Update IUCN status data (#4013)

bims/admin.py

@@ -364,9 +364,11 @@ def save_model(self, request, obj, form, change):
         obj.save()
 
 
-class IUCNStatusAdmin(admin.ModelAdmin):
-    list_display = ('get_category_display', 'sensitive',
+class IUCNStatusAdmin(OrderedModelAdmin):
+    list_display = ('id', 'get_category_display', 'move_up_down_links',
+                    'order', 'sensitive',
                     'iucn_colour', 'national', 'total_species')
+    ordering = ('order',)
 
     list_filter = (
         'national',

bims/migrations/0412_alter_iucnstatus_options_iucnstatus_order_and_more.py

@@ -0,0 +1,28 @@
+# Generated by Django 4.2.8 on 2024-06-24 15:25
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('bims', '0411_importtask_cancel'),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name='iucnstatus',
+            options={'ordering': ['order'], 'verbose_name': 'IUCN Status', 'verbose_name_plural': 'IUCN Status'},
+        ),
+        migrations.AddField(
+            model_name='iucnstatus',
+            name='order',
+            field=models.PositiveIntegerField(db_index=True, default=0, editable=False, verbose_name='order'),
+            preserve_default=False,
+        ),
+        migrations.AlterField(
+            model_name='iucnstatus',
+            name='category',
+            field=models.CharField(blank=True, choices=[('LC', 'Least Concern'), ('NT', 'Near Threatened'), ('VU', 'Vulnerable'), ('EN', 'Endangered'), ('CR', 'Critically Endangered'), ('CR PE', 'Critically Endangered, Possibly Extinct'), ('EW', 'Extinct in the Wild'), ('EX', 'Extinct'), ('RE', 'Regionally Extinct'), ('CA', 'Critically Rare'), ('RA', 'Rare'), ('D', 'Declining'), ('DD', 'Data Deficient'), ('DDD', 'Data Deficient - Insufficient Information'), ('DDT', 'Data Deficient - Taxonomically Problematic'), ('NE', 'Not Evaluated')], default='', max_length=50),
+        ),
+    ]

bims/models/iucn_status.py

@@ -6,6 +6,7 @@
 from django.db import models
 from django.dispatch import receiver
 from colorfield.fields import ColorField
+from ordered_model.models import OrderedModel
 
 SENSITIVE_STATUS = ['CR', 'EN', 'VU']
 IUCN_CATEGORIES = {
@@ -14,40 +15,48 @@
     'vulnerable': 'VU',
     'endangered': 'EN',
     'critically endangered': 'CR',
+    'critically endangered, possibly extinct': 'CR PE',
     'extinct in the wild': 'EW',
     'extinct': 'EX',
     'regionally extinct': 'RE',
-    'critically endangered, possibly extinct': 'CE',
     'critically rare': 'CA',
     'rare': 'RA',
+    'declining': 'D',
     'data deficient': 'DD',
-    'data deficient - insufficient information': 'DI',
-    'data deficient - taxonomically problematic': 'DT',
-    'not evaluated': 'NE'
+    'data deficient - insufficient information': 'DDD',
+    'data deficient - taxonomically problematic': 'DDT',
+    'not evaluated': 'NE',
+    'conservation dependent': 'LR/cd',
+    'near threatened - legacy': 'LR/nt',
+    'least concern - legacy': 'LR/lc',
 }
 
 
-class IUCNStatus(models.Model):
+class IUCNStatus(OrderedModel):
     """IUCN status model."""
     CATEGORY_CHOICES = (
-        (IUCN_CATEGORIES['least concern'], 'Least concern'),
-        (IUCN_CATEGORIES['near threatened'], 'Near threatened'),
+        (IUCN_CATEGORIES['least concern'], 'Least Concern'),
+        (IUCN_CATEGORIES['near threatened'], 'Near Threatened'),
         (IUCN_CATEGORIES['vulnerable'], 'Vulnerable'),
         (IUCN_CATEGORIES['endangered'], 'Endangered'),
-        (IUCN_CATEGORIES['critically endangered'], 'Critically endangered'),
-        (IUCN_CATEGORIES['extinct in the wild'], 'Extinct in the wild'),
-        (IUCN_CATEGORIES['extinct'], 'Extinct'),
-        (IUCN_CATEGORIES['data deficient'], 'Data deficient'),
-        (IUCN_CATEGORIES['not evaluated'], 'Not evaluated'),
-        (IUCN_CATEGORIES['regionally extinct'], 'Regionally Extinct'),
+        (IUCN_CATEGORIES['critically endangered'], 'Critically Endangered'),
         (IUCN_CATEGORIES['critically endangered, possibly extinct'],
          'Critically Endangered, Possibly Extinct'),
+        (IUCN_CATEGORIES['extinct in the wild'], 'Extinct in the Wild'),
+        (IUCN_CATEGORIES['extinct'], 'Extinct'),
+        (IUCN_CATEGORIES['regionally extinct'], 'Regionally Extinct'),
         (IUCN_CATEGORIES['critically rare'], 'Critically Rare'),
         (IUCN_CATEGORIES['rare'], 'Rare'),
+        (IUCN_CATEGORIES['declining'], 'Declining'),
+        (IUCN_CATEGORIES['data deficient'], 'Data Deficient'),
         (IUCN_CATEGORIES['data deficient - insufficient information'],
          'Data Deficient - Insufficient Information'),
         (IUCN_CATEGORIES['data deficient - taxonomically problematic'],
          'Data Deficient - Taxonomically Problematic'),
+        (IUCN_CATEGORIES['not evaluated'], 'Not Evaluated'),
+        (IUCN_CATEGORIES['conservation dependent'], 'Conservation Dependent'),
+        (IUCN_CATEGORIES['near threatened - legacy'], 'Near Threatened - Legacy'),
+        (IUCN_CATEGORIES['least concern - legacy'], 'Least Concern - Legacy'),
     )
 
     category = models.CharField(
@@ -83,6 +92,7 @@ class Meta:
         app_label = 'bims'
         verbose_name_plural = 'IUCN Status'
         verbose_name = 'IUCN Status'
+        ordering = ['order']
 
 
 @receiver(models.signals.pre_save, sender=IUCNStatus)

bims/views/map.py

@@ -89,7 +89,7 @@ def get_context_data(self, **kwargs):
 
         # Get all the iucn conservation status
         iucn_statuses = IUCNStatus.objects.all().distinct(
-            'category', 'national')
+            'category', 'national', 'order').order_by('order')
         conservation_status_data = []
         conservation_status_desc = {
             'CR': 'A taxon is Critically Endangered when the best '

deployment/docker/entrypoint.sh

@@ -14,9 +14,7 @@ python manage.py migrate sites --noinput
 python manage.py migrate --noinput
 python manage.py gruntserver
 python manage.py collectstatic --noinput
-python manage.py update_site_domain
-python manage.py add_default_location_site_view
-python manage.py add_location_site_view_geoserver
+python manage.py create_or_update_iucn_status
 popd
 
 exec "$@"

scripts/management/commands/create_or_update_iucn_status.py

@@ -0,0 +1,61 @@
+# -*- coding: utf-8 -*-
+from django.core.management.base import BaseCommand
+from django.db.models import signals
+from django_tenants.utils import get_tenant_model, schema_context
+
+from bims.models import (
+    BiologicalCollectionRecord, collection_post_save_handler, IUCNStatus
+)
+from bims.utils.logger import log
+
+
+class Command(BaseCommand):
+
+    def create_or_update_iucn_status(self):
+        categories = [
+            {'category': 'EX', 'national': False, 'sensitive': False, 'colour': '#606060', 'order': 0},
+            {'category': 'EW', 'national': False, 'sensitive': False, 'colour': '#808080', 'order': 1},
+            {'category': 'CR', 'national': False, 'sensitive': True, 'colour': '#B00000', 'order': 2},
+            {'category': 'EN', 'national': False, 'sensitive': True, 'colour': '#D00000', 'order': 3},
+            {'category': 'VU', 'national': False, 'sensitive': True, 'colour': '#FF0000', 'order': 4},
+            {'category': 'NT', 'national': False, 'sensitive': False, 'colour': '#FFC000', 'order': 5},
+            {'category': 'LC', 'national': False, 'sensitive': False, 'colour': '#009106', 'order': 6},
+            {'category': 'DD', 'national': False, 'sensitive': False, 'colour': '#808000', 'order': 7},
+            {'category': 'NE', 'national': False, 'sensitive': False, 'colour': '#808000', 'order': 8},
+
+            {'category': 'EX', 'national': True, 'sensitive': False, 'colour': '#606060', 'order': 9},
+            {'category': 'EW', 'national': True, 'sensitive': False, 'colour': '#606060', 'order': 10},
+            {'category': 'RE', 'national': True, 'sensitive': False, 'colour': '#404040', 'order': 11},
+            {'category': 'CR PE', 'national': True, 'sensitive': True, 'colour': '#A00000', 'order': 12},
+            {'category': 'EN', 'national': True, 'sensitive': True, 'colour': '#D00000', 'order': 13},
+            {'category': 'VU', 'national': True, 'sensitive': True, 'colour': '#FF0000', 'order': 14},
+            {'category': 'NT', 'national': True, 'sensitive': False, 'colour': '#FFC000', 'order': 15},
+            {'category': 'CA', 'national': True, 'sensitive': False, 'colour': '#FFC000', 'order': 16},
+            {'category': 'RA', 'national': True, 'sensitive': False, 'colour': '#FF8000', 'order': 17},
+            {'category': 'D', 'national': True, 'sensitive': False, 'colour': '#FF4000', 'order': 18},
+            {'category': 'DDD', 'national': True, 'sensitive': False, 'colour': '#808000', 'order': 19},
+            {'category': 'DDT', 'national': True, 'sensitive': False, 'colour': '#808000', 'order': 20},
+            {'category': 'LC', 'national': True, 'sensitive': False, 'colour': '#009106', 'order': 21},
+        ]
+        for cat in categories:
+            iucn_status, created = IUCNStatus.objects.update_or_create(
+                category=cat['category'], national=cat['national'],
+                defaults={
+                    'sensitive': cat['sensitive'],
+                    'colour': cat['colour'],
+                    'order': cat['order']
+                }
+            )
+            if created:
+                print(f'Created {cat["category"]} (national={cat["national"]})')
+            else:
+                print(f'Updated {cat["category"]} (national={cat["national"]})')
+
+    def handle(self, *args, **options):
+
+        TenantModel = get_tenant_model()
+        tenants = TenantModel.objects.all().exclude(schema_name='public')
+
+        for tenant in tenants:
+            with schema_context(tenant.schema_name):
+                self.create_or_update_iucn_status()