Merge discordance triage extended work

classification/admin/classification_admin.py

@@ -895,7 +895,6 @@ def ensure_bulk(self, request):
         ensure_discordance_report_triages_bulk()
 
 
-
 @admin.register(DiscordanceNotification)
 class DiscordanceNotificationAdmin(ModelAdminBasics):
     list_display = ("lab", "discordance_report", "notification_sent_date")

classification/migrations/0109_discordancereporttriage_closed_and_more.py

@@ -0,0 +1,23 @@
+# Generated by Django 4.2.2 on 2023-09-08 00:05
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('classification', '0108_discordancereporttriage'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='discordancereporttriage',
+            name='closed',
+            field=models.BooleanField(default=False),
+        ),
+        migrations.AlterField(
+            model_name='discordancereporttriage',
+            name='triage_status',
+            field=models.TextField(choices=[('P', 'Pending Triage'), ('F', 'Will Amend'), ('D', 'For Joint Discussion'), ('R', 'Confident in Classification'), ('X', 'Low Penetrance/Risk Allele etc')], default='P', max_length=1),
+        ),
+    ]

classification/migrations/0110_merge_20230912_1033.py

@@ -0,0 +1,14 @@
+# Generated by Django 4.2.2 on 2023-09-12 01:03
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('classification', '0109_condition_matching_override_blank condition'),
+        ('classification', '0109_discordancereporttriage_closed_and_more'),
+    ]
+
+    operations = [
+    ]

classification/models/clinical_context_models.py

@@ -268,12 +268,17 @@ class ClinicalContextRecalcTrigger(Enum):
     DELAYED = "delayed"
     OTHER = "other"
     PENDING_CS_CHANGE = "pending_cs_change"
+    RE_OPEN = "reopen"
 
 
 @dataclass(frozen=True)
 class ClinicalContextChangeData:
     cause_text: str
     cause_code: ClinicalContextRecalcTrigger
+    notify_worthy: bool = True
+
+    def with_notify_worthy(self, notify: bool) -> 'ClinicalContextChangeData':
+        return ClinicalContextChangeData(cause_text=self.cause_text, cause_code=self.cause_code, notify_worthy=notify)
 
 
 class ClinicalContext(FlagsMixin, TimeStampedModel):

classification/models/discordance_lab_summaries.py

@@ -75,4 +75,19 @@ def for_discordance_report(discordance_report: DiscordanceReport, perspective: L
         for triage in discordance_report.discordancereporttriage_set.select_related('lab').all():
             triage_by_lab[triage.lab] = triage
 
-        return [dls._with_triage(triage_by_lab.pop(dls.lab, None)) for dls in dlses]
+        # apply triages to the first (non withdrawn row) for each lab
+        # in case a lab has both withdrawn and non-withdrawn records
+        with_triages = []
+        for dl in dlses:
+            if not dl.clinical_significance_to == 'withdrawn':
+                dl = dl._with_triage(triage_by_lab.pop(dl.lab, None))
+            with_triages.append(dl)
+
+        if triage_by_lab:
+            # there are some triages for purely withdrawn labs
+            for dl in with_triages:
+                if not dl.triage:
+                    dl = dl._with_triage(triage_by_lab.pop(dl.lab, None))
+            with_triages.append(dl)
+
+        return with_triages