Update edit form, fix taxon group experts (#4196)

bims/api_views/taxon.py

@@ -15,6 +15,7 @@
 from rest_framework.pagination import PageNumberPagination
 from taggit.models import Tag
 
+from bims.api_views.taxon_update import is_expert
 from bims.models.taxonomy import Taxonomy, TaxonTag, CustomTaggedTaxonomy
 from bims.serializers.taxon_detail_serializer import TaxonDetailSerializer
 from bims.serializers.taxon_serializer import TaxonSerializer
@@ -655,12 +656,17 @@ def get(self, request, *args):
         page = self.paginate_queryset(taxon_list)
         validated = ast.literal_eval(request.GET.get('validated', 'True'))
         if page is not None:
+            taxon_group_id = request.GET.get('taxonGroup', None)
             serializer = self.get_paginated_response(
                 TaxonSerializer(page, many=True, context={
-                    'taxon_group_id': request.GET.get('taxonGroup', None),
+                    'taxon_group_id': taxon_group_id,
                     'user': request.user.id,
                     'validated': validated
                 }).data)
+            serializer.data['is_expert'] = is_expert(
+                self.request.user,
+                TaxonGroup.objects.get(id=taxon_group_id)
+            ) if taxon_group_id else False
         else:
             serializer = TaxonSerializer(
                 taxon_list,

bims/api_views/taxon_update.py

@@ -43,12 +43,21 @@ def create_taxon_proposal(
         'Taxonomic Comments',
         'Conservation Comments',
         'Biogeographic Comments',
-        'Environmental Comments'
+        'Environmental Comments',
+        'Taxonomic References',
+        'Conservation References',
+        'Biogeographic References',
+        'Environmental References'
     ]
     for additional_key in additional_data_to_check:
         if data.get(additional_key):
             additional_data[additional_key] = data.get(additional_key)
 
+    canonical_name = data.get('canonical_name', taxon.canonical_name)
+    if taxon.is_species:
+        if taxon.genus_name not in canonical_name:
+            canonical_name = taxon.genus_name + ' ' + canonical_name
+
     proposal, created = TaxonomyUpdateProposal.objects.get_or_create(
         original_taxonomy=taxon,
         taxon_group=taxon_group,
@@ -57,15 +66,15 @@ def create_taxon_proposal(
             'author': data.get('author', taxon.author),
             'rank': data.get('rank', taxon.rank),
             'scientific_name': data.get('scientific_name', taxon.scientific_name),
-            'canonical_name': data.get('canonical_name', taxon.canonical_name),
+            'canonical_name': canonical_name,
             'origin': data.get('origin', taxon.origin),
             'iucn_status': iucn_status,
             'endemism': endemism,
             'taxon_group_under_review': taxon_group,
             'taxonomic_status': taxonomic_status,
             'accepted_taxonomy': accepted_taxonomy,
             'parent': data.get('parent', taxon.parent),
-            'hierarchical_data': taxon.hierarchical_data,
+            'hierarchical_data': {},
             'gbif_data': taxon.gbif_data,
             'collector_user': creator,
             'additional_data': additional_data
@@ -114,6 +123,8 @@ def update_taxon_proposal(
 def is_expert(user, taxon_group):
     if user.is_superuser:
         return True
+    if not taxon_group:
+        return False
     return taxon_group.experts.filter(
         id=user.id
     ).exists()

bims/models/taxonomy.py

@@ -338,6 +338,12 @@ def sub_tribe_name(self):
     def variety_name(self):
         self.get_taxon_rank_name(TaxonomicRank.VARIETY.name)
 
+    @property
+    def taxon_name(self):
+        if self.is_species and self.genus_name:
+            return self.canonical_name.split(self.genus_name)[-1].strip()
+        return self.canonical_name
+
     @property
     def is_species(self):
         return (
@@ -483,18 +489,24 @@ def save(self, *args, **kwargs):
         if self.additional_data and 'fetch_gbif' in self.additional_data:
             update_taxon_with_gbif = True
             del self.additional_data['fetch_gbif']
+        species_name = ''
+        if not self.hierarchical_data or 'species_name' not in self.hierarchical_data:
+            species_name = self.species_name
+            genus_name = self.genus_name
+            if genus_name in species_name and genus_name:
+                species_name = species_name.split(genus_name)[-1].strip()
         if not self.hierarchical_data:
             self.hierarchical_data = {
                 'family_name': self.get_taxon_rank_name(TaxonomicRank.FAMILY.name),
                 'genus_name': self.get_taxon_rank_name(TaxonomicRank.GENUS.name),
-                'species_name': self.get_taxon_rank_name(TaxonomicRank.SPECIES.name),
+                'species_name': species_name
             }
         elif 'family_name' not in self.hierarchical_data:
             self.hierarchical_data['family_name'] = self.get_taxon_rank_name(TaxonomicRank.FAMILY.name)
         elif 'genus_name' not in self.hierarchical_data:
             self.hierarchical_data['genus_name'] = self.get_taxon_rank_name(TaxonomicRank.GENUS.name)
         elif 'species_name' not in self.hierarchical_data:
-            self.hierarchical_data['species_name'] = self.get_taxon_rank_name(TaxonomicRank.SPECIES.name)
+            self.hierarchical_data['species_name'] = species_name
 
         super(Taxonomy, self).save(*args, **kwargs)
 

bims/models/taxonomy_update_proposal.py

@@ -310,6 +310,7 @@ def approve(self, reviewer: settings.AUTH_USER_MODEL):
                     setattr(
                         self.original_taxonomy,
                         field, getattr(self, field))
+            self.original_taxonomy.hierarchical_data = {}
             self.original_taxonomy.save()
             self.status = 'approved'
             self.save()

bims/static/js/taxa_management/taxa_management.js

@@ -357,6 +357,12 @@ export const taxaManagement = (() => {
                     success: function (response) {
                         loading.hide();
                         taxaData = response.results;
+                        $('#add-taxon-btn').hide();
+
+                        if (response['is_expert']) {
+                            $('#add-taxon-btn').show();
+                        }
+
                         $.each(response.results, function (index, data) {
                             let name = data.canonical_name || data.scientific_name;
                             let taxonomicStatusHTML = (data.taxonomic_status && data.taxonomic_status.toLowerCase() === 'synonym') ?
@@ -366,7 +372,6 @@ export const taxaManagement = (() => {
                             let validatedHTML = !data.validated ? '<span class="badge badge-secondary">Unvalidated</span>' : '';
 
                             data.nameHTML = name + '<br/>' + gbifHTML + iucnHTML + validatedHTML + `<input type="hidden" class="proposal-id" value="${data.proposal_id}" />`;
-
                             if (data['can_edit']) {
                                 let $rowAction = $('.row-action').clone(true, true).removeClass('row-action');
                                 if (!data['validated']) {

bims/templates/edit_taxon.html

@@ -85,7 +85,8 @@ <h2>
                 <div class="col-sm-10">
                     <input type="text" name="canonical_name" id="canonical_name"
                            class="form-control form-control-sm"
-                           placeholder="" value="{{ object.canonical_name }}" >
+                           placeholder=""
+                           value="{{ object.taxon_name }}" >
                 </div>
             </div>
 
@@ -218,13 +219,13 @@ <h2>
 
             <div class="form-group row">
                 <label for="rank" class="col-sm-2 col-form-label col-form-label">
-                    Conservation Comments
+                    Taxonomic References
                 </label>
                 <div class="col-sm-10">
-                    <input type="text" name="additional_data__Conservation_Comments" id="additional_data__Conservation_Comments"
+                    <input type="text" name="additional_data__Taxonomic_References" id="additional_data__Taxonomic_References"
                            class="form-control form-control-sm"
                            placeholder=""
-                           value="{% with object.additional_data as data %}{% if data|value_by_key:'Conservation Comments' %}{{ data|value_by_key:'Conservation Comments' }}{% elif data|value_by_key:'Conservation comments' %}{{ data|value_by_key:'Conservation comments' }}{% else %}{% endif %}{% endwith %}" >
+                           value="{% with object.additional_data as data %}{% if data|value_by_key:'Taxonomic References' %}{{ data|value_by_key:'Taxonomic References' }}{% endif %}{% endwith %}" >
                 </div>
             </div>
 
@@ -239,6 +240,18 @@ <h2>
                 </div>
             </div>
 
+            <div class="form-group row">
+                <label for="rank" class="col-sm-2 col-form-label col-form-label">
+                    Biogeographic References
+                </label>
+                <div class="col-sm-10">
+                    <input type="text" name="additional_data__Biogeographic_References" id="additional_data__Biogeographic_References"
+                           class="form-control form-control-sm"
+                           placeholder=""
+                           value="{% with object.additional_data as data %}{% if data|value_by_key:'Biogeographic References' %}{{ data|value_by_key:'Biogeographic References' }}{% endif %}{% endwith %}" >
+                </div>
+            </div>
+
             <div class="form-group row">
                 <label for="rank" class="col-sm-2 col-form-label col-form-label">
                     Environmental Comments
@@ -250,6 +263,42 @@ <h2>
                 </div>
             </div>
 
+            <div class="form-group row">
+                <label for="rank" class="col-sm-2 col-form-label col-form-label">
+                    Environmental References
+                </label>
+                <div class="col-sm-10">
+                    <input type="text" name="additional_data__Environmental_References" id="additional_data__Environmental_References"
+                           class="form-control form-control-sm"
+                           placeholder=""
+                           value="{% with object.additional_data as data %}{% if data|value_by_key:'Environmental References' %}{{ data|value_by_key:'Environmental References' }}{% endif %}{% endwith %}" >
+                </div>
+            </div>
+
+            <div class="form-group row">
+                <label for="rank" class="col-sm-2 col-form-label col-form-label">
+                    Conservation Comments
+                </label>
+                <div class="col-sm-10">
+                    <input type="text" name="additional_data__Conservation_Comments" id="additional_data__Conservation_Comments"
+                           class="form-control form-control-sm"
+                           placeholder=""
+                           value="{% with object.additional_data as data %}{% if data|value_by_key:'Conservation Comments' %}{{ data|value_by_key:'Conservation Comments' }}{% elif data|value_by_key:'Conservation comments' %}{{ data|value_by_key:'Conservation comments' }}{% else %}{% endif %}{% endwith %}" >
+                </div>
+            </div>
+
+            <div class="form-group row">
+                <label for="rank" class="col-sm-2 col-form-label col-form-label">
+                    Conservation References
+                </label>
+                <div class="col-sm-10">
+                    <input type="text" name="additional_data__Conservation_References" id="additional_data__Conservation_References"
+                           class="form-control form-control-sm"
+                           placeholder=""
+                           value="{% with object.additional_data as data %}{% if data|value_by_key:'Conservation References' %}{{ data|value_by_key:'Conservation References' }}{% endif %}{% endwith %}" >
+                </div>
+            </div>
+
             <div class="form-group submit-holder">
                 {% if update %}
                     {% if allow_to_edit %}

bims/templates/taxa_management.html

@@ -273,10 +273,10 @@ <h2>Taxon Management</h2>
                     </div>
                     <!-- Download button -->
                     <div class="float-right download-button-container"
-                         style="margin-top: -47px; display: none">
-                        {% if perms.bims.add_taxonomy or is_expert %}
+                         style="margin-top: -47px;">
                         <button id="add-taxon-btn"
                                 class="btn btn-outline-success" data-toggle="modal"
+                                style="display: none"
                                 data-target="#addNewTaxonModal">Add a taxon
                         </button>
                         <div class="btn-group">
@@ -289,7 +289,6 @@ <h2>Taxon Management</h2>
                                 <a class="dropdown-item disabled" href="#" id="download-pdf">PDF Report</a>
                             </div>
                         </div>
-                        {% endif %}
                     </div>
                     <div class="taxa-table">
                         <table id="taxaTable" class="table stripe">
@@ -306,18 +305,9 @@ <h2>Taxon Management</h2>
                                 <th scope="col">Biographic distributions</th>
                                 <th scope="col">Accepted Taxon</th>
                                 <th scope="col">Rank</th>
-{#                                <th scope="col">Origin#}
-{#                                </th>#}
-{#                                <th scope="col">Endemism#}
-{#                                </th>#}
-{#                                <th scope="col">Records#}
-{#                                </th>#}
-
                                 <th scope="col">
                                     {% if fada_site %}Environmental Information{% else %}Tags{% endif %}</th>
-                                {% if perms.bims.change_taxonomy or is_expert %}
-                                    <th scope="col"></th>
-                                {% endif %}
+                                <th scope="col"></th>
                             </tr>
                             </thead>
                             <tbody id="taxa-list"></tbody>
@@ -340,7 +330,6 @@ <h2>Taxon Management</h2>
                     </div>
                 </div>
 
-                {% if perms.bims.change_taxonomy or is_expert %}
                 {% with preferences.SiteSetting.project_name as project_name %}
                 <div class="row-action" style="display: none">
                     <div class="btn-validated-container">
@@ -360,9 +349,6 @@ <h2>Taxon Management</h2>
                                     <i class="fa fa-pencil-square-o" aria-hidden="true"></i> Edit in Admin
                                 </a>
                                 {% endif %}
-{#                                <button class="dropdown-item add-tag" title="Manage tags">#}
-{#                                    <i class="fa fa-tags" aria-hidden="true"></i> Manage tags#}
-{#                                </button>#}
                             </div>
                         </div>
                     </div>
@@ -386,7 +372,6 @@ <h2>Taxon Management</h2>
                     </div>
                 </div>
                 {% endwith %}
-                {% endif %}
 
             </div>
         </div>

bims/templatetags/jsonify.py

@@ -63,6 +63,8 @@ def get_html_for_radio_group_headings(column_count):
 
 @register.filter
 def value_by_key(d, key):
+    if not d:
+        return ''
     if key in d:
         return d[key]
     return ''

bims/views/edit_taxon_view.py

@@ -101,12 +101,20 @@ def form_valid(self, form):
 
         data['Taxonomic Comments'] = (
             self.request.POST.get('additional_data__Taxonomic_Comments', '')).strip()
-        data['Conservation Comments'] = (
-            self.request.POST.get('additional_data__Conservation_Comments', '')).strip()
+        data['Taxonomic References'] = (
+            self.request.POST.get('additional_data__Taxonomic_References', '')).strip()
         data['Biogeographic Comments'] = (
             self.request.POST.get('additional_data__Biogeographic_Comments', '')).strip()
+        data['Biogeographic References'] = (
+            self.request.POST.get('additional_data__Biogeographic_References', '')).strip()
         data['Environmental Comments'] = (
             self.request.POST.get('additional_data__Environmental_Comments', '')).strip()
+        data['Environmental References'] = (
+            self.request.POST.get('additional_data__Environmental_References', '')).strip()
+        data['Conservation Comments'] = (
+            self.request.POST.get('additional_data__Conservation_Comments', '')).strip()
+        data['Conservation References'] = (
+            self.request.POST.get('additional_data__Conservation_References', '')).strip()
 
         new_proposal = False