Replace legacy primary filter with is_canonical and add synonym filter in ConditionFilter

- Introduced a new `canonical` ForeignKey field in the Condition model to manage alias relationships.
- Enhanced synonym retrieval methods to prefer canonical names and handle aliases more effectively.
- Updated condition detail templates to reflect canonical status and improved synonym display.
- Implemented migration scripts to establish canonical relationships based on existing synonym links.

atlas/filters.py

@@ -164,13 +164,16 @@ class SeriesFilter(django_filters.FilterSet):
 
 
 class ConditionFilter(django_filters.FilterSet):
+    # Replace legacy `primary` filter with `is_canonical` and provide a
+    # `synonym` filter which will filter by the canonical group of the
+    # selected condition.
+    is_canonical = django_filters.BooleanFilter(method="filter_is_canonical", label="Canonical")
+    synonym = django_filters.ModelChoiceFilter(queryset=Condition.objects.all(), method="filter_synonym", label="Synonym group")
+
     class Meta:
         model = Condition
         fields = {
             "name": ["icontains"],
-            "primary": ["exact"],
-            "synonym": ["exact"],
-            #"parent": ["exact"],
             "subspecialty": ["exact"],
             "rcr_curriculum": ["exact"],
         }
@@ -189,6 +192,21 @@ class ConditionFilter(django_filters.FilterSet):
         )
         pass
 
+    def filter_is_canonical(self, queryset, name, value):
+        if value in (True, "True", "true", 1, "1"):
+            return queryset.filter(canonical__isnull=True)
+        if value in (False, "False", "false", 0, "0"):
+            return queryset.filter(canonical__isnull=False)
+        return queryset
+
+    def filter_synonym(self, queryset, name, value):
+        # value is a Condition instance selected in the filter. Return all
+        # Conditions that belong to the same canonical group as `value`.
+        if not value:
+            return queryset
+        master = value.canonical if value.canonical else value
+        return queryset.filter(Q(canonical=master) | Q(pk=master.pk))
+
 
 class FindingFilter(django_filters.FilterSet):
     class Meta:

atlas/migrations/0086_add_canonical.py

@@ -0,0 +1,69 @@
+from django.db import migrations, models
+
+
+def forwards(apps, schema_editor):
+    Condition = apps.get_model("atlas", "Condition")
+    # Build connected components using existing M2M 'synonym' links
+    visited = set()
+
+    for cond in Condition.objects.all():
+        if cond.pk in visited:
+            continue
+        # BFS/DFS to collect component
+        stack = [cond]
+        comp = []
+        while stack:
+            c = stack.pop()
+            if c.pk in visited:
+                continue
+            visited.add(c.pk)
+            comp.append(c)
+            # access existing M2M relations
+            for s in c.synonym.all():
+                if s.pk not in visited:
+                    stack.append(s)
+
+        # choose canonical: prefer primary==True else lowest pk
+        canon = None
+        for c in comp:
+            if getattr(c, "primary", False):
+                canon = c
+                break
+        if not canon:
+            canon = min(comp, key=lambda x: x.pk)
+
+        # set canonical for all non-canonical members
+        for c in comp:
+            if c.pk != canon.pk:
+                c.canonical_id = canon.pk
+                c.save()
+
+
+def backwards(apps, schema_editor):
+    Condition = apps.get_model("atlas", "Condition")
+    for c in Condition.objects.all():
+        if c.canonical_id:
+            c.canonical_id = None
+            c.save()
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("atlas", "0085_rename_case_detail_caseprior_casedetail_and_more"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="condition",
+            name="canonical",
+            field=models.ForeignKey(
+                related_name="aliases",
+                null=True,
+                on_delete=models.SET_NULL,
+                to="atlas.condition",
+                blank=True,
+            ),
+        ),
+        migrations.RunPython(forwards, backwards),
+    ]

atlas/migrations/0087_alter_condition_canonical.py

@@ -0,0 +1,19 @@
+# Generated by Django 5.2.7 on 2025-11-20 22:35
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0086_add_canonical'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='condition',
+            name='canonical',
+            field=models.ForeignKey(blank=True, help_text='If set, this Condition is an alias and points to the canonical Condition.', null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='aliases', to='atlas.condition'),
+        ),
+    ]

atlas/models.py

@@ -116,30 +116,66 @@ class SynMixin(object):
             return f"{self.name} [syn]"
 
     def get_old_str(self) -> str:
+        # Prefer using a model-specific get_synonyms (e.g. Condition.get_synonyms)
+        try:
+            syns = self.get_synonyms()
+        except Exception:
+            syns = None
+
         if self.primary:
-            if self.synonym.count() == 0:
+            if syns is None:
+                if getattr(self, "synonym", None) is None or self.synonym.count() == 0:
                     return self.name
-            else:
                 synonyms = ",".join([i.name for i in self.synonym.all()])
                 return f"{self.name} ({synonyms})"
+            else:
+                if not syns:
+                    return self.name
+                synonyms = ",".join([i.name for i in syns])
+                return f"{self.name} ({synonyms})"
         else:
             return f"{self.name} [syn]"
 
     def get_synonym(self):
-        if self.primary:
+        # Return a readable synonym string. For models that implement
+        # get_synonyms (Condition with canonical/aliases), use that.
+        try:
+            syns = self.get_synonyms()
+        except Exception:
+            syns = None
+
+        if getattr(self, "primary", False):
             return "[Primary]"
         else:
+            if syns is None:
                 s = self.synonym.filter(primary=True).values_list("name", flat=True)
                 return ", ".join(s)
+            else:
+                # prefer primary names among synonyms if present
+                primary_names = [i.name for i in syns if getattr(i, "primary", False)]
+                if primary_names:
+                    return ", ".join(primary_names)
+                return ", ".join([i.name for i in syns])
 
     def get_synonym_link(self):
-        if self.primary:
+        try:
+            syns = self.get_synonyms()
+        except Exception:
+            syns = None
+
+        if getattr(self, "primary", False):
             return "[Primary]"
         else:
-            syns = self.synonym.filter(primary=True)
-            return ", ".join(
-                [f"<a href='{s.get_absolute_url()}'>{s.name}</a>" for s in syns]
-            )
+            if syns is None:
+                # fall back to all M2M synonyms (not just primary) for models
+                # that still use the old synonym field (e.g. Finding, Structure)
+                syns_qs = self.synonym.all()
+                items = [f"<a href='{s.get_absolute_url()}'>{s.name}</a>" for s in syns_qs]
+                return ", ".join(items)
+            else:
+                # render links for synonyms/canonical group
+                items = [f"<a href='{s.get_absolute_url()}'>{s.name}</a>" for s in syns]
+                return ", ".join(items)
 
     def get_link(self):
         return format_html("<a href='{}'>{}</a>", self.get_absolute_url(), self.name)
@@ -163,6 +199,16 @@ class Condition(SynMixin, models.Model):
         blank=True,
         help_text="Use if a direct synonym for the condition exists, e.g. 'Wegener granulomatosis' and 'Granulomatosis with Polyangitis'.",
     )
+    # New canonical/alias field (Option B): if set, this Condition is an alias
+    # and points to the canonical/master Condition.
+    canonical = models.ForeignKey(
+        "self",
+        null=True,
+        blank=True,
+        on_delete=models.SET_NULL,
+        related_name="aliases",
+        help_text="If set, this Condition is an alias and points to the canonical Condition.",
+    )
     parent = models.ManyToManyField(
         "self",
         blank=True,
@@ -198,6 +244,23 @@ class Condition(SynMixin, models.Model):
     def get_absolute_url(self):
         return reverse("atlas:condition_detail", kwargs={"pk": self.pk})
 
+    @property
+    def canonical_condition(self):
+        """Return the canonical/master condition for this Condition (self if none)."""
+        return self.canonical if self.canonical else self
+
+    def get_synonyms(self):
+        """Return other Conditions that are synonyms/aliases for this concept.
+
+        Behaviour:
+        - If this Condition is an alias (canonical set), return the canonical and
+          any other aliases (excluding self).
+        - If this Condition is canonical, return all aliases (and exclude self).
+        """
+        master = self.canonical_condition
+        qs = Condition.objects.filter(models.Q(canonical=master) | models.Q(pk=master.pk)).exclude(pk=self.pk)
+        return qs
+
     def get_children(self):
         return self.child.all()
 

atlas/templates/atlas/condition_detail.html

@@ -18,7 +18,7 @@
                 <h5 class="mb-2">Details</h5>
                 <dl class="row">
                         <dt class="col-sm-4">Primary name</dt>
-                        <dd class="col-sm-8">{{ condition.primary }}</dd>
+                        <dd class="col-sm-8">{% if condition.canonical %}No (alias of <a href="{{ condition.canonical.get_absolute_url }}">{{ condition.canonical.name }}</a>){% else %}Yes{% endif %}</dd>
 
                         <dt class="col-sm-4">Subspecialty</dt>
                         <dd class="col-sm-8">
@@ -31,33 +31,9 @@
 
                         <dt class="col-sm-4">Synonyms</dt>
                         <dd class="col-sm-8">
-                            {% for syn in condition.synonym.all %}
-                                <a class="badge bg-secondary text-decoration-none text-white me-1" href="{{ syn.get_absolute_url }}">{{ syn }}</a>
-                            {% empty %}
-                                &mdash;
-                            {% endfor %}
-                            {% if request.user.is_authenticated and can_merge %}
-                                <div class="mt-2">
-                                    <a class="btn btn-sm btn-outline-primary" data-bs-toggle="collapse" href="#addSynonymCollapse" role="button" aria-expanded="false" aria-controls="addSynonymCollapse">Add synonym</a>
+                            <div id="synonyms-container">
+                                {% include 'atlas/partials/_synonyms_list.html' %}
                             </div>
-                                <div class="collapse mt-2" id="addSynonymCollapse">
-                                    <div class="card card-body">
-                                        <form method="POST">
-                                            {% csrf_token %}
-                                            <input type="hidden" name="action" value="add_synonym" />
-                                            <div class="mb-2">
-                                                <label class="form-label small">Select existing condition</label>
-                                                {{ synonym_form.condition }}
-                                            </div>
-                                            <div class="mb-2">
-                                                <label class="form-label small">Or create new synonym name</label>
-                                                <input class="form-control" type="text" name="synonym_name" placeholder="e.g. Granulomatosis with Polyangiitis" />
-                                            </div>
-                                            <button class="btn btn-primary btn-sm" type="submit">Add</button>
-                                        </form>
-                                    </div>
-                                </div>
-                            {% endif %}
                         </dd>
 
                         <dt class="col-sm-4">Parent</dt>

atlas/templates/atlas/finding_detail.html

@@ -12,8 +12,8 @@
     </div>
     <div>
         <h3>Name: {{finding.name}}</h3>
-        Primary name: {{finding.primary}}<br />
-        Synonyms: {{finding.synonym.all|join:", "}}<br />
+    Primary name: {% if finding.canonical %}No (alias of <a href="{{ finding.canonical.get_absolute_url }}">{{ finding.canonical.name }}</a>){% else %}Yes{% endif %}<br />
+    Synonyms: {{ finding.get_synonym_link|safe }}<br />
     </div>
     {% if finding.seriesfinding_set.all %}
         <h4>Associated Cases</h4>

atlas/templates/atlas/partials/_synonyms_list.html

@@ -0,0 +1,56 @@
+{% comment %}Partial that renders the synonyms list + add form. Used by condition_detail and HTMX responses.{% endcomment %}
+{% load static %}
+
+{% with syns=condition.get_synonyms %}
+    {% if syns %}
+        {% for syn in syns %}
+            <a class="badge bg-secondary text-decoration-none text-white me-1" href="{{ syn.get_absolute_url }}">{{ syn }}</a>
+        {% endfor %}
+    {% else %}
+        &mdash;
+    {% endif %}
+{% endwith %}
+
+{% if request.user.is_authenticated and can_merge %}
+    <div class="mt-2 d-flex gap-2">
+        <!-- Button to add an existing condition as a synonym -->
+        <a class="btn btn-sm btn-outline-primary" data-bs-toggle="collapse" href="#addSynonymCollapse" role="button" aria-expanded="false" aria-controls="addSynonymCollapse">Add synonym</a>
+
+        <!-- Button to create a new condition and add it as a synonym -->
+        <a class="btn btn-sm btn-outline-success" data-bs-toggle="collapse" href="#createSynonymCollapse" role="button" aria-expanded="false" aria-controls="createSynonymCollapse">Create synonym</a>
+    </div>
+
+    <!-- Collapse: add existing condition -->
+    <div class="collapse mt-2" id="addSynonymCollapse">
+        <div class="card card-body">
+            <form method="POST"
+                  hx-post="{% url 'atlas:condition_detail' condition.pk %}"
+                  hx-target="#synonyms-container" hx-swap="innerHTML">
+                {% csrf_token %}
+                <input type="hidden" name="action" value="add_synonym" />
+                <div class="mb-2">
+                    <label class="form-label small">Select existing condition</label>
+                    {{ synonym_form.condition }}
+                </div>
+                <button class="btn btn-primary btn-sm" type="submit">Add</button>
+            </form>
+        </div>
+    </div>
+
+    <!-- Collapse: create new condition -->
+    <div class="collapse mt-2" id="createSynonymCollapse">
+        <div class="card card-body">
+            <form method="POST"
+                  hx-post="{% url 'atlas:condition_detail' condition.pk %}"
+                  hx-target="#synonyms-container" hx-swap="innerHTML">
+                {% csrf_token %}
+                <input type="hidden" name="action" value="add_synonym" />
+                <div class="mb-2">
+                    <label class="form-label small">Create new synonym name</label>
+                    <input class="form-control" type="text" name="synonym_name" placeholder="e.g. Granulomatosis with Polyangitis" required />
+                </div>
+                <button class="btn btn-success btn-sm" type="submit">Create</button>
+            </form>
+        </div>
+    </div>
+{% endif %}

atlas/templates/atlas/structure_detail.html

@@ -14,8 +14,8 @@
     </div>
     <div>
         <h3>Name: {{structure.name}}</h3>
-        Primary name: {{structure.primary}}<br />
-        Synonyms: {{structure.synonym.all|join:", "}}<br />
+    Primary name: {% if structure.canonical %}No (alias of <a href="{{ structure.canonical.get_absolute_url }}">{{ structure.canonical.name }}</a>){% else %}Yes{% endif %}<br />
+    Synonyms: {{ structure.get_synonym_link|safe }}<br />
     </div>
     <h4>Associated Cases</h4>
     <ul>

atlas/views.py

@@ -860,19 +860,50 @@ def condition_detail(request, pk):
         if form.is_valid():
             other = form.cleaned_data.get("condition")
 
+        # keep the form (possibly with errors) to render back in HTMX responses
+        synonym_form = form
+
         # If no autocomplete selection, accept a free-text name
         synonym_name = request.POST.get("synonym_name")
         if not other and synonym_name:
             other, created = Condition.objects.get_or_create(name=synonym_name)
             if created:
-                # mark created synonym as non-primary
-                other.primary = False
-                other.save()
+                # created condition: treat as alias by setting canonical below
+                pass
 
         if other and other != condition:
-            # add mutual synonym relationship
-            condition.synonym.add(other)
-            other.synonym.add(condition)
+            # Option B: treat synonym as alias/canonical relationship.
+            # Determine canonical/master for the current condition
+            master = condition.canonical if condition.canonical else condition
+
+            # If `other` belongs to a different canonical group, move its group
+            # to point at our master. If `other` has no canonical, set it.
+            if other.canonical:
+                # move the whole other group (canonical + aliases) to our master
+                    group_master = other.canonical
+                    members = Condition.objects.filter(Q(canonical=group_master) | Q(pk=group_master.pk))
+                    for m in members:
+                        if m.pk != master.pk:
+                            m.canonical = master
+                            m.save()
+            else:
+                # other is standalone; make it an alias of our master
+                other.canonical = master
+                other.save()
+
+            # Master is indicated by having no `canonical` pointer. Ensure
+            # it remains canonical (no save required unless changed elsewhere).
+
+        # If this was an HTMX request return the updated synonyms partial so the
+        # page can be updated without a full redirect. Otherwise perform the
+        # existing redirect back to the detail page.
+        if request.htmx:
+            html = render_to_string(
+                "atlas/partials/_synonyms_list.html",
+                {"condition": condition, "synonym_form": synonym_form, "can_merge": can_merge},
+                request=request,
+            )
+            return HttpResponse(html)
 
         return redirect("atlas:condition_detail", pk=condition.pk)