Improve validation workflow (#4233)

* Fix and improve validation workflow

* User taxon group id from current taxa when editing

bims/api_views/taxon.py

@@ -295,6 +295,14 @@ def post(self, request, *args):
                 get_vernacular=True
             )
         elif taxon_name and rank:
+            if rank.lower() == 'species' and parent and parent.rank.lower() == 'genus':
+                if parent.canonical_name not in taxon_name:
+                    taxon_name = parent.canonical_name + ' ' + taxon_name
+            elif rank.lower() == 'subspecies' and parent and parent.rank.lower() == 'species':
+                species_name = parent.species_name
+                if species_name not in taxon_name:
+                    taxon_name = species_name + ' ' + taxon_name
+            taxon_name = taxon_name.strip()
             try:
                 taxonomy, created = Taxonomy.objects.get_or_create(
                     scientific_name=taxon_name,
@@ -549,14 +557,6 @@ def get_taxa_by_parameters(request):
                         taxongrouptaxonomy__is_validated=False,
                         taxongrouptaxonomy__taxongroup__in=taxon_group_ids
                     )
-
-                    rejected_taxa = list(TaxonomyUpdateProposal.objects.filter(
-                        taxon_group_id__in=taxon_group_ids,
-                        status='rejected'
-                    ).values_list('original_taxonomy_id', flat=True))
-
-                    if rejected_taxa:
-                        taxon_list = taxon_list.exclude(id__in=rejected_taxa)
                 else:
                     taxon_list = taxon_list.filter(
                         taxongrouptaxonomy__is_validated=True,

bims/api_views/taxon_update.py

@@ -39,6 +39,8 @@ def create_taxon_proposal(
             accepted_taxonomy = accepted_taxonomy[0]
 
     additional_data = taxon.additional_data
+    if not additional_data:
+        additional_data = {}
     additional_data_to_check = [
         'Taxonomic Comments',
         'Conservation Comments',
@@ -54,9 +56,13 @@ def create_taxon_proposal(
             additional_data[additional_key] = data.get(additional_key)
 
     canonical_name = data.get('canonical_name', taxon.canonical_name)
-    if taxon.is_species:
+    if taxon.rank.lower() == 'species':
         if taxon.genus_name not in canonical_name:
             canonical_name = taxon.genus_name + ' ' + canonical_name
+    elif taxon.rank.lower() == 'subspecies':
+        if taxon.full_species_name not in canonical_name:
+            canonical_name = taxon.full_species_name + ' ' + canonical_name
+    canonical_name = canonical_name.strip()
 
     proposal, created = TaxonomyUpdateProposal.objects.get_or_create(
         original_taxonomy=taxon,

bims/models/taxonomy.py

@@ -345,6 +345,14 @@ def genus_name(self):
     def sub_genus_name(self):
         return self.get_taxon_rank_name(TaxonomicRank.SUBGENUS.name)
 
+    @cached_property
+    def full_species_name(self):
+        genus_name = self.get_taxon_rank_name(TaxonomicRank.GENUS.name)
+        species_name = self.species_name
+        if genus_name not in species_name:
+            return genus_name + ' ' + species_name
+        return species_name
+
     @property
     def species_name(self):
         return self.get_taxon_rank_name(TaxonomicRank.SPECIES.name)
@@ -371,6 +379,8 @@ def variety_name(self):
 
     @property
     def taxon_name(self):
+        if self.rank.lower() == 'subspecies':
+            return self.canonical_name.split(self.full_species_name)[-1].strip()
         if self.is_species and self.genus_name:
             return self.canonical_name.split(self.genus_name)[-1].strip()
         return self.canonical_name

bims/models/taxonomy_update_proposal.py

@@ -1,3 +1,5 @@
+from datetime import datetime
+
 from django.contrib.auth import get_user_model
 from django.db import models
 from django.conf import settings
@@ -254,11 +256,7 @@ def approve(self, reviewer: settings.AUTH_USER_MODEL):
         )
         top_level_taxon_group = self.taxon_group.get_top_level_parent()
 
-        if self.taxon_group_under_review:
-            self.taxon_group_under_review = top_level_taxon_group
-            self.save()
-
-        if top_level_taxon_group != self.taxon_group:
+        if top_level_taxon_group != self.taxon_group_under_review:
             parent_expert = list(top_level_taxon_group.experts.values_list(
                 'email', flat=True
             ))
@@ -272,59 +270,127 @@ def approve(self, reviewer: settings.AUTH_USER_MODEL):
             from_email = settings.DEFAULT_FROM_EMAIL
             message = (f"Dear Validator,\n\nThe taxon '{self.original_taxonomy.canonical_name}' "
                        f"has been validated by the current expert.\n\nIt now requires "
-                       f"validation to be added to the taxon group '{self.taxon_group.name}'.")
+                       f"validation to be added to the taxon group '{top_level_taxon_group.name}'.")
             send_mail_notification.delay(
                 subject,
                 message,
                 from_email,
                 recipients
             )
-
-        # Only top level experts can approve data
-        if top_level_taxon_group.experts.filter(
-            id=reviewer.id
-        ).exists() or reviewer.is_superuser:
-            fields_to_update = [
-                'scientific_name',
-                'canonical_name',
-                'legacy_canonical_name',
-                'rank',
-                'taxonomic_status',
-                'endemism',
-                'iucn_status',
-                'accepted_taxonomy',
-                'parent',
-                'tags',
-                'biographic_distributions',
-                'additional_data',
-                'vernacular_names',
-                'origin']
-            for field in fields_to_update:
-                if field == 'tags':
-                    self.original_taxonomy.tags.clear()
-                    self.original_taxonomy.tags.set(getattr(self, field).all())
-                elif field == 'biographic_distributions':
-                    self.original_taxonomy.biographic_distributions.clear()
-                    self.original_taxonomy.biographic_distributions.set(
-                        getattr(self, field).all())
-                elif field == 'vernacular_names':
-                    self.original_taxonomy.vernacular_names.clear()
-                    self.original_taxonomy.vernacular_names.set(
-                        getattr(self, field).all())
-                else:
-                    setattr(
-                        self.original_taxonomy,
-                        field, getattr(self, field))
-            self.original_taxonomy.hierarchical_data = {}
-            self.original_taxonomy.save()
-            self.status = 'approved'
+            self.taxon_group_under_review = top_level_taxon_group
             self.save()
+        else:
+            # Only top level experts can approve data
+            if top_level_taxon_group.experts.filter(
+                id=reviewer.id
+            ).exists() or reviewer.is_superuser:
+                fields_to_update = [
+                    'scientific_name',
+                    'canonical_name',
+                    'legacy_canonical_name',
+                    'rank',
+                    'taxonomic_status',
+                    'endemism',
+                    'iucn_status',
+                    'accepted_taxonomy',
+                    'parent',
+                    'tags',
+                    'biographic_distributions',
+                    'additional_data',
+                    'vernacular_names',
+                    'origin']
+                for field in fields_to_update:
+                    if field == 'tags':
+                        self.original_taxonomy.tags.clear()
+                        self.original_taxonomy.tags.set(getattr(self, field).all())
+                    elif field == 'biographic_distributions':
+                        self.original_taxonomy.biographic_distributions.clear()
+                        self.original_taxonomy.biographic_distributions.set(
+                            getattr(self, field).all())
+                    elif field == 'vernacular_names':
+                        self.original_taxonomy.vernacular_names.clear()
+                        self.original_taxonomy.vernacular_names.set(
+                            getattr(self, field).all())
+                    else:
+                        setattr(
+                            self.original_taxonomy,
+                            field, getattr(self, field))
+                self.original_taxonomy.hierarchical_data = {}
+                self.original_taxonomy.save()
+                self.status = 'approved'
+                self.save()
+
+                self.validate_taxon(
+                    self.taxon_group,
+                    self.original_taxonomy
+                )
+
+                self.send_success_emails(reviewer)
+                return
 
-            self.validate_taxon(
-                self.taxon_group,
-                self.original_taxonomy
+    def send_success_emails(self, reviewer, comments: str = "",):
+        """
+        Send notification emails to the collector and staff upon successful validation.
+
+        Args:
+            reviewer (User, optional): User reviewing the taxon
+            comments (str, optional): Comments regarding the approval.
+        """
+        current_site = get_current_domain()
+        from_email = settings.DEFAULT_FROM_EMAIL
+
+        # Email to the collector
+        if self.collector_user:
+            submission_type = 'Addition' if self.new_data else 'Update'
+            collector_subject = f'[{current_site}] Taxon {submission_type} Submission Approved'
+            collector_message = (
+                f"Dear {self.collector_user.get_full_name()},\n\n"
+                f"Your submission for the taxon '{self.canonical_name}' "
+                f"has been successfully approved by "
+                f"the experts at {current_site}.\n\n"
             )
-            return
+            send_mail_notification.delay(
+                collector_subject,
+                collector_message,
+                from_email,
+                [self.collector_user.email]
+            )
+
+        # Email to staff and experts
+        staff_subject = (
+            f'[{current_site}] Taxon '
+            f'{"Addition" if self.new_data else "Update"} Submission Approved'
+        )
+
+        # Gather all expert emails
+        recipients = []
+        experts = self.taxon_group.get_all_experts()
+        for expert in experts:
+            if expert.email not in recipients:
+                recipients.append(expert.email)
+        superusers = list(
+            get_user_model().objects.filter(
+                is_superuser=True).values_list('email', flat=True)
+        )
+        recipients = list(set(superusers + recipients))
+
+        staff_message = (
+            f"Dear Staff/Expert,\n\n"
+            f"The taxon '{self.canonical_name}' has been successfully validated and "
+            f"approved at {current_site}.\n\n"
+            f"Submission Details:\n"
+            f"Taxon Name: {self.canonical_name}\n\n"
+            f"Taxon Group: {self.taxon_group.name}\n\n"
+            f"Approved by: {reviewer.get_full_name()}\n"
+            f"Date: {datetime.now().strftime('%Y-%m-%d')}\n\n"
+        )
+
+        send_mail_notification.delay(
+            staff_subject,
+            staff_message,
+            from_email,
+            recipients
+        )
 
 
 class TaxonomyUpdateReviewer(models.Model):

bims/serializers/taxon_detail_serializer.py

@@ -42,7 +42,15 @@ def get_species_group(self, obj: Taxonomy):
         return ''
 
     def get_subspecies(self, obj: Taxonomy):
-        return obj.sub_species_name
+        sub_species_name = obj.sub_species_name
+        if sub_species_name:
+            genus_name = obj.genus_name
+            if genus_name:
+                sub_species_name = sub_species_name.replace(genus_name, '', 1).strip()
+            species_name = self.get_species(obj)
+            if species_name:
+                sub_species_name = sub_species_name.replace(species_name, '', 1).strip()
+        return sub_species_name
 
     def get_subgenus(self, obj: Taxonomy):
         return obj.sub_genus_name

bims/serializers/taxon_serializer.py

@@ -305,14 +305,28 @@ def get_taxon_group(self, obj: Taxonomy):
         taxon_group_id = self.context.get('taxon_group_id', None)
         if taxon_group_id:
             taxon_group = TaxonGroup.objects.get(id=taxon_group_id)
+            if not TaxonGroupTaxonomy.objects.filter(
+                taxongroup_id=taxon_group_id,
+                taxonomy=obj
+            ).exists():
+                children = taxon_group.get_all_children()
+                children_ids = [child.id for child in children]
+                taxon_group_taxa = TaxonGroupTaxonomy.objects.filter(
+                    taxongroup_id__in=children_ids,
+                    taxonomy=obj
+                )
+                if taxon_group_taxa.exists():
+                    taxon_group = taxon_group_taxa.first().taxongroup
             return {
+                'id': taxon_group.id,
                 'logo': taxon_group.logo.name,
                 'name': taxon_group.name
             }
         taxonomy_obj = self.taxonomy_obj(obj)
         taxon_module = taxonomy_obj.taxongroup_set.first()
         if taxon_module:
             return {
+                'id': taxon_module.id,
                 'logo': taxon_module.logo.name,
                 'name': taxon_module.name
             }

bims/static/js/taxa_management/taxa_management.js

@@ -293,7 +293,7 @@ export const taxaManagement = (() => {
                     if (!taxaData) return false;
                     let data = taxaData.find(taxon => taxon.id === $(this).parent().data('id'));
                     if (data) {
-                        window.location.href = `/taxonomy/edit/${selectedTaxonGroup}/${data.id}/?next=${encodeURIComponent(location.href)}`;
+                        window.location.href = `/taxonomy/edit/${data.taxon_group.id}/${data.id}/?next=${encodeURIComponent(location.href)}`;
                     }
                 });
 

bims/views/edit_taxon_view.py

@@ -1,6 +1,7 @@
 from django.contrib import messages
 from django.contrib.auth.mixins import LoginRequiredMixin, UserPassesTestMixin
 from django.db import transaction
+from django.http import Http404
 from django.shortcuts import get_object_or_404, redirect
 from django.urls import reverse
 from django.views.generic import UpdateView