Add ecosystem type

bims/admin.py

@@ -442,7 +442,8 @@ class Media:
         'taxonomy',
         'taxonomy__origin',
         'record_type',
-        'sampling_method'
+        'sampling_method',
+        'ecosystem_type'
     )
     search_fields = (
         'taxonomy__scientific_name',

bims/api_views/search.py

@@ -307,6 +307,14 @@ def modules(self):
         else:
             return None
 
+    @property
+    def ecosystem_type(self):
+        ecosystem_type = self.get_request_data('ecosystemType')
+        if ecosystem_type:
+            return ecosystem_type.split(',')
+        else:
+            return None
+
     @property
     def spatial_filter(self):
         spatial_filters = self.parse_request_json('spatialFilter')
@@ -661,6 +669,12 @@ def process_search(self):
                 ))
                 bio_filtered = True
 
+        if self.ecosystem_type:
+            bio = bio.filter(
+               ecosystem_type__in=self.ecosystem_type
+            )
+            bio_filtered = True
+
         if self.modules:
             # For Intersection methods :
             if len(self.modules) > 1:

bims/enums/ecosystem_type.py

@@ -0,0 +1,9 @@
+ECOSYSTEM_RIVER = 'River'
+ECOSYSTEM_WETLAND = 'Wetland'
+ECOSYSTEM_OPEN_WATERBODY = 'Open waterbody'
+
+ECOSYSTEM_TYPE_CHOICES = (
+    (ECOSYSTEM_RIVER, ECOSYSTEM_RIVER),
+    (ECOSYSTEM_WETLAND, ECOSYSTEM_WETLAND),
+    (ECOSYSTEM_OPEN_WATERBODY, ECOSYSTEM_OPEN_WATERBODY)
+)

bims/migrations/0342_biologicalcollectionrecord_ecosystem_type_and_more.py

@@ -0,0 +1,19 @@
+# Generated by Django 4.1.10 on 2023-08-22 02:30
+
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+        ('bims', '0341_remove_bimsdocument_profile_locationsite_wetland_id_and_more'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='biologicalcollectionrecord',
+            name='ecosystem_type',
+            field=models.CharField(blank=True, choices=[('River', 'River'), ('Wetland', 'Wetland'), ('Open waterbody', 'Open waterbody')], default='', max_length=128, null=True),
+     ), ]

bims/migrations/0343_locationsite_ecosystem_type_and_more.py

@@ -0,0 +1,20 @@
+# Generated by Django 4.1.10 on 2023-08-23 01:01
+
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+        ('bims', '0342_biologicalcollectionrecord_ecosystem_type_and_more'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='locationsite',
+            name='ecosystem_type',
+            field=models.CharField(blank=True, choices=[('River', 'River'), ('Wetland', 'Wetland'), ('Open waterbody', 'Open waterbody')], default='', max_length=128, null=True),
+        ),
+    ]

bims/models/biological_collection_record.py

@@ -20,6 +20,7 @@
 from bims.enums.taxonomic_group_category import TaxonomicGroupCategory
 from bims.models.bims_document import BimsDocument
 from bims.models.survey import Survey
+from bims.enums.ecosystem_type import ECOSYSTEM_TYPE_CHOICES
 from td_biblio.models import Entry
 
 
@@ -321,6 +322,14 @@ class BiologicalCollectionRecord(AbstractValidation):
         null=True
     )
 
+    ecosystem_type = models.CharField(
+        max_length=128,
+        blank=True,
+        choices=ECOSYSTEM_TYPE_CHOICES,
+        default='',
+        null=True
+    )
+
     @property
     def data_name(self):
         return self.original_species_name

bims/models/location_site.py

@@ -20,11 +20,11 @@
 from bims.models.location_type import LocationType
 from bims.utils.get_key import get_key
 from bims.models.document_links_mixin import DocumentLinksMixin
-from bims.models.search_process import SearchProcess
 from bims.enums.geomorphological_zone import GeomorphologicalZoneCategory
 from bims.models.location_context import LocationContext
 from bims.models.location_context_group import LocationContextGroup
 from bims.utils.decorator import prevent_recursion
+from bims.enums.ecosystem_type import ECOSYSTEM_TYPE_CHOICES
 
 LOGGER = logging.getLogger(__name__)
 
@@ -173,6 +173,14 @@ class LocationSite(DocumentLinksMixin, AbstractValidation):
         max_length=256
     )
 
+    ecosystem_type = models.CharField(
+        max_length=128,
+        blank=True,
+        choices=ECOSYSTEM_TYPE_CHOICES,
+        default='',
+        null=True
+    )
+
     @property
     def location_site_identifier(self):
         """

bims/scripts/collection_csv_keys.py

@@ -27,6 +27,7 @@
 BROAD_BIOTOPE = 'Broad biotope'
 SPECIFIC_BIOTOPE = 'Specific biotope'
 SUBSTRATUM = 'Substratum'
+ECOSYSTEM_TYPE = 'Ecosystem type'
 
 # Chemical records
 TEMP = 'TEMP'

bims/scripts/occurrences_upload.py

@@ -228,6 +228,11 @@ def process_survey(self, record, location_site, sampling_date, collector):
     def location_site(self, record):
         """ Process location site data """
         location_site = None
+
+        # -- Ecosystem type
+        ecosystem_type = DataCSVUpload.row_value(
+            record, ECOSYSTEM_TYPE)
+
         location_type, status = LocationType.objects.get_or_create(
             name='PointObservation',
             allowed_geometry='POINT'
@@ -292,21 +297,24 @@ def location_site(self, record):
             if len(str(latitude)) > 5 and len(str(longitude)) > 5:
                 location_site = LocationSite.objects.filter(
                     latitude__startswith=latitude,
-                    longitude__startswith=longitude
+                    longitude__startswith=longitude,
+                    ecosystem_type=ecosystem_type
                 ).first()
 
         if not location_site:
             try:
                 location_site, status = (
                     LocationSite.objects.get_or_create(
                         location_type=location_type,
-                        geometry_point=record_point
+                        geometry_point=record_point,
+                        ecosystem_type=ecosystem_type
                     )
                 )
             except LocationSite.MultipleObjectsReturned:
                 location_site = LocationSite.objects.filter(
                     location_type=location_type,
-                    geometry_point=record_point
+                    geometry_point=record_point,
+                    ecosystem_type=ecosystem_type
                 ).first()
         if not location_site.name and location_site_name:
             location_site.name = location_site_name
@@ -700,9 +708,14 @@ def process_data(self, row):
         if self.module_group:
             record.module_group = self.module_group
 
+        # -- Ecosystem type
+        record.ecosystem_type = DataCSVUpload.row_value(
+            row, ECOSYSTEM_TYPE)
+
         # -- Additional data
         record.additional_data = json.dumps(row)
         record.validated = True
+
         record.save()
 
         if not str(record.site.id) in self.site_ids:

bims/serializers/bio_collection_serializer.py

@@ -605,6 +605,7 @@ class Meta:
             'river_name',
             'user_site_code',
             'site_code',
+            'ecosystem_type',
             'site_description',
             'refined_geomorphological_zone',
             'latitude',

bims/static/js/router.js

@@ -13,32 +13,19 @@ define(['backbone', 'views/olmap', 'utils/events_connector', 'shared'], function
             "site/:params": "showSingleSiteDetail"
         },
         initializeParameters: function () {
-            this.parameters['taxon'] = '';
-            this.parameters['months'] = '';
-            this.parameters['siteId'] = '';
-            this.parameters['search'] = '';
-            this.parameters['collector'] = '';
-            this.parameters['category'] = '';
-            this.parameters['yearFrom'] = '';
-            this.parameters['yearTo'] = '';
-            this.parameters['userBoundary'] = '';
-            this.parameters['referenceCategory'] = '';
-            this.parameters['boundary'] = '';
-            this.parameters['reference'] = '';
-            this.parameters['endemic'] = '';
-            this.parameters['conservationStatus'] = '';
-            this.parameters['spatialFilter'] = '';
-            this.parameters['taxon'] = '';
-            this.parameters['validated'] = '';
-            this.parameters['modules'] = '';
-            this.parameters['sourceCollection'] = '';
-            this.parameters['ecologicalCategory'] = '';
-            this.parameters['module'] = '';
-            this.parameters['rank'] = '';
-            this.parameters['orderBy'] = '';
-            this.parameters['siteIdOpen'] = '';
-            this.parameters['polygon'] = '';
-            this.parameters['dst'] = '';
+            const parameterKeys = [
+                'taxon', 'months', 'siteId', 'search', 'collector',
+                'category', 'yearFrom', 'yearTo', 'userBoundary', 'referenceCategory',
+                'boundary', 'reference', 'endemic', 'conservationStatus', 'spatialFilter',
+                'taxon', 'validated', 'modules', 'sourceCollection', 'ecologicalCategory',
+                'module', 'rank', 'orderBy', 'siteIdOpen', 'polygon',
+                'dst', 'ecosystemType'
+            ];
+
+            parameterKeys.forEach(key => {
+                this.parameters[key] = '';
+            });
+
             if (typeof filterParameters !== 'undefined') {
                 filterParameters = $.extend(true, {}, this.parameters);
             }

bims/static/js/shared.js

@@ -12,7 +12,7 @@ define(['backbone', 'underscore', 'utils/storage', 'utils/color', 'utils/url', '
             "&reference=<%= reference %>&endemic=<%= endemic %>&conservationStatus=<%= conservationStatus %>" +
             "&modules=<%= modules %>&validated=<%= validated %>&sourceCollection=<%= sourceCollection %>" +
             "&module=<%= module %>&ecologicalCategory=<%= ecologicalCategory %>&rank=<%= rank %>"+
-            "&siteIdOpen=<%= siteIdOpen %>&orderBy=<%= orderBy %>&polygon=<%= polygon %>&dst=<%= dst %>",
+            "&siteIdOpen=<%= siteIdOpen %>&orderBy=<%= orderBy %>&polygon=<%= polygon %>&dst=<%= dst %>&ecosystemType=<%= ecosystemType %>",
         LocationSiteDetailXHRRequest: null,
         MultiSitesOverviewXHRRequest: null,
         TaxonDetailXHRRequest: null,

bims/static/js/utils/filter_list.js

@@ -23,6 +23,10 @@ let filterParametersJSON = {
         'label': 'Site Id',
         'type': 'comma'
     },
+    'ecosystemType': {
+        'label': 'Ecosystem Type',
+        'type': 'comma'
+    },
     'collector': {
         'label': 'Collector',
         'type': 'json'

bims/static/js/views/detail_dashboard/site_detail.js

@@ -1446,8 +1446,7 @@ define([
                             continue;
                         }
                     }
-
-                    if(keys[i] === 'DOI/URL' && document && source[keys[i]].indexOf('/uploaded/') > -1) {
+                    if(keys[i] === 'DOI/URL' && document && source[keys[i]] && source[keys[i]].indexOf('/uploaded/') > -1) {
                         itemDiv.append('<td><a href="'+ source[keys[i]] + '" target="_blank">Download</a></td>')
                     } else if (keys[i] === 'DOI/URL' && source[keys[i]] && source[keys[i]].substring(0, 4) !== 'http') {
                         itemDiv.append(`<td><a href="http://dx.doi.org/${source[keys[i]]}" target="_blank">${source[keys[i]]}</a></td>`);

bims/static/js/views/search.js

@@ -86,6 +86,7 @@ define([
                 }
             }
             let occurrencesFilter = [
+                'ecosystem-type-container',
                 'biodiversity-module-container',
                 'data-source-container',
                 'validation-status-container',
@@ -515,6 +516,20 @@ define([
             }
             filterParameters['validated'] = validated;
 
+            // Ecosystem type filter
+            let ecosystemTypeFilter = [];
+            let ecosystemType = '';
+            $('[name=filter-ecosystem-type]:checked').each(function () {
+                ecosystemTypeFilter.push($(this).attr('value'));
+            });
+            if (ecosystemTypeFilter.length > 0 && $('[name=filter-ecosystem-type]').length !== ecosystemTypeFilter.length) {
+                ecosystemType = ecosystemTypeFilter.join();
+                self.highlightPanel('.ecosystem-type-row', true);
+            } else {
+                self.highlightPanel('.ecosystem-type-row', false);
+            }
+            filterParameters['ecosystemType'] = ecosystemType;
+
             // ecological category
             var ecologicalConditions = '';
             if (self.selectedEcologicalConditions.length > 0) {
@@ -556,29 +571,18 @@ define([
             Shared.Dispatcher.trigger('map:closeHighlight');
             Shared.Dispatcher.trigger(Shared.EVENTS.SEARCH.HIT, filterParameters);
             Shared.Dispatcher.trigger('sidePanel:closeSidePanel');
-            if (!filterParameters['search']
-                && !filterParameters['collector']
-                && !filterParameters['validated']
-                && !filterParameters['category']
-                && !filterParameters['yearFrom']
-                && !filterParameters['yearTo']
-                && !filterParameters['userBoundary']
-                && !filterParameters['referenceCategory']
-                && !filterParameters['reference']
-                && !filterParameters['endemic']
-                && !filterParameters['modules']
-                && !filterParameters['conservationStatus']
-                && !filterParameters['spatialFilter']
-                && !filterParameters['ecologicalCategory']
-                && !filterParameters['sourceCollection']
-                && !filterParameters['abioticData']
-                && !filterParameters['polygon']
-                && !filterParameters['boundary']
-                && !filterParameters['dst']
-                && !filterParameters['thermalModule']) {
+            const keysToCheck = [
+                'search', 'collector', 'validated', 'ecosystemType', 'category',
+                'yearFrom', 'yearTo', 'userBoundary', 'referenceCategory', 'reference',
+                'endemic', 'modules', 'conservationStatus', 'spatialFilter',
+                'ecologicalCategory', 'sourceCollection', 'abioticData', 'polygon',
+                'boundary', 'dst', 'thermalModule'
+            ];
+            const hasAnyTruthyValue = keysToCheck.some(key => filterParameters[key]);
+            if (!hasAnyTruthyValue) {
                 Shared.Dispatcher.trigger('cluster:updateAdministrative', '');
                 Shared.Router.clearSearch();
-                return false
+                return false;
             }
             this.searchResultCollection.search(
                 this.searchPanel,
@@ -651,6 +655,8 @@ define([
             this.searchPanel.clearSidePanel();
             this.clearClickedOriginButton();
 
+            $('[name=filter-ecosystem-type]').prop('checked', true);
+
             Shared.Dispatcher.trigger('politicalRegion:clear');
 
             Shared.Dispatcher.trigger('spatialFilter:clearSelected');
@@ -855,6 +861,18 @@ define([
                 $('[name="module"]').trigger('change');
             }
 
+            // Search module
+            if (allFilters.hasOwnProperty('ecosystemType')) {
+                let ecosystemTypes = allFilters['ecosystemType'].split(',');
+                $('[name=filter-ecosystem-type]').each(function () {
+                    if (ecosystemTypes.includes($(this).attr('value'))) {
+                        $(this).prop('checked', true);
+                    } else {
+                        $(this).prop('checked', false);
+                    }
+                });
+            }
+
             // Collectors
             self.initialSelectedCollectors = [];
             if (allFilters.hasOwnProperty('collector')) {