Fix add new taxon (#4060)

bims/api_views/taxon_update.py

@@ -54,7 +54,7 @@ def create_taxon_proposal(taxon, taxon_group, data={}, iucn_status=None, endemis
         if data.get('tags'):
             proposal.tags.set(data.get('tags'))
         else:
-            proposal.tags.set(taxon.tags.all())
+            proposal.tags.clear()
         proposal.biographic_distributions.set(taxon.biographic_distributions.all())
         proposal.save()
 

bims/models/taxonomy.py

@@ -238,90 +238,6 @@ class AbstractTaxonomy(AbstractValidation):
     class Meta:
         abstract = True
 
-
-class Taxonomy(AbstractTaxonomy):
-    CATEGORY_CHOICES = (
-        (ORIGIN_CATEGORIES['non-native'], 'Non-Native'),
-        (ORIGIN_CATEGORIES['native'], 'Native'),
-        (ORIGIN_CATEGORIES['unknown'], 'Unknown'),
-        (ORIGIN_CATEGORIES['non-native: invasive'], 'Non-native: invasive'),
-        (
-            ORIGIN_CATEGORIES['non-native: non-invasive'],
-            'Non-native: non-invasive'
-        )
-    )
-    CATEGORY_CHOICES_DICT = {
-        ORIGIN_CATEGORIES['non-native']: 'Non-Native',
-        ORIGIN_CATEGORIES['native']: 'Native',
-        ORIGIN_CATEGORIES['unknown']: 'Unknown',
-        ORIGIN_CATEGORIES['non-native: invasive']: 'Non-native: invasive',
-        ORIGIN_CATEGORIES['non-native: non-invasive']: 'Non-native: non-invasive'
-    }
-
-    def save_json_data(self, json_field):
-        max_allowed = 10
-        attempt = 0
-        is_dictionary = False
-        json_data = {}
-        if not json_field:
-            return json_data
-        while not is_dictionary and attempt < max_allowed:
-            if not json_field:
-                break
-            if isinstance(json_field, dict):
-                is_dictionary = True
-                json_data = json_field
-            else:
-                json_data = json.loads(json_field)
-                attempt += 1
-        return json_data
-
-    # noinspection PyClassicStyleClass
-    class Meta:
-        """Meta class for project."""
-        app_label = 'bims'
-        verbose_name_plural = 'Taxa'
-        verbose_name = 'Taxonomy'
-
-    def __unicode__(self):
-        return '%s - %s' % (
-            self.scientific_name,
-            self.rank
-        )
-
-    def __str__(self):
-        return '%s - %s' % (
-            self.scientific_name,
-            self.rank
-        )
-
-    def get_direct_children(self):
-        children = Taxonomy.objects.filter(
-            parent=self
-        )
-        return children
-
-    def get_all_children(self):
-        query = {}
-        parent = ''
-        or_condition = models.Q()
-        for i in range(6):  # species to class
-            parent += 'parent__'
-            query[parent + 'in'] = [self]
-        for key, value in query.items():
-            or_condition |= models.Q(**{key: value})
-        return Taxonomy.objects.filter(or_condition)
-
-    def parent_by_rank(self, rank):
-        taxon = self
-        current_rank = taxon.rank
-        while current_rank != rank and taxon.parent:
-            taxon = taxon.parent
-            current_rank = taxon.rank
-        if current_rank == rank:
-            return taxon
-        return None
-
     @property
     def data_name(self):
         return self.canonical_name
@@ -421,6 +337,123 @@ def name(self):
             return self.scientific_name
         return '-'
 
+
+class Taxonomy(AbstractTaxonomy):
+    CATEGORY_CHOICES = (
+        (ORIGIN_CATEGORIES['non-native'], 'Non-Native'),
+        (ORIGIN_CATEGORIES['native'], 'Native'),
+        (ORIGIN_CATEGORIES['unknown'], 'Unknown'),
+        (ORIGIN_CATEGORIES['non-native: invasive'], 'Non-native: invasive'),
+        (
+            ORIGIN_CATEGORIES['non-native: non-invasive'],
+            'Non-native: non-invasive'
+        )
+    )
+    CATEGORY_CHOICES_DICT = {
+        ORIGIN_CATEGORIES['non-native']: 'Non-Native',
+        ORIGIN_CATEGORIES['native']: 'Native',
+        ORIGIN_CATEGORIES['unknown']: 'Unknown',
+        ORIGIN_CATEGORIES['non-native: invasive']: 'Non-native: invasive',
+        ORIGIN_CATEGORIES['non-native: non-invasive']: 'Non-native: non-invasive'
+    }
+
+    def save_json_data(self, json_field):
+        max_allowed = 10
+        attempt = 0
+        is_dictionary = False
+        json_data = {}
+        if not json_field:
+            return json_data
+        while not is_dictionary and attempt < max_allowed:
+            if not json_field:
+                break
+            if isinstance(json_field, dict):
+                is_dictionary = True
+                json_data = json_field
+            else:
+                json_data = json.loads(json_field)
+                attempt += 1
+        return json_data
+
+    # noinspection PyClassicStyleClass
+    class Meta:
+        """Meta class for project."""
+        app_label = 'bims'
+        verbose_name_plural = 'Taxa'
+        verbose_name = 'Taxonomy'
+
+    def __unicode__(self):
+        return '%s - %s' % (
+            self.scientific_name,
+            self.rank
+        )
+
+    def __str__(self):
+        return '%s - %s' % (
+            self.scientific_name,
+            self.rank
+        )
+
+    def get_direct_children(self):
+        children = Taxonomy.objects.filter(
+            parent=self
+        )
+        return children
+
+    def get_all_children(self):
+        query = {}
+        parent = ''
+        or_condition = models.Q()
+        for i in range(6):  # species to class
+            parent += 'parent__'
+            query[parent + 'in'] = [self]
+        for key, value in query.items():
+            or_condition |= models.Q(**{key: value})
+        return Taxonomy.objects.filter(or_condition)
+
+    def parent_by_rank(self, rank):
+        taxon = self
+        current_rank = taxon.rank
+        while current_rank != rank and taxon.parent:
+            taxon = taxon.parent
+            current_rank = taxon.rank
+        if current_rank == rank:
+            return taxon
+        return None
+
+
+    def save(self, *args, **kwargs):
+        update_taxon_with_gbif = False
+        if self.gbif_data:
+            self.gbif_data = self.save_json_data(self.gbif_data)
+        if self.additional_data:
+            self.additional_data = self.save_json_data(self.additional_data)
+        if self.additional_data and 'fetch_gbif' in self.additional_data:
+            update_taxon_with_gbif = True
+            del self.additional_data['fetch_gbif']
+        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),
+            }
+        elif 'family_name' not in self.hierarchical_data:
+            self.hierarchical_data['family_name'] = self.get_taxon_rank_name(TaxonomicRank.FAMILY.name)
+        elif 'species_name' not in self.hierarchical_data:
+            self.hierarchical_data['species_name'] = self.get_taxon_rank_name(TaxonomicRank.SPECIES.name)
+        elif 'genus_name' not in self.hierarchical_data:
+            self.hierarchical_data['genus_name'] = self.get_taxon_rank_name(TaxonomicRank.GENUS.name)
+
+        super(Taxonomy, self).save(*args, **kwargs)
+
+        if update_taxon_with_gbif:
+            from bims.utils.fetch_gbif import fetch_all_species_from_gbif
+            fetch_all_species_from_gbif(
+                species=self.scientific_name,
+                parent=self.parent,
+                gbif_key=self.gbif_key,
+                fetch_vernacular_names=True)
+
     def send_new_taxon_email(self, taxon_group_id=None):
         from bims.models import TaxonGroup
         from bims.tasks.send_notification import send_mail_notification

bims/models/taxonomy_update_proposal.py

@@ -208,6 +208,7 @@ def approve(self, reviewer: settings.AUTH_USER_MODEL):
                 'origin']
             for field in fields_to_update:
                 if field == 'tags':
+                    self.original_taxonomy.tags.clear()
                     self.original_taxonomy.tags.set(getattr(self, field).all())
                 else:
                     setattr(

bims/static/js/non_requirejs/helpers.js

@@ -1,37 +1,50 @@
 const speciesAutoComplete = (inputDiv, additionalFilters = "") => {
-    return new Promise(function (resolve, reject) {
-        inputDiv.autocomplete({
-            source: function (request, response) {
-                $.ajax({
-                    url: (
-                        `/species-autocomplete/?` +
-                        `term=${encodeURIComponent(request.term)}` +
-                        `${additionalFilters}`
-                    ),
-                    type: 'get',
-                    dataType: 'json',
-                    success: function (data) {
-                        response($.map(data, function (item) {
-                            return {
-                                label: item.species,
-                                value: item.id
-                            }
-                        }));
-                    }
-                });
+
+    const parseAdditionalFilters = (filterString) => {
+        const params = new URLSearchParams(filterString);
+        let filterObject = {};
+        for (const [key, value] of params.entries()) {
+            filterObject[key] = value;
+        }
+        return filterObject;
+    };
+    return new Promise((resolve, reject) => {
+        // Ensure inputDiv is a jQuery object
+        const $inputDiv = $(inputDiv);
+
+        if (typeof $inputDiv.select2 !== 'function') {
+            console.error('Select2 is not loaded.');
+            return reject(new Error('Select2 is not loaded.'));
+        }
+
+        const filters = parseAdditionalFilters(additionalFilters);
+
+        $inputDiv.select2({
+            ajax: {
+                url: '/species-autocomplete/',
+                dataType: 'json',
+                delay: 250,
+                data: (params) => ({
+                    term: params.term,
+                    ...filters
+                }),
+                processResults: (data) => ({
+                    results: data.map(item => ({
+                        id: item.id,
+                        text: item.species
+                    }))
+                }),
+                cache: true
             },
-            minLength: 3,
-            open: function (event, ui) {
-                setTimeout(function () {
-                    $('.ui-autocomplete').css('z-index', 9999)
-                }, 0);
-            },
-            select: function (e, u) {
-                e.preventDefault();
-                console.log('clicked');
-                inputDiv.val(u.item.label)
-                resolve(u.item.value)
-            }
-        })
-    })
-}
+            minimumInputLength: 3,
+            templateResult: (item) => item.text,
+            templateSelection: (item) => item.text
+        }).on('select2:select', (e) => {
+            resolve(e.params.data.id);
+        }).on('select2:open', () => {
+            setTimeout(() => {
+                $('.select2-results').css('z-index', 9999);
+            }, 0);
+        });
+    });
+};

bims/static/js/taxa_management/add_new_taxon.js

@@ -9,7 +9,7 @@ export const addNewTaxon = (() => {
 
     function showNewTaxonForm(taxonName) {
         let capitalizedTaxonName = taxonName.substr(0, 1).toUpperCase() + taxonName.substr(1).toLowerCase();
-        speciesAutoComplete($newTaxonFamilyInput, '&rank=family').then(value => {
+        speciesAutoComplete($newTaxonFamilyInput, '&rank=family&taxonGroupId=' + selectedTaxonGroup).then(value => {
             $newTaxonFamilyIdInput.val(value);
         })
         $newTaxonNameInput.val(capitalizedTaxonName);

bims/templates/edit_taxon.html

@@ -147,7 +147,15 @@ <h2>
                 <div class="col-sm-10">
                     <select name="iucn_status" id="iucn_status" class="form-control form-control-sm">
                         {% for iucn_status in iucn_status_choices %}
-                            <option value="{{ iucn_status.id }}" {% if iucn_status == object.iucn_status %}selected{% endif %}>{{ iucn_status.get_status }}</option>
+                            <option value="{{ iucn_status.id }}"
+                                    {% if object.iucn_status %}
+                                        {% if iucn_status == object.iucn_status %}selected{% endif %}
+                                    {% else %}
+                                        {% if iucn_status.category == 'NE' %}
+                                            selected
+                                        {% endif %}
+                                    {% endif %}
+                            >{{ iucn_status.get_status }}</option>
                         {% endfor %}
                     </select>
                 </div>

bims/templates/taxa_management.html

@@ -411,9 +411,13 @@ <h5 class="modal-title">Add New Taxon</h5>
                             </thead>
                             <tbody>
                             <tr>
-                                <td><input type="text" class="form-control new-taxon-family-name" placeholder="Family">
-                                    <input type="hidden" class="new-taxon-family-id"></td>
-                                <td><input type="text" class="form-control" placeholder="Taxon Name" id="new-taxon-name"></td>
+                                <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">
+                                </td>
+                                <td>
+                                    <input type="text" class="form-control" placeholder="Taxon Name" id="new-taxon-name">
+                                </td>
                                 <td>
 
                                     <div>
@@ -773,7 +777,7 @@ <h5 class="modal-title" id="statusModalLabel">Status</h5>
     </script>
     <script src="{% static "js/libs/jquery/jquery-3.3.1.min.js" %}"></script>
     <script src="https://cdn.jsdelivr.net/npm/[email protected]/underscore-umd-min.js"></script>
-    <script src="{% static "js/libs/jquery-ui-1.12.1/jquery-ui.min.js" %}"></script>
+   <script src="https://code.jquery.com/ui/1.13.3/jquery-ui.js"></script>
 
     <script src="https://cdn.datatables.net/v/dt/jq-3.7.0/dt-2.0.8/fc-5.0.1/fh-4.0.1/datatables.min.js"></script>
     <script src="{% static "library/popper.js/1.11.0/popper.min.js" %}" crossorigin="anonymous"></script>

bims/templatetags/site.py

@@ -111,4 +111,7 @@ def is_fada_site():
 
 @register.filter
 def get_attr(obj, attr_name):
-    return getattr(obj, attr_name)
+    try:
+        return getattr(obj, attr_name)
+    except AttributeError:
+        return ''