Add checkbox restricting genes to those having PTM muts #97

website/templates/gene/list.html

@@ -40,7 +40,7 @@ <h3>Gene list: {{ list_name }}</h3>
 <div>
   <div id="toolbar" class="gene-widgets">
     <form method="GET" class="widget-form" id="toolbar_form">
-      {% with widgets=[widgets.dataset, widgets.ptm_type, widgets.cancer] %}
+      {% with widgets=[widgets.dataset, widgets.ptm_type, widgets.cancer, widgets.has_ptm] %}
         {% include 'filters/bar.html' %}
       {% endwith %}
       <input type="hidden" name="fallback" value="True">

website/views/gene.py

@@ -3,6 +3,8 @@
 from flask import request
 from flask_classful import FlaskView
 from flask_classful import route
+from sqlalchemy.sql.elements import TextClause
+
 from models import Protein, MC3Mutation, Cancer
 from models import Mutation
 from models import Gene
@@ -24,6 +26,13 @@
 import sqlalchemy
 
 
+def select_textual_filters(filters):
+    return [
+        filter_ for filter_ in filters
+        if type(filter_) is TextClause
+    ]
+
+
 def select_filters(filters, models):
     """Selects filters which are applicable to at least one of given models."""
     selected = set()
@@ -137,6 +146,11 @@ def __init__(self, **kwargs):
                 choices=Site.types,
                 as_sqlalchemy=True
             ),
+            Filter(
+                Gene, 'has_ptm_muts',
+                comparators=['eq'],
+                as_sqlalchemy=lambda self, value: text('ptm_muts_cnt > 0') if value else text('ptm_muts_cnt > -1')
+            ),
             SourceDependentFilter(
                 [Mutation, MC3Mutation], 'mc3_cancer_code',
                 comparators=['in'],
@@ -163,7 +177,13 @@ def make_widgets(filter_manager, cancer=False):
             'Type of PTM site', 'select',
             filter=filter_manager.filters['Site.type'],
             disabled_label='all sites'
-        )
+        ),
+        'has_ptm': FilterWidget(
+            'Genes with PTM mutations only', 'checkbox',
+            filter=filter_manager.filters['Gene.has_ptm_muts'],
+            disabled_label='all genes',
+            labels=['Genes with PTM mutations only']
+        ),
     }
     if cancer:
         base_widgets.update({
@@ -184,6 +204,8 @@ def ajax_query(sql_filters):
 
     muts, ptm_muts, sites = prepare_subqueries(sql_filters)
 
+    textutal_filters = select_textual_filters(sql_filters)
+
     query = (
         db.session.query(
             Gene.name,
@@ -195,6 +217,7 @@ def ajax_query(sql_filters):
         .select_from(Gene)
         .join(Protein, Protein.id == Gene.preferred_isoform_id)
         .group_by(Gene.id)
+        .having(and_(*textutal_filters))
     )
     return query
 
@@ -241,6 +264,9 @@ def list_data(self, list_name):
         def query_constructor(sql_filters):
             muts, ptm_muts, sites = prepare_subqueries(sql_filters)
 
+            textutal_filters = select_textual_filters(sql_filters)
+            textutal_filters.append(text('muts_cnt > 0'))
+
             return (
                 db.session.query(
                     Gene.name,
@@ -255,23 +281,27 @@ def query_constructor(sql_filters):
                 .filter(GeneListEntry.gene_list_id == gene_list.id)
                 .join(Gene, Gene.id == GeneListEntry.gene_id)
                 .join(Protein, Protein.id == Gene.preferred_isoform_id)
-                .having(text('muts_cnt > 0'))
+                .having(and_(*textutal_filters))
                 .group_by(Gene.id)
             )
 
         def count_query_constructor(sql_filters):
             muts, ptm_muts, sites = prepare_subqueries(sql_filters)
 
+            textutal_filters = select_textual_filters(sql_filters)
+            textutal_filters.append(text('muts_cnt > 0'))
+
             return (
                 db.session.query(
                     GeneListEntry.id,
+                    ptm_muts,
                     muts
                 )
                 .select_from(GeneListEntry)
                 .join(Gene, GeneListEntry.gene_id == Gene.id)
                 .join(Protein, Protein.id == Gene.preferred_isoform_id)
                 .filter(GeneListEntry.gene_list_id == gene_list.id)
-                .having(text('muts_cnt > 0'))
+                .having(and_(*textutal_filters))
             )
 
         ajax_view = AjaxTableView.from_query(