% url_replace request 'page' compounds.previous_page_number %}" aria-label="Previous">
+ <a class="page-link" href="?{% url_replace request 'page' page_obj.previous_page_number %}" aria-label="Previous">
<span aria-hidden="true">«</span>
<span class="sr-only">Previous</span>
</a>
@@ -131,12 +131,12 @@
{% endif %}
<li class="page-item disabled">
- <span class="page-link">Page {{ compounds.number }} of {{ compounds.paginator.num_pages }}.</span>
+ <span class="page-link">Page {{ page_obj.number }} of {{ paginator.num_pages }}.</span>
</li>
- {% if compounds.has_next %}
+ {% if page_obj.has_next %}
<li class="page-item">
- <a class="page-link" href="?{% url_replace request 'page' compounds.next_page_number %}" aria-label="Next">
+ <a class="page-link" href="?{% url_replace request 'page' page_obj.next_page_number %}" aria-label="Next">
<span aria-hidden="true">»</span>
<span class="sr-only">Next</span>
</a>
@@ -145,7 +145,7 @@
<li class="page-item ml-3">
<div class="input-group input-group-sm">
- <input id="pageNumber" type="number" min="1" max="{{compounds.paginator.num_pages}}" step="1" placeholder="page #" style="width: 4em;" aria-label="Page number">
+ <input id="pageNumber" type="number" min="1" max="{{ paginator.num_pages }}" step="1" placeholder="page #" style="width: 4em;" aria-label="Page number">
<div class="input-group-append">
<button class="btn btn-outline-primary" type="button" onclick="modifyUrl('page',$('#pageNumber').val())">Go</button>
</div>
@@ -155,11 +155,11 @@
</ul>
</nav>
- {% include "multiselection_modal.html" with label="PPI Family" selected_list=selected_families unselected_list=families param_name="family" all_param_name="families_all" all_param_value=families_all %}
- {% include "multiselection_modal.html" with label="PPI" selected_list=selected_ppis unselected_list=ppis param_name="ppi" all_param_name="ppis_all" all_param_value=ppis_all %}
- {% include "multiselection_modal.html" with label="Disease" selected_list=selected_diseases unselected_list=diseases param_name="disease" all_param_name="diseases_all" all_param_value=diseases_all %}
- {% include "multiselection_modal.html" with label="Organism" selected_list=selected_taxonomies unselected_list=taxonomies param_name="taxonomy" all_param_name="taxonomies_all" all_param_value=taxonomies_all %}
- {% include "multiselection_modal.html" with label="Bound complex" selected_list=selected_boundcomplexes unselected_list=boundcomplexes param_name="boundcomplex" all_param_name="boundcomplexes_all" all_param_value=boundcomplexes_all %}
+ {% include "multiselection_modal.html" with label="PPI Family" selected_list=selected_family unselected_list=family param_name="family" all_param_name="family_all" all_param_value=family_all %}
+ {% include "multiselection_modal.html" with label="PPI" selected_list=selected_ppi unselected_list=ppi param_name="ppi" all_param_name="ppi_all" all_param_value=ppi_all %}
+ {% include "multiselection_modal.html" with label="Disease" selected_list=selected_disease unselected_list=disease param_name="disease" all_param_name="disease_all" all_param_value=disease_all %}
+ {% include "multiselection_modal.html" with label="Organism" selected_list=selected_taxonomy unselected_list=taxonomy param_name="taxonomy" all_param_name="taxonomy_all" all_param_value=taxonomy_all %}
+ {% include "multiselection_modal.html" with label="Bound complex" selected_list=selected_boundcomplex unselected_list=boundcomplex param_name="boundcomplex" all_param_name="boundcomplex_all" all_param_value=boundcomplex_all %}
{% 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'%}
diff --git a/ippisite/ippidb/urls.py b/ippisite/ippidb/urls.py
index 82df36de..db1fb11d 100644
--- a/ippisite/ippidb/urls.py
+++ b/ippisite/ippidb/urls.py
@@ -11,7 +11,7 @@ urlpatterns = [
url(r'^$', views.index, name='index'),
url(r'^about$', views.about, name='about'),
url(r'^about/general/$', views.general, name='general'),
- url(r'^compounds/$', views.compound_list, name='compound_list'),
+ url(r'^compounds/$', views.CompoundListView.as_view(), name='compound_listbeta'),
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'),
diff --git a/ippisite/ippidb/views.py b/ippisite/ippidb/views.py
index 6ae89210..62077cb8 100644
--- a/ippisite/ippidb/views.py
+++ b/ippisite/ippidb/views.py
@@ -7,6 +7,7 @@ from django.shortcuts import render
from django.http import HttpResponseRedirect, Http404
from django.core.paginator import Paginator, EmptyPage, PageNotAnInteger
from django.contrib.auth.mixins import LoginRequiredMixin
+from django.views.generic.list import ListView
from formtools.wizard.views import SessionWizardView, NamedUrlSessionWizardView
import ippidb
@@ -143,99 +144,151 @@ class IppiWizard(LoginRequiredMixin, NamedUrlSessionWizardView):
'form_data': [form.cleaned_data for form in form_list],
})
+class CompoundListFilterHandler(object):
+
+ def __init__(self, filter_class, relation_from_compound, relation_to_compound, parameter_name, filter_context, request_get):
+ self.filter_class = filter_class
+ self.relation_from_compound = relation_from_compound
+ self.parameter_name = parameter_name
+ self.filter_context = filter_context
+ self.relation_from_compound = relation_from_compound
+ self.relation_to_compound = relation_to_compound
+ self.value = request_get.getlist(parameter_name)
+
+ def process(self, queryset):
+ """ to be called during queryset filtering """
+ # if a value has been set for this filter
+ if self.value:
+ # filter queryset on the ID values specified
+ queryset = queryset.filter(**{self.relation_from_compound + '__id__in': self.value})
+ # selected objects on the ID values specified
+ self.filter_context['selected_' + self.parameter_name] = self.filter_class.objects.filter(id__in = self.value)
+ # unselected objects on the ID values not specified
+ self.filter_context[self.parameter_name] = self.filter_class.objects.exclude(id__in = self.value)
+ return queryset
+
+ def post_process(self, compound_ids, queryset):
+ """ to be called after queryset filtering """
+ # if no value has been set for this filter
+ if not self.value:
+ # selected objects is an empty queryset
+ self.filter_context['selected_' + self.parameter_name] = self.filter_class.objects.none()
+ if compound_ids:
+ # unselected objects is the range related to the current queryset
+ self.filter_context[self.parameter_name] = self.filter_class.objects.filter(**{self.relation_to_compound + '__id__in':compound_ids}).distinct()
+ else:
+ # unselected objects are all objects if no filter is set
+ self.filter_context[self.parameter_name] = self.filter_class.objects.all()
+
+
+class CompoundCutoffFilterHandler(object):
+
+ def __init__(self, parameter_name, cutoff_dir, filter_context, request_get):
+ self.parameter_name = parameter_name
+ self.cutoff_dir = cutoff_dir
+ self.filter_context = filter_context
+ self.value = request_get.get(parameter_name)
+
+ def process(self, queryset):
+ """ to be called during queryset filtering """
+ # if a value has been set for this filter
+ if self.value:
+ # filter queryset on the ID values specified
+ self.filter_context[self.parameter_name] = self.value
+ filter_dict = {self.parameter_name + '__' + self.cutoff_dir + 'te': self.value}
+ queryset = queryset.filter(**filter_dict)
+ # max and min value are the max and min for
+ self.filter_context[self.parameter_name+'_max'] = str(int(math.ceil(float(Compound.objects.aggregate(Max(self.parameter_name))[self.parameter_name + '__max'] or 0))))
+ self.filter_context[self.parameter_name+'_min'] = str(int(math.floor(float(Compound.objects.aggregate(Min(self.parameter_name))[self.parameter_name + '__min'] or 0))))
+ return queryset
+
+ def post_process(self, compound_ids, queryset):
+ """ to be called after queryset filtering """
+ # if no value has been set for this filter
+ if not self.value:
+ self.filter_context[self.parameter_name+'_max'] = str(int(math.ceil(float(queryset.aggregate(Max(self.parameter_name))[self.parameter_name + '__max'] or 0))))
+ self.filter_context[self.parameter_name+'_min'] = str(int(math.floor(float(queryset.aggregate(Min(self.parameter_name))[self.parameter_name + '__min'] or 0))))
+ if self.cutoff_dir == 'l':
+ self.filter_context[self.parameter_name] = self.filter_context[self.parameter_name+'_max']
+ else:
+ self.filter_context[self.parameter_name] = self.filter_context[self.parameter_name+'_min']
+
+
+class CompoundListView(ListView):
+
+ model = Compound
+ template_name = "compound_list.html"
+ paginate_by = 15
+
+ table_view_default_fields = ['id', 'common_name', 'molecular_weight', 'a_log_p', 'compound_action_pdb_ids', 'pubs']
-def process_cutoff_value(name, context, request, cutoff_dir='l'):
- c = context['compounds']
- context[name+'_max'] = str(int(math.ceil(float(c.aggregate(Max(name))[name + '__max'] or 0))))
- context[name+'_min'] = str(int(math.floor(float(c.aggregate(Min(name))[name + '__min'] or 0))))
- if request.GET.get(name):
- context[name] = request.GET.get(name)
- filter_dict = {name + '__' + cutoff_dir + 'te': context[name]}
- context['compounds'] = context['compounds'].filter(**filter_dict)
- elif cutoff_dir == 'l':
- context[name] = context[name+'_max']
- else:
- context[name] = context[name+'_min']
- return context
-
-def compound_list(request):
- """
- Display the list of compounds
- """
- context = {}
- # 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'):
- context['compounds'] = context['compounds'].filter(compoundaction__ppi__family__id__in=request.GET.getlist('family'))
- if request.GET.get('ppi'):
- context['compounds'] = context['compounds'].filter(compoundaction__ppi__id__in=request.GET.getlist('ppi'))
- if request.GET.get('disease'):
- context['compounds'] = context['compounds'].filter(compoundaction__ppi__diseases__id__in=request.GET.getlist('disease'))
- if request.GET.get('taxonomy'):
- context['compounds'] = context['compounds'].filter(compoundaction__ppi_id__ppicomplex__complex__protein__organism__id__in=request.GET.getlist('taxonomy'))
- if request.GET.get('boundcomplex'):
- 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, 'g')
- 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'))
- ppis = Ppi.objects.exclude(id__in=request.GET.getlist('ppi'))
- selected_diseases = Disease.objects.filter(id__in=request.GET.getlist('disease'))
- diseases = Disease.objects.exclude(id__in=request.GET.getlist('disease'))
- selected_taxonomies = Taxonomy.objects.filter(id__in=request.GET.getlist('taxonomy'))
- taxonomies = Taxonomy.objects.exclude(id__in=request.GET.getlist('taxonomy'))
- selected_boundcomplexes = ProteinDomainBoundComplex.objects.filter(id__in=request.GET.getlist('boundcomplex'))
- 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')
- context['compounds'] = context['compounds'].order_by(sort_by)
- context['compounds'] = context['compounds'].distinct()
- # handle pagination in compounds list
- paginator = Paginator(context['compounds'], 15)
- page = request.GET.get('page')
- try:
- context['compounds'] = paginator.page(page)
- except PageNotAnInteger:
- # If page is not an integer, deliver first page.
- context['compounds'] = paginator.page(1)
- except EmptyPage:
- # If page is out of range (e.g. 9999), deliver last page of results.
- context['compounds'] = paginator.page(paginator.num_pages)
- display = request.GET.get('display')
- if display not in ['l', 't']:
- display = 'v'
- context['display']=display
- compound_fields = {f.name: f.verbose_name for f in Compound._meta.get_fields() if not(f.is_relation)}
- sort_by_options = OrderedDict()
- for sort_by_option_id in sort_by_option_ids:
- if sort_by_option_id == 'pubs':
- name = 'Number of publications'
+
+ def get_ordering(self):
+ sort_by = self.request.GET.get('sort_by', 'id')
+ return sort_by
+
+ def get_context_data(self, **kwargs):
+ context = super().get_context_data(**kwargs)
+ # process display configuration
+ display = self.request.GET.get('display')
+ if display not in ['l', 't']:
+ display = 'v'
+ context['display']=display
+ # displayed fields in "table" mode
+ fields = self.request.GET.getlist('fields', self.table_view_default_fields)
+ if 'id' not in fields:
+ fields.append('id')
+ context['fields'] = fields
+ # filters
+ context.update(self.filter_context)
+ # sort by options
+ compound_fields = {f.name: f.verbose_name for f in Compound._meta.get_fields() if not(f.is_relation)}
+ sort_by_options = OrderedDict()
+ for sort_by_option_id in self.sort_by_option_ids:
+ if sort_by_option_id == 'pubs':
+ name = 'Number of publications'
+ else:
+ name = compound_fields.get(sort_by_option_id)
+ sort_by_options[sort_by_option_id] = {'name': name, 'order':'ascending', 'id': sort_by_option_id}
+ sort_by_options['-'+sort_by_option_id] = {'name': name, 'order':'descending', 'id': sort_by_option_id}
+ context['sort_by'] = self.get_ordering()
+ context['sort_by_options'] = sort_by_options
+ # return context
+ return context
+
+ def get_queryset(self):
+ self.filter_context = {}
+ # get queryset
+ qs = super().get_queryset()
+ # annotate
+ qs = qs.annotate(pubs=Count('refcompoundbiblio'))
+ # add filters
+ cfhs = [\
+ CompoundListFilterHandler(PpiFamily, 'compoundaction__ppi__family', 'ppi__compoundaction__compound', 'family', self.filter_context, self.request.GET),
+ CompoundListFilterHandler(Ppi, 'compoundaction__ppi', 'compoundaction__compound', 'ppi', self.filter_context, self.request.GET),
+ CompoundListFilterHandler(Disease, 'compoundaction__ppi__diseases', 'ppi__compoundaction__compound', 'disease', self.filter_context, self.request.GET),
+ CompoundListFilterHandler(Taxonomy, 'compoundaction__ppi_id__ppicomplex__complex__protein__organism', 'protein__proteindomaincomplex__ppicomplex__ppi__compoundaction__compound', 'taxonomy', self.filter_context, self.request.GET),
+ CompoundListFilterHandler(ProteinDomainBoundComplex, 'compoundaction__ppi_id__ppicomplex__complex', 'ppicomplex__ppi__compoundaction__compound', 'boundcomplex', self.filter_context, self.request.GET),
+ CompoundCutoffFilterHandler('molecular_weight', 'l', self.filter_context, self.request.GET),
+ CompoundCutoffFilterHandler('a_log_p', 'l', self.filter_context, self.request.GET),
+ CompoundCutoffFilterHandler('nb_donor_h', 'l', self.filter_context, self.request.GET),
+ CompoundCutoffFilterHandler('pubs', 'g', self.filter_context, self.request.GET),
+ ]
+ for cfh in cfhs:
+ qs = cfh.process(qs)
+ # sort results
+ # post filter filters
+ if self.filter_context:
+ # compound ids in the final selection if a selection has happened
+ cids = [c for c in qs.all().values_list('id', flat=True)]
else:
- name = compound_fields.get(sort_by_option_id)
- sort_by_options[sort_by_option_id] = {'name': name, 'order':'ascending', 'id': sort_by_option_id}
- sort_by_options['-'+sort_by_option_id] = {'name': name, 'order':'descending', 'id': sort_by_option_id}
-
- fields = request.GET.getlist('fields',['id', 'common_name', 'molecular_weight', 'a_log_p', 'compound_action_pdb_ids', 'pubs'])
- if 'id' not in fields:
- fields.append('id')
- context['selected_ppis'] = selected_ppis
- context['ppis'] = ppis
- context['selected_families'] = selected_families
- context['families'] = families
- context['selected_diseases'] = selected_diseases
- context['diseases'] = diseases
- context['selected_taxonomies'] = selected_taxonomies
- context['taxonomies'] = taxonomies
- context['selected_boundcomplexes'] = selected_boundcomplexes
- context['boundcomplexes'] = boundcomplexes
- context['fields'] = fields
- context['sort_by'] = sort_by
- context['sort_by_options'] = sort_by_options
- return render(request, 'compound_list.html', context)
+ cids = None
+ for cfh in cfhs:
+ cfh.post_process(cids, qs)
+ # return queryset
+ return qs
+
def compound_card(request, compound_id):
try:
--
GitLab