handle "compound replacement" in DB and interface

- replaced compounds can only be viewed by superusers
- and are clearly indicated as such

FIX #241

ippisite/ippidb/migrations/0065_compound_replaced_with.py

+# Generated by Django 2.2.1 on 2020-09-14 18:02
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('ippidb', '0064_proteindomaincomplex_polymorphic_ctype'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='compound',
+            name='replaced_with',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.PROTECT, to='ippidb.Compound', verbose_name='Replacement ID'),
+        ),
+    ]

ippisite/ippidb/models.py

@@ -570,11 +570,13 @@ class CompoundsManager(models.Manager):
         qs = self.get_queryset()
         if current_user.is_anonymous:
             qs = qs.exclude(compoundaction__ppi__contribution__validated=False)
+            qs = qs.filter(replaced_with__isnull=True)
         elif not current_user.is_superuser:
             qs = qs.exclude(
                 Q(compoundaction__ppi__contribution__validated=False),
                 ~Q(compoundaction__ppi__contribution__contributor=current_user),
             )
+            qs = qs.filter(replaced_with__isnull=True)
         return qs
 
     def validated(self):
@@ -865,6 +867,14 @@ class Compound(AutoFillableModel):
         verbose_name="Number of tests available", null=True, blank=True
     )
 
+    replaced_with = models.ForeignKey(
+        "self",
+        verbose_name="Replacement ID",
+        null=True,
+        blank=True,
+        on_delete=models.PROTECT,
+    )
+
     class Meta:
         ordering = ["id"]
         indexes = [
@@ -1097,7 +1107,9 @@ class Compound(AutoFillableModel):
         Replace the references to a given compound in the data with
         references to another new compound. used to deal with
         duplicates in the database
+        also delete this object
         """
+        self.replaced_with = replacing_compound
         for ref in RefCompoundBiblio.objects.filter(compound=self):
             ref.compound = replacing_compound
             ref.save()

ippisite/ippidb/templates/compound_card.html

@@ -37,7 +37,9 @@
       {% include "compound_smiles_draw.html" with id=compound.id smile=compound.canonical_smile width=250 height=250%}
       <div style="display: flex;
       align-items: center;">
-        {% if compound.is_validated is False %}
+        {% if compound.replaced_with is not None %}
+        <h1 class="page-title-warning" style="margin: 0;">Compound {{ compound.id }} - This compound is replaced with <a href="/compounds/{{ compound.replaced_with.id }}">compound {{ compound.replaced_with.id }}</a> </h1>
+        {% elif compound.is_validated is False %}
         <h1 class="page-title-warning" style="margin: 0;">Compound {{ compound.id }} - This compound has not been
           validated by a curator yet, data might be incomplete or
           inaccurate</h1>

ippisite/ippidb/templates/compound_l_item.html

 <div class="row m-2 border border-info bg-light border_card" style="box-shadow: 0 3px 5px 0 rgba(0, 0, 0, 0.2);">
   {%if show_detail != True %}
-  <div class="col-sm-3 border-info d-flex justify-content-center align-content-center">
+  <div class="col-sm-3 border-info d-flex justify-content-center align-content-center {% if compound.replaced_with or compound.is_validated is False %}bg_warning{% endif %}">
     <a href="/compounds/{{ compound.id }}">{% include "compound_smiles_draw.html" with id=compound.id smile=compound.canonical_smile %}</a>
-    <h2 class="position-absolute" style="top:0.3em; left:0.3em;"><span class="badge badge-light"><a href="/compounds/{{ compound.id }}">{{ compound.id }}</a></span></h2>
+    <h2 class="position-absolute" style="top:0.3em; left:0.3em;"><span class="badge badge-light"><a href="/compounds/{{ compound.id }}">{{ compound.id }}</a></span>{% if compound.replaced_with is not None %}
+      <span style="font-size: 26px; color:#fa8005; font-size: 75%;">replaced with <a href="/compounds/{{ compound.replaced_with.id }}">{{ compound.replaced_with.id }}</a></span>{% elif compound.is_validated is False %}<span
+          style="font-size: 26px; color:#fa8005;">not validated</span>{% endif %}</h2>
     {% if compound.tanimoto != None %}
     <h2 class="position-absolute" style="top:0.3em; right:0.3em;" title="tanimoto similarity value"><span class="badge badge-light text-warning">{{ compound.tanimoto }}</span></h2>
     {% endif %}

ippisite/ippidb/templates/compound_t_list.html

@@ -28,11 +28,13 @@
   </thead>
   <tbody>
     {% for compound in compounds %}
-      <tr>
+      <tr class="{% if compound.replaced_with or compound.is_validated is False %}bg_warning{% endif %}">
         {% if compound.tanimoto != None %}
         <td title="tanimoto similarity value">{{ compound.tanimoto }}</td>
         {% endif %}
-        <td scope="col"><span class="badge badge-light"><a href="/compounds/{{ compound.id }}">{{ compound.id }}</a></span></td>
+        <td scope="col"><span class="badge badge-light"><a href="/compounds/{{ compound.id }}">{{ compound.id }}</a>{% if compound.replaced_with is not None %}
+          <span style="font-size: 26px; color:#fa8005; font-size: 75%;">replaced with <a href="/compounds/{{ compound.replaced_with.id }}">{{ compound.replaced_with.id }}</a></span>{% elif compound.is_validated is False %}<span
+              style="font-size: 26px; color:#fa8005;">not validated</span>{% endif %}</span></td>
       {% if "canonical_smiles" in fields %}
         <td scope="col" style="width:150px">{% include "compound_smiles_draw.html" with id=compound.id smile=compound.canonical_smile width="150" height="150"%}</td>
       {% endif %}

ippisite/ippidb/templates/compound_v_item.html

 <div class="p-2">
-    <div class="card border border-info border_card {% if compound.is_validated is False %}bg_warning{% endif %}">
-        <a href="/compounds/{{ compound.id }}">{% include "compound_smiles_draw.html" with id=compound.id smile=compound.canonical_smile %}</a>
-        <h2 class="position-absolute" style="top:0.3em; left:0.3em;"><span class="badge badge-light"><a href="/compounds/{{ compound.id }}">{{ compound.id }}</a></span>{% if compound.is_validated is False %}<span style="font-size: 26px; color:#fa8005;">not validated</span>{% endif %}</h2>
+    <div class="card border border-info border_card {% if compound.replaced_with or compound.is_validated is False %}bg_warning{% endif %}">
+        <a
+            href="/compounds/{{ compound.id }}">{% include "compound_smiles_draw.html" with id=compound.id smile=compound.canonical_smile %}</a>
+        <h2 class="position-absolute" style="top:0.3em; left:0.3em;"><span class="badge badge-light"><a
+                    href="/compounds/{{ compound.id }}">{{ compound.id }}</a></span>{% if compound.replaced_with is not None %}
+            <span style="font-size: 26px; color:#fa8005; font-size: 75%;">replaced with <a href="/compounds/{{ compound.replaced_with.id }}">{{ compound.replaced_with.id }}</a></span>{% elif compound.is_validated is False %}<span
+                style="font-size: 26px; color:#fa8005;">not validated</span>{% endif %}</h2>
         {% if compound.tanimoto != None %}
-        <h2 class="position-absolute" style="top:0.3em; right:0.3em;" title="tanimoto similarity value"><span class="badge badge-dark text-warning">{{ compound.tanimoto }}</span></h2>
+        <h2 class="position-absolute" style="top:0.3em; right:0.3em;" title="tanimoto similarity value"><span
+                class="badge badge-dark text-warning">{{ compound.tanimoto }}</span></h2>
         {% endif %}
         <div class="card-body desc_card" style="overflow:hidden; word-wrap:break-word;">
-            {%if compound.common_name %}<p title="Common name"><span style="font-family:'BrandonGrotesqueBlk';">Common name : </span>{{ compound.common_name }}</p>{%else%}<p></br></p>{% endif %}
-            <p title="PPI Family"><span style="font-family:'BrandonGrotesqueBlk';">PPI Family : </span>{{ compound.best_activity_ppi_family_name }}</p>
-            <p title="Molecular Weight"><span style="font-family:'BrandonGrotesqueBlk';">Molecular weight: </span>{{ compound.molecular_weight }} g/mol</p>
+            {%if compound.common_name %}<p title="Common name"><span style="font-family:'BrandonGrotesqueBlk';">Common
+                    name : </span>{{ compound.common_name }}</p>{%else%}<p></br></p>{% endif %}
+            <p title="PPI Family"><span style="font-family:'BrandonGrotesqueBlk';">PPI Family :
+                </span>{{ compound.best_activity_ppi_family_name }}</p>
+            <p title="Molecular Weight"><span style="font-family:'BrandonGrotesqueBlk';">Molecular weight:
+                </span>{{ compound.molecular_weight }} g/mol</p>
             <p style="text-align:right;"><a class="read-more" href="/compounds/{{ compound.id }}">Read more</a></p>
         </div>
     </div>
-</div>
+</div>
\ No newline at end of file