875: ensure that site.species site-settings does not remove in-use taxonomy

app/modules/site_settings/helpers.py

@@ -57,12 +57,18 @@
             AutogeneratedNameType,
         )
 
-        from .models import SiteSetting
+        from .models import SiteSetting, Taxonomy
 
         assert isinstance(value, list)
         # we have to start with *all* autogen names (not just auto_species) for sake of validation
         new_autogen_names = SiteSetting.get_value('autogenerated_names') or {}
 
+        existing = {str(guid) for guid in Taxonomy.usage().keys() if guid}
+        for spec in value:
+            existing.discard(spec.get('id'))
+        if len(existing):
+            raise ValueError(f'Missing taxonomies in use: {existing}')
+
         species_fields = [
             ('commonNames', list, True),
             ('scientificName', str, True),
@@ -93,7 +99,13 @@
             AutogeneratedNameType,
         )
 
-        from .models import SiteSetting
+        from .models import SiteSetting, Taxonomy
+
+        existing = {str(guid) for guid in Taxonomy.usage().keys() if guid}
+        for spec in value:
+            existing.discard(spec.get('id'))
+        if len(existing):
+            raise ValueError(f'Missing taxonomies in use: {existing}')
 
         # we have to start with *all* autogen names (not just auto_species) for sake of setting
         new_autogen_names = SiteSetting.get_value('autogenerated_names') or {}

app/modules/site_settings/models.py

@@ -1043,6 +1043,25 @@
                 return
         raise ValueError('unknown id')
 
+    # this will return taxonomy_guid values *even if they are not* in site_settings! ymmv?
+    @classmethod
+    def usage(cls):
+        from app.extensions import db
+
+        counts = {}
+        # these are the places taxonomy_guid can be used:
+        tables = ['individual', 'encounter', 'sighting_taxonomies']
+        for table_name in tables:
+            res = db.session.execute(
+                f'SELECT taxonomy_guid, COUNT(*) FROM {table_name} GROUP BY taxonomy_guid'
+            )
+            for row in res:
+                if row[0] in counts:
+                    counts[row[0]] += row[1]
+                else:
+                    counts[row[0]] = row[1]
+        return counts
+
     @classmethod
     def get_configuration_value(cls):
         from app.modules.site_settings.models import SiteSetting

tests/modules/site_settings/resources/test_read_configurations.py

@@ -41,7 +41,9 @@ def test_read_site_settings(flask_app_client, researcher_1):
 @pytest.mark.skipif(
     module_unavailable('site_settings'), reason='Site-settings module disabled'
 )
-def test_alter_settings(flask_app_client, admin_user):
+def test_alter_settings(flask_app_client, admin_user, db):
+    from app.modules.individuals.models import Individual
+
     response = conf_utils.read_main_settings(flask_app_client, admin_user)
     assert 'value' in response.json['site.species']
     vals = response.json['site.species']['value']
@@ -65,6 +67,22 @@ def test_alter_settings(flask_app_client, admin_user):
         'site.species',
     )
 
+    # create a faux individual with random taxonomy_guid to test failing update site.species without it
+    indiv = Individual()
+    indiv.taxonomy_guid = '00000000-eb82-471e-b3be-000000000000'
+    with db.session.begin():
+        db.session.add(indiv)
+    with pytest.raises(ValueError) as ve:
+        response = conf_utils.modify_main_settings(
+            flask_app_client,
+            admin_user,
+            vals,
+            'site.species',
+        )
+    assert 'Missing taxonomies' in str(ve)
+    with db.session.begin():
+        db.session.delete(indiv)
+
 
 # TODO sort this out as part of DEX 1306
 #      note: some of this may have been picked up by test_alter_custom_field_categories() below