From 722baacc622ee2de801b7333de0e90abbfba7a1c Mon Sep 17 00:00:00 2001
From: Dimas Ciputra <dimas.ciputra@gmail.com>
Date: Thu, 25 Jul 2024 07:26:01 +0100
Subject: [PATCH] Add ability to add new taxon with higher taxonomic ranks
 (#4103)

---
 bims/api_views/taxon.py                       | 26 +++++--
 bims/enums/taxonomic_rank.py                  | 26 +++----
 .../js/taxa_management/add_new_taxon.js       | 36 ++++++---
 bims/static/js/taxa_management/taxa_table.js  |  3 +-
 bims/templates/taxa_management.html           | 14 ++--
 bims/tests/test_add_new_taxon.py              | 73 +++++++++++++++++++
 6 files changed, 140 insertions(+), 38 deletions(-)
 create mode 100644 bims/tests/test_add_new_taxon.py

diff --git a/bims/api_views/taxon.py b/bims/api_views/taxon.py
index 3b42a72fe..a68c446b7 100644
--- a/bims/api_views/taxon.py
+++ b/bims/api_views/taxon.py
@@ -260,9 +260,12 @@ def post(self, request, *args):
         author_name = self.request.POST.get('authorName', '')
         rank = self.request.POST.get('rank', None)
         family_id = self.request.POST.get('familyId', None)
-        family = None
+        parent = None
         if family_id:
-            family = Taxonomy.objects.get(id=int(family_id))
+            parent = Taxonomy.objects.get(id=int(family_id))
+        parent_id = self.request.POST.get('parentId', None)
+        if parent_id:
+            parent = Taxonomy.objects.get(id=int(parent_id))
         if gbif_key:
             taxonomy = update_taxonomy_from_gbif(
                 key=gbif_key,
@@ -277,12 +280,23 @@ def post(self, request, *args):
             )
         if taxon_group_id:
             taxon_group = TaxonGroup.objects.get(id=taxon_group_id)
-            taxon_group.taxonomies.add(taxonomy)
+            taxon_group.taxonomies.add(
+                taxonomy,
+                through_defaults={
+                    'is_validated': False
+                }
+            )
         else:
             if taxon_group:
                 try:
                     taxon_group = TaxonGroup.objects.get(name=taxon_group)
-                    taxon_group.taxonomies.add(taxonomy)
+                    taxon_group.taxonomies.add(
+                        taxonomy,
+                        through_defaults={
+                            'is_validated': False
+                        }
+                    )
+                    taxon_group_id = taxon_group.id
                 except TaxonGroup.DoesNotExist:
                     pass
         if taxonomy:
@@ -302,8 +316,8 @@ def post(self, request, *args):
                 taxonomy.ready_to_be_validate()
                 taxonomy.send_new_taxon_email(taxon_group_id)
 
-            if family:
-                taxonomy.parent = family
+            if parent:
+                taxonomy.parent = parent
                 taxonomy.save()
 
         with transaction.atomic():
diff --git a/bims/enums/taxonomic_rank.py b/bims/enums/taxonomic_rank.py
index e5aa2f561..fdfbc2f13 100644
--- a/bims/enums/taxonomic_rank.py
+++ b/bims/enums/taxonomic_rank.py
@@ -3,26 +3,26 @@
 
 class TaxonomicRank(Enum):
 
-    SUBSPECIES = 'Sub Species'
-    SPECIES = 'Species'
-    GENUS = 'Genus'
-    SUBGENUS = 'Sub Genus'
-    FAMILY = 'Family'
-    SUPERFAMILY = 'Super Family'
-    ORDER = 'Order'
-    CLASS = 'Class'
-    SUBCLASS = 'Sub Class'
+    DOMAIN = 'Domain'
+    KINGDOM = 'Kingdom'
     PHYLUM = 'Phylum'
     SUBPHYLUM = 'SubPhylum'
-    KINGDOM = 'Kingdom'
-    DOMAIN = 'Domain'
+    CLASS = 'Class'
+    SUBCLASS = 'Sub Class'
+    ORDER = 'Order'
     SUBORDER = 'Sub Order'
     INFRAORDER = 'Infra Order'
+    SUPERFAMILY = 'Super Family'
+    FAMILY = 'Family'
     SUBFAMILY = 'Sub Family'
-    VARIETY = 'Variety'
-    FORMA = 'Forma'
     TRIBE = 'Tribe'
     SUBTRIBE = 'Sub Tribe'
+    GENUS = 'Genus'
+    SUBGENUS = 'Sub Genus'
+    SPECIES = 'Species'
+    SUBSPECIES = 'Sub Species'
+    VARIETY = 'Variety'
+    FORMA = 'Forma'
 
     @staticmethod
     def hierarchy():
diff --git a/bims/static/js/taxa_management/add_new_taxon.js b/bims/static/js/taxa_management/add_new_taxon.js
index c06f9585a..087b6d4b7 100644
--- a/bims/static/js/taxa_management/add_new_taxon.js
+++ b/bims/static/js/taxa_management/add_new_taxon.js
@@ -1,25 +1,28 @@
 export const addNewTaxon = (() => {
-    const $newTaxonFamilyIdInput = $('.new-taxon-family-id');
+    const $newTaxonParentIdInput = $('.new-taxon-parent-id');
     const $newTaxonFamilyInput = $('.new-taxon-family-name');
+    const $newTaxonParent = $('#new-taxon-parent');
     const $taxonForm = $('.new-taxon-form');
     const $addNewTaxonBtn = $taxonForm.find('.add-new-taxon-btn');
     const $newTaxonNameInput = $('#new-taxon-name');
 
     let selectedTaxonGroup = '';
 
+
     function showNewTaxonForm(taxonName) {
         let capitalizedTaxonName = taxonName.substr(0, 1).toUpperCase() + taxonName.substr(1).toLowerCase();
-        speciesAutoComplete($newTaxonFamilyInput, '&rank=family&taxonGroupId=' + currentSelectedTaxonGroup).then(value => {
-            $newTaxonFamilyIdInput.val(value);
-        })
         $newTaxonNameInput.val(capitalizedTaxonName);
+        $newTaxonParentIdInput.val($newTaxonParent.val())
         $taxonForm.show();
         const authorAutoComplete = $('#author-auto-complete');
         authorAutoComplete.empty();
         authorAutoComplete.val(null).trigger('change');
+
+        $newTaxonParent.empty();
+        $newTaxonParent.val(null).trigger('change');
     }
 
-    function addNewTaxonToObservedList(name, gbifKey, rank, taxaId = null, familyId = "", authorName = "") {
+    function addNewTaxonToObservedList(name, gbifKey, rank, taxaId = null, parentId = "", authorName = "") {
         let postData = {
             'gbifKey': gbifKey,
             'taxonName': name,
@@ -27,8 +30,8 @@ export const addNewTaxon = (() => {
             'taxonGroupId': currentSelectedTaxonGroup,
             'authorName': authorName
         };
-        if (familyId) {
-            postData['familyId'] = familyId
+        if (parentId) {
+            postData['parentId'] = parentId
         }
         let table = $('.find-taxon-table');
         table.hide();
@@ -149,18 +152,27 @@ export const addNewTaxon = (() => {
     function handleAddNewTaxon(event) {
         let $rank = $taxonForm.find('.new-taxon-rank');
         let $author = $taxonForm.find('#author-auto-complete');
-        const familyId = $newTaxonFamilyIdInput.val();
-        if (!familyId) {
-            alert("Missing family");
+        const parentId = $newTaxonParent.val();
+        if (!parentId) {
+            alert("Missing parent");
             return
         }
-        addNewTaxonToObservedList($newTaxonNameInput.val(), '', $rank.val(), null, familyId, $author.val());
+        addNewTaxonToObservedList($newTaxonNameInput.val(), '', $rank.val(), null, parentId, $author.val());
         $taxonForm.hide();
         $newTaxonFamilyInput.val("")
-        $newTaxonFamilyIdInput.val("")
+        $newTaxonParentIdInput.val("")
     }
 
     function init(_selectedTaxonGroup) {
+
+        $('#addNewTaxonModal').on('shown.bs.modal', function (e) {
+            const authorAutoComplete = $('#author-auto-complete');
+            authorAutoComplete.empty();
+            authorAutoComplete.val(null).trigger('change');
+
+            $newTaxonParent.empty();
+            $newTaxonParent.val(null).trigger('change');
+        });
         selectedTaxonGroup = _selectedTaxonGroup
 
         $('#find-taxon-button').on('click', handleFindTaxonButton)
diff --git a/bims/static/js/taxa_management/taxa_table.js b/bims/static/js/taxa_management/taxa_table.js
index d4d119347..69d5d8d42 100644
--- a/bims/static/js/taxa_management/taxa_table.js
+++ b/bims/static/js/taxa_management/taxa_table.js
@@ -107,7 +107,8 @@ export const taxaTable = (() => {
                 data: function (params) {
                     return {
                         term: params.term,
-                        rank: $(this).data('rank')
+                        rank: $(this).data('rank'),
+                        taxonGroupId: currentSelectedTaxonGroup
                     }
                 },
                 processResults: function (data) {
diff --git a/bims/templates/taxa_management.html b/bims/templates/taxa_management.html
index 7c65720d5..e1104f293 100644
--- a/bims/templates/taxa_management.html
+++ b/bims/templates/taxa_management.html
@@ -451,7 +451,7 @@ <h5 class="modal-title">Add New Taxon</h5>
                             </tbody>
                         </table>
                     </div>
-                    <div class="container new-taxon-form" style="margin-top: 15px; display: none">
+                    <div class="container new-taxon-form" style="margin-top: 15px;">
                         <div class="alert alert-info" role="alert">
                             Whilst the system will accept taxa that are not listed in GBIF,
                             you should use the capability only for taxa where the classification is partly unresolved.
@@ -462,7 +462,7 @@ <h5 class="modal-title">Add New Taxon</h5>
                         <table class="table table-sm">
                             <thead>
                                 <tr>
-                                    <th scope="col" style="width: 25%">Family</th>
+                                    <th scope="col" style="width: 25%">Parent</th>
                                     <th scope="col" style="width: 25%">Taxon Name</th>
                                     <th scope="col" style="width: 25%">Author</th>
                                     <th scope="col" style="width: 25%">Rank</th>
@@ -472,8 +472,8 @@ <h5 class="modal-title">Add New Taxon</h5>
                             <tbody>
                             <tr>
                                 <td>
-                                    <select name="newTaxonFamilyName" class="new-taxon-family-name form-control" data-add-new-tag="false" style="width: 100%"></select>
-                                    <input type="hidden" class="new-taxon-family-id">
+                                    <select name="newTaxonFamilyName" class="taxon-auto-complete form-control" id="new-taxon-parent" style="width: 100%"></select>
+                                    <input type="hidden" class="new-taxon-parent-id">
                                 </td>
                                 <td>
                                     <input type="text" class="form-control" placeholder="Taxon Name" id="new-taxon-name">
@@ -486,8 +486,10 @@ <h5 class="modal-title">Add New Taxon</h5>
                                 </td>
                                 <td>
                                     <select class="form-control new-taxon-rank">
-                                        {% for rank in taxon_rank %}
+                                        {% for rank in all_ranks %}
+                                            {% if rank != 'DOMAIN' %}
                                             <option value="{{ rank }}" {% if rank == 'SPECIES' %}selected{% endif %}>{{ rank }}</option>
+                                            {% endif %}
                                         {% endfor %}
                                     </select>
                                 </td>
@@ -500,7 +502,7 @@ <h5 class="modal-title">Add New Taxon</h5>
                             </tr>
                             <tr>
                                 <td style="border-top-width: 0"><span class="text-muted" style="font-size: 10pt; font-style: italic">
-                                    This is an autocomplete search, if the family does not exist in the system, please add it first.</span>
+                                    This is an autocomplete search, if the taxon does not exist in the system, please add it first.</span>
                                 </td>
                             </tr>
                             </tbody>
diff --git a/bims/tests/test_add_new_taxon.py b/bims/tests/test_add_new_taxon.py
new file mode 100644
index 000000000..0c6207d0d
--- /dev/null
+++ b/bims/tests/test_add_new_taxon.py
@@ -0,0 +1,73 @@
+from django.test import TestCase
+from django.urls import reverse
+from django_tenants.test.cases import FastTenantTestCase
+from django_tenants.test.client import TenantClient
+from rest_framework.test import APIClient
+from unittest.mock import patch
+
+from django.contrib.auth.models import User
+from bims.tests.model_factories import TaxonomyF, TaxonGroupF, UserF, IUCNStatusF
+
+
+def mock_update_taxonomy_from_gbif(key, fetch_parent=True, get_vernacular=True):
+    iucn_status = IUCNStatusF.create()
+    taxonomy = TaxonomyF.create(
+        gbif_key=key,
+        scientific_name="Mocked Scientific Name",
+        canonical_name="Mocked Canonical Name",
+        iucn_status=iucn_status
+    )
+    return taxonomy
+
+class AddNewTaxonTestCase(FastTenantTestCase):
+    def setUp(self):
+        self.client = TenantClient(self.tenant)
+        self.user = UserF.create(username='testuser', password='testpassword')
+        self.client.login(username='testuser', password='testpassword')
+        self.taxon_group = TaxonGroupF.create(
+            name='test'
+        )
+        self.taxonomy = TaxonomyF()
+
+    @patch('bims.api_views.taxon.update_taxonomy_from_gbif', side_effect=mock_update_taxonomy_from_gbif)
+    def test_add_new_taxon_with_gbif_key(self, mock_update):
+        data = {
+            'gbifKey': '1',
+            'taxonName': 'Test Taxon',
+            'taxonGroup': self.taxon_group.name,
+            'rank': 'species',
+            'authorName': 'Test Author',
+        }
+        response = self.client.post(reverse('add-new-taxon'), data)
+        self.assertEqual(response.status_code, 200)
+        self.assertTrue('id' in response.data)
+        self.assertTrue('taxon_name' in response.data)
+        self.assertEqual(response.data['taxon_name'], 'Mocked Canonical Name')
+
+    @patch('bims.api_views.taxon.update_taxonomy_from_gbif', side_effect=mock_update_taxonomy_from_gbif)
+    def test_add_new_taxon_without_gbif_key(self, mock_update):
+        data = {
+            'taxonName': 'Test Taxon Without GBIF',
+            'taxonGroup': self.taxon_group.name,
+            'rank': 'species',
+            'parentId': self.taxonomy.id,
+            'authorName': 'Test Author Without GBIF',
+        }
+        response = self.client.post(reverse('add-new-taxon'), data)
+        self.assertEqual(response.status_code, 200)
+        self.assertTrue('id' in response.data)
+        self.assertTrue('taxon_name' in response.data)
+        self.assertEqual(response.data['taxon_name'], 'Test Taxon Without GBIF')
+
+        data = {
+            'taxonName': 'Test Taxon Without GBIF 2',
+            'taxonGroupId': self.taxon_group.id,
+            'rank': 'species',
+            'familyId': self.taxonomy.id,
+            'authorName': 'Test Author Without GBIF 2',
+        }
+        response = self.client.post(reverse('add-new-taxon'), data)
+        self.assertEqual(response.status_code, 200)
+        self.assertTrue('id' in response.data)
+        self.assertTrue('taxon_name' in response.data)
+        self.assertEqual(response.data['taxon_name'], 'Test Taxon Without GBIF 2')