add compound "summary" to list view, + cytotox and pk in card

fixes #251, and adds missing data to compound card :)

ippisite/ippidb/models.py

@@ -8,6 +8,7 @@ import operator
 import re
 import sys
 
+from boltons.iterutils import flatten, unique_iter
 from django.conf import settings
 from django.contrib.auth import get_user_model
 from django.core.exceptions import ValidationError
@@ -985,6 +986,20 @@ class Compound(AutoFillableModel):
             .count()
         )
 
+    @property
+    def pk_tests_count(self):
+        """
+        Return the number of associated pharmacokinetic tests
+        """
+        return self.compoundpkresult_set.all().count()
+
+    @property
+    def cytotoxicity_tests_count(self):
+        """
+        Return the number of associated cytotoxicity tests
+        """
+        return self.compoundcytotoxicityresult_set.all().count()
+
     @property
     def sorted_similar_drugbank_compounds(self):
         """
@@ -1183,6 +1198,60 @@ class Compound(AutoFillableModel):
         CompoundTanimoto.objects.filter(compound=self).delete()
         DrugbankCompoundTanimoto.objects.filter(compound=self).delete()
 
+    def get_target_activities_table(self):
+        """
+        Return test activity result data as a list of
+        items containing for each PPI family the compound
+        was tested against, the best activity, the linked diseases
+        and the modulation types
+        """
+        ppi_families = [
+            item["test_activity_description__ppi__family"]
+            for item in self.compoundactivityresult_set.filter(
+                ~Q(activity_type="KdRat")
+            )
+            .order_by()
+            .values("test_activity_description__ppi__family")
+            .distinct()
+        ]
+        results = []
+        for ppi_family in ppi_families:
+            family_compound_activity_results = self.compoundactivityresult_set.filter(
+                ~Q(activity_type="KdRat")
+            ).filter(test_activity_description__ppi__family__id=ppi_family)
+            best_activity = (
+                family_compound_activity_results.order_by("-activity")
+                .values("activity")
+                .first()["activity"]
+            )
+            diseases = list(
+                unique_iter(
+                    flatten(
+                        [
+                            list(fcar.test_activity_description.ppi.diseases.all())
+                            for fcar in family_compound_activity_results
+                        ]
+                    )
+                )
+            )
+            modulation_types = list(
+                set(
+                    [
+                        fcar.get_modulation_type_display()
+                        for fcar in family_compound_activity_results
+                    ]
+                )
+            )
+            results.append(
+                {
+                    "family": PpiFamily.objects.get(id=ppi_family),
+                    "best_activity": best_activity,
+                    "diseases": diseases,
+                    "modulation_types": modulation_types,
+                }
+            )
+        return results
+
 
 class CompoundTanimoto(models.Model):
     canonical_smiles = models.TextField("Canonical Smile")

ippisite/ippidb/templates/compound_card.html

@@ -382,20 +382,7 @@
         <div class="row d-flex justify-content-center">
           <div class="col-sm-12 col-md-9" style="margin: 10px;">
             <h5 class="card_title">Summary</h5>
-            <div class="card_border row" style="text-align: center;">
-              <div class="col-md-4">
-                <h6 class="card_title">Bibliographic ressources</h6>
-                <p>{{ compound.biblio_refs.count }}</p>
-              </div>
-              <div class="col-md-4">
-                <h6 class="card_title">Biochemical tests</h6>
-                <p>{{ compound.bioch_tests_count }}</p>
-              </div>
-              <div class="col-md-4">
-                <h6 class="card_title">Cellular tests</h6>
-                <p>{{ compound.cell_tests_count }}</p>
-              </div>
-            </div>
+            {% include "compound_test_counts.html" with compound=compound show_bibrefs=True %}
           </div>
         </div>
         <div class="row d-flex justify-content-center">

ippisite/ippidb/templates/compound_l_item.html

@@ -38,7 +38,7 @@
     {% include "compound_dbsearch_links.html" %}
     {% endif %}
     {% if compound.biblio_refs %}
-    <h4 class="pt-2 compound_list_title">Bibliography</h4>
+    <h4 class="pt-2 compound_list_title">Bibliography ({{compound.biblio_refs.count}})</h4>
     <table class="table">
       <thead>
         <tr>
@@ -55,7 +55,39 @@
         {% endfor %}
       </tbody>
     </table>
-    </ul>
+    <h4 class="pt-2 compound_list_title">Pharmacological data</h4>
+    {% include "compound_test_counts.html" with compound=compound show_bibrefs=False %}
+    <h4 class="pt-2 compound_list_title">Targets</h4>
+    <table class="table">
+      <thead>
+        <tr>
+          <th scope="col">PPI family</th>
+          <th scope="col">Best activity</th>
+          <th scope="col">Diseases</th>
+          <th scope="col" title="Molecular Mechanism of Action">MMoA</th>
+        </tr>
+      </thead>
+      <tbody>
+        {% for row in compound.get_target_activities_table %}
+        <tr>
+          <td scope="col">{{ row.family.name }}</td>
+          <td scope="col">{{ row.best_activity }}</td>
+          <td scope="col">
+            {% for disease in row.diseases %}
+            {{ disease.name }}
+            {% if not forloop.last %}, {% endif %}
+            {% endfor %}
+          </td>
+          <td scope="col">
+            {% for modulation_type in row.modulation_types %}
+            {{ modulation_type }}
+            {% if not forloop.last %}, {% endif %}
+            {% endfor %}
+          </td>
+        </tr>
+        {% endfor %}
+      </tbody>
+    </table>
     {% endif %}
   </div>
 </div>

ippisite/ippidb/templates/compound_test_counts.html

+<div class="card_border row" style="text-align: center;">
+    {% if show_bibrefs %}
+    <div class="col-md-4">
+        <h6 class="card_title">Bibliographic ressources</h6>
+        <p>{{ compound.biblio_refs.count }}</p>
+    </div>
+    {% endif %}
+    <div class="col-md-{% if show_bibrefs %}2{%else%}3{%endif%}">
+        <h6 class="card_title" title="Biochemical tests">Biochemical tests</h6>
+        <p>{{ compound.bioch_tests_count }}</p>
+    </div>
+    <div class="col-md-{% if show_bibrefs %}2{%else%}3{%endif%}">
+        <h6 class="card_title" title="Cellular tests">Cellular tests</h6>
+        <p>{{ compound.cell_tests_count }}</p>
+    </div>
+    <div class="col-md-{% if show_bibrefs %}2{%else%}3{%endif%}">
+        <h6 class="card_title" title="Pharmacokinetic tests">PK tests</h6>
+        <p>{{ compound.pk_tests_count }}</p>
+    </div>
+    <div class="col-md-{% if show_bibrefs %}2{%else%}3{%endif%}">
+        <h6 class="card_title" title="Cytotoxicity tests">Cytotoxicity tests</h6>
+        <p>{{ compound.cytotoxicity_tests_count }}</p>
+    </div>
+</div>
\ No newline at end of file

ippisite/requirements-core.txt

@@ -29,3 +29,4 @@ git+https://gitlab.pasteur.fr/hmenager/django-diu.git#egg=django_diu
 django-crispy-forms
 celery==4.4.7
 django-polymorphic
+boltons