Fix duplicate TaxaList names causing MultipleObjectsReturned

ami/main/management/commands/import_taxa.py

@@ -166,7 +166,9 @@ class Command(BaseCommand):
     This is a very specific command for importing taxa from an exiting format. A more general
     import command with support for all taxon ranks & fields should be written.
 
-
+    @TODO: Add --project parameter(s) to scope the taxa list to specific projects.
+    This would allow multiple projects to have taxa lists with the same name.
+    Usage would be: --project project-slug --project another-project-slug
 
     Example taxa.json
     ```
@@ -234,7 +236,8 @@ def handle(self, *args, **options):
         else:
             list_name = pathlib.Path(fname).stem
 
-        taxalist, created = TaxaList.objects.get_or_create(name=list_name)
+        # Uses get_or_create_for_project with project=None to create a global list
+        taxalist, created = TaxaList.objects.get_or_create_for_project(name=list_name, project=None)
         if created:
             self.stdout.write(self.style.SUCCESS('Successfully created taxa list "%s"' % taxalist))
 

ami/main/management/commands/update_taxa.py

@@ -91,6 +91,10 @@ class Command(BaseCommand):
     ```
 
     You can include any column that exists in the Taxon model.
+
+    @TODO: Add --project parameter(s) to scope the taxa list to specific projects.
+    This would allow multiple projects to have taxa lists with the same name.
+    Usage would be: --project project-slug --project another-project-slug
     """
 
     help = "Update existing taxa with new data from a CSV file."
@@ -123,10 +127,11 @@ def handle(self, *args, **options):
         incoming_taxa = read_csv(fname)
 
         # Get or create taxa list if specified
+        # Uses get_or_create_for_project with project=None to create a global list
         taxalist = None
         if options["list"]:
             list_name = options["list"]
-            taxalist, created = TaxaList.objects.get_or_create(name=list_name)
+            taxalist, created = TaxaList.objects.get_or_create_for_project(name=list_name, project=None)
             if created:
                 self.stdout.write(self.style.SUCCESS(f"Created new taxa list '{list_name}'"))
             else:

ami/main/models.py

@@ -3595,6 +3595,44 @@ def save(self, update_calculated_fields=True, *args, **kwargs):
             self.update_calculated_fields(save=True)
 
 
+class TaxaListQuerySet(BaseQuerySet):
+    def get_or_create_for_project(
+        self, name: str, project: "Project | None" = None, **defaults
+    ) -> tuple["TaxaList", bool]:
+        """
+        Get or create a TaxaList with uniqueness scoped to project.
+
+        - If project is None: looks for/creates a global list (no project associations)
+        - If project is provided: looks for/creates a list associated with that project
+
+        Returns:
+            Tuple of (TaxaList, created: bool)
+        """
+        if project is None:
+            # Global list: find list with this name that has no project associations
+            qs = self.filter(name=name).annotate(project_count=models.Count("projects")).filter(project_count=0)
+        else:
+            # Project-specific: find list with this name in this project
+            qs = self.filter(name=name, projects=project)
+
+        try:
+            return qs.get(), False
+        except self.model.DoesNotExist:
+            taxa_list = self.create(name=name, **defaults)
+            if project:
+                taxa_list.projects.add(project)
+            return taxa_list, True
+        except self.model.MultipleObjectsReturned:
+            # Handle existing duplicates gracefully - return the oldest one
+            taxa_list = qs.order_by("created_at").first()
+            assert taxa_list is not None  # We know there's at least one
+            return taxa_list, False
+
+
+class TaxaListManager(models.Manager.from_queryset(TaxaListQuerySet)):
+    pass
+
+
 @final
 class TaxaList(BaseModel):
     """A checklist of taxa"""
@@ -3605,6 +3643,8 @@ class TaxaList(BaseModel):
     taxa = models.ManyToManyField(Taxon, related_name="lists")
     projects = models.ManyToManyField("Project", related_name="taxa_lists")
 
+    objects: TaxaListManager = TaxaListManager()
+
     class Meta:
         ordering = ["-created_at"]
         verbose_name_plural = "Taxa Lists"

ami/ml/models/pipeline.py

@@ -555,8 +555,9 @@ def get_or_create_taxon_for_classification(
 
     :return: The Taxon object
     """
-    taxa_list, created = TaxaList.objects.get_or_create(
+    taxa_list, created = TaxaList.objects.get_or_create_for_project(
         name=f"Taxa returned by {algorithm.name}",
+        project=None,  # Algorithm taxa lists are global
     )
     if created:
         logger.info(f"Created new taxa list {taxa_list}")