Merge pull request #9 from KWB-R/feature/many-to-many-references

add m2m field for QMRAReference in QMRATreatment

Author: adaurat

.gitignore

@@ -9,4 +9,5 @@ qmra-prod.db
 dump*
 prod-migrations/
 *.tar
-.vscode
+.vscode
+test.zip

infra/helm/qmra/templates/deployment.yaml

@@ -19,15 +19,6 @@ spec:
         {{- include "app.labels" . | nindent 8 }}
     spec:
       initContainers:
-        - name: move-static
-          image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
-          envFrom:
-          - configMapRef:
-              name: {{ .Values.configmap_name }}
-          volumeMounts:
-            - name: static
-              mountPath: {{ .Values.static.mount_path }}
-          command: [ python, manage.py, collectstatic, --noinput ]
         - name: migrate
           image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
           envFrom:
@@ -46,6 +37,15 @@ spec:
             - name: qmra-default
               mountPath: {{ .Values.qmra_default.mount_path }}
           command: [ python, manage.py, migrate, --database, qmra ]
+        - name: move-static
+          image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
+          envFrom:
+            - configMapRef:
+                name: {{ .Values.configmap_name }}
+          volumeMounts:
+            - name: static
+              mountPath: {{ .Values.static.mount_path }}
+          command: [ python, manage.py, collectstatic, --noinput ]
       containers:
         - name: {{ .Chart.Name }}
           image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"

qmra/risk_assessment/admin.py

@@ -64,10 +64,14 @@ class QMRATreatmentAdmin(admin.ModelAdmin):
         ("name", "group"),
         ("bacteria_min", "bacteria_max"),
         "bacteria_reference",
+        "bacteria_references",
         ("viruses_min", "viruses_max"),
         "viruses_reference",
+        "viruses_references",
         ("protozoa_min", "protozoa_max"),
-        "protozoa_reference"
+        "protozoa_reference",
+        "protozoa_references"
     ]
+    filter_horizontal = ["bacteria_references", "viruses_references", "protozoa_references"]
 
     save_model = save_model

qmra/risk_assessment/dbrouter.py

@@ -17,4 +17,5 @@ def allow_migrate(self, db, app_label, model_name=None, **hints):
         """
         if model_name is not None and "qmra" in model_name:
             return db == "qmra"
-        return db == "default"
+        # model_name is None when the migration is a RunPython or a RunSQL
+        return db == "default" or model_name is None

qmra/risk_assessment/migrations/0007_qmratreatment_bacteria_references_and_more.py

@@ -0,0 +1,28 @@
+# Generated by Django 5.0.6 on 2026-01-15 12:42
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('risk_assessment', '0006_qmrapathogen_qmrareference_qmrasource_qmraexposure_and_more'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='qmratreatment',
+            name='bacteria_references',
+            field=models.ManyToManyField(related_name='bacteria_lrvs', to='risk_assessment.qmrareference'),
+        ),
+        migrations.AddField(
+            model_name='qmratreatment',
+            name='protozoa_references',
+            field=models.ManyToManyField(related_name='protozoa_lrvs', to='risk_assessment.qmrareference'),
+        ),
+        migrations.AddField(
+            model_name='qmratreatment',
+            name='viruses_references',
+            field=models.ManyToManyField(related_name='viruses_lrvs', to='risk_assessment.qmrareference'),
+        ),
+    ]

qmra/risk_assessment/migrations/0008_auto_20260115_1342.py

@@ -0,0 +1,25 @@
+# Generated by Django 5.0.6 on 2026-01-15 12:42
+
+from django.db import migrations
+
+
+def migrate_references(apps, schema_editor):
+    if schema_editor.connection.alias != "qmra":
+        return
+    QMRATreatment = apps.get_model("risk_assessment", "QMRATreatment")
+    for treatment in QMRATreatment.objects.all():
+
+        treatment.bacteria_references.add(treatment.bacteria_reference)
+        treatment.viruses_references.add(treatment.viruses_reference)
+        treatment.protozoa_references.add(treatment.protozoa_reference)
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('risk_assessment', '0007_qmratreatment_bacteria_references_and_more'),
+    ]
+
+    operations = [
+        migrations.RunPython(migrate_references),
+    ]

qmra/risk_assessment/migrations/0009_auto_20260121_1454.py

@@ -0,0 +1,31 @@
+# Generated by Django 5.0.6 on 2026-01-15 12:42
+from django.core.management import call_command
+from django.db import migrations
+
+
+def migrate_references(apps, schema_editor):
+    if schema_editor.connection.alias != "qmra":
+        return
+    QMRATreatment = apps.get_model("risk_assessment", "QMRATreatment")
+    all_treatments = QMRATreatment.objects.all()
+    if len(all_treatments) == 0:
+        call_command("seed_default_db")
+        all_treatments = QMRATreatment.objects.all()
+    for treatment in all_treatments:
+
+        treatment.bacteria_references.add(treatment.bacteria_reference)
+        treatment.viruses_references.add(treatment.viruses_reference)
+        treatment.protozoa_references.add(treatment.protozoa_reference)
+        treatment.save()
+    call_command("export_default")
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('risk_assessment', '0008_auto_20260115_1342'),
+    ]
+
+    operations = [
+        migrations.RunPython(migrate_references),
+    ]

qmra/risk_assessment/qmra_models.py

@@ -270,14 +270,19 @@ class QMRATreatment(models.Model):
     bacteria_max: Optional[float] = models.FloatField(blank=True, null=True)
     bacteria_reference = models.ForeignKey(QMRAReference, blank=True, null=True, on_delete=models.CASCADE,
                                            related_name="bacteria_lrv")
+    bacteria_references = models.ManyToManyField(QMRAReference, related_name="bacteria_lrvs")
+
     viruses_min: Optional[float] = models.FloatField(blank=True, null=True)
     viruses_max: Optional[float] = models.FloatField(blank=True, null=True)
     viruses_reference = models.ForeignKey(QMRAReference, blank=True, null=True, on_delete=models.CASCADE,
                                           related_name="viruses_lrv")
+    viruses_references = models.ManyToManyField(QMRAReference, related_name="viruses_lrvs")
+
     protozoa_min: Optional[float] = models.FloatField(blank=True, null=True)
     protozoa_max: Optional[float] = models.FloatField(blank=True, null=True)
     protozoa_reference = models.ForeignKey(QMRAReference, blank=True, null=True, on_delete=models.CASCADE,
                                            related_name="protozoa_lrv")
+    protozoa_references = models.ManyToManyField(QMRAReference, related_name="protozoa_lrvs")
 
     @classmethod
     def from_dict(cls, data):
@@ -288,6 +293,7 @@ def from_dict(cls, data):
             description=data['description'],
             bacteria_min=data['bacteria_min'],
             bacteria_max=data['bacteria_max'],
+            # TODO: *_referenceS (m2m fields...)
             bacteria_reference_id=int(data["bacteria_reference"]) \
                 if data["bacteria_reference"] is not None else None,
             viruses_min=data['viruses_min'],
@@ -303,8 +309,11 @@ def from_dict(cls, data):
     def to_dict(self):
         data = model_to_dict(self)
         data["bacteria_reference"] = str(self.bacteria_reference.pk) if self.bacteria_reference is not None else None
+        data["bacteria_references"] = [str(ref.pk) for ref in self.bacteria_references.all()]
         data["viruses_reference"] = str(self.viruses_reference.pk) if self.viruses_reference is not None else None
+        data["viruses_references"] = [str(ref.pk) for ref in self.viruses_references.all()]
         data["protozoa_reference"] = str(self.protozoa_reference.pk) if self.protozoa_reference is not None else None
+        data["protozoa_references"] = [str(ref.pk) for ref in self.protozoa_references.all()]
         return data
 
 

qmra/risk_assessment/templates/treatments-form-js.html

@@ -388,22 +388,24 @@
             var inner = "";
             for (const treatment of this.treatments){
                 if (!uniques.has(treatment.name)){
-                    const virus_ref = this.references[treatment.viruses_reference]
-                    const bacteria_ref = this.references[treatment.bacteria_reference]
-                    const protozoa_ref = this.references[treatment.protozoa_reference]
+                    const all_refs_id = new Set();
+                    for (const r of [...treatment.viruses_references, ...treatment.bacteria_references, ...treatment.protozoa_references]){
+                        all_refs_id.add(r);
+                    }
+                    const superscripts = [...all_refs_id].map((r, i) => { return `<sup>[${i+1}]</sup>` }).join('');
+                    const ref_footnotes = [...all_refs_id].map((r, i) => {
+                        const ref = this.references[r];
+                        return `<div class="small"><sup>[${i+1}]</sup>values taken from <a href="${ref.ReferenceLink}">${ref.ReferenceName}</a></div>`;
+                    }).join('');
                     uniques.add(treatment.name)
-                    const ref = virus_ref === undefined ?
-                        bacteria_ref === undefined ? protozoa_ref === undefined ? "#" : protozoa_ref : bacteria_ref : virus_ref
-                    const link = ref.ReferenceLink;
-                    const name = ref.ReferenceName;
                     inner += `<li>
-                    <h5>${treatment.name}</h5>
+                    <h5>${treatment.name}${superscripts}</h5>
                     <div class="text-muted small mb-4">${treatment.description}</div>
                     <table class="table small">
                         <tr>
                             <th>Pathogen group</th>
-                            <th>Minimum LRV<sup>[1]</sup></th>
-                            <th>Maximum LRV<sup>[1]</sup></th>
+                            <th>Minimum LRV</th>
+                            <th>Maximum LRV</th>
                         </tr>
                         <tr>
                             <td>Viruses</td>
@@ -422,7 +424,7 @@ <h5>${treatment.name}</h5>
                         </tr>
                         
                     </table>
-                    <div class="small"><sup>[1]</sup>values taken from <a href="${link}">${name}</a></p>
+                    ${ref_footnotes}
                     </li>
                     `
                 }

qmra/risk_assessment/tests/test_assess_risk.py

@@ -77,7 +77,7 @@ def test_with_all_pathogens(self):
             ) for p, _ in QMRAPathogens.data.items()
         ]
         given_treatments = [
-            Treatment.from_default(QMRATreatments.get("Conventional clarification"), given_ra),
+            Treatment.from_default(QMRATreatments.get("Coagulation, flocculation and media filtration"), given_ra),
             Treatment.from_default(QMRATreatments.get("Slow sand filtration"), given_ra),
         ]
         given_ra.inflows.set(given_inflows, bulk=False)