Bump sentry-sdk from 1.40.0 to 2.8.0 in /deployment/production

bims/admin.py

@@ -1901,7 +1901,11 @@ class TaxonomyUpdateProposalAdmin(admin.ModelAdmin):
         'original_taxonomy',
         'scientific_name',
         'canonical_name',
-        'status'
+        'status',
+        'created_at'
+    )
+    autocomplete_fields = (
+        'vernacular_names',
     )
 
 

bims/api_views/checklist.py

@@ -2,14 +2,24 @@
 import os
 from django.conf import settings
 from django.http import Http404
+from django.template.loader import render_to_string
 from preferences import preferences
+from reportlab.lib import colors
+from reportlab.lib.pagesizes import A4, landscape
+from reportlab.lib.styles import getSampleStyleSheet
+from reportlab.lib.units import cm
+from reportlab.platypus import SimpleDocTemplate, TableStyle, Table, Spacer
+from reportlab.platypus.para import Paragraph
 from rest_framework.response import Response
 from rest_framework.views import APIView
 
 from bims.api_views.search import CollectionSearch
 from bims.models.taxonomy import Taxonomy
 from bims.models.download_request import DownloadRequest
-from bims.serializers.checklist_serializer import ChecklistSerializer
+from bims.serializers.checklist_serializer import (
+    ChecklistSerializer,
+    ChecklistPDFSerializer
+)
 from bims.utils.url import parse_url_to_filters
 from bims.tasks.checklist import download_checklist
 from bims.tasks.email_csv import send_csv_via_email
@@ -61,10 +71,22 @@ def generate_checklist(download_request_id):
     batch_size = 1000
     collection_records = search.process_search().distinct('taxonomy')
 
+    if (
+        download_request.resource_type and
+        download_request.resource_type.lower() == 'pdf'
+    ):
+        return generate_pdf_checklist(
+            download_request, collection_records, batch_size)
+    else:
+        return generate_csv_checklist(
+            download_request, collection_records, batch_size)
+
+
+def generate_csv_checklist(download_request, collection_records, batch_size):
     csv_file_path = os.path.join(
         settings.MEDIA_ROOT,
         'checklists',
-        f'checklist_{download_request_id}.csv')
+        f'checklist_{download_request.id}.csv')
     os.makedirs(os.path.dirname(csv_file_path), exist_ok=True)
 
     fieldnames = [key for key in get_serializer_keys(ChecklistSerializer) if key != 'id']
@@ -83,14 +105,81 @@ def generate_checklist(download_request_id):
             batch = collection_records[start:start + batch_size]
             process_batch(batch, writer, written_taxa_ids)
 
-    # Save file path to download_request
     download_request.processing = False
     download_request.request_file = csv_file_path
     download_request.save()
 
     return True
 
 
+def generate_pdf_checklist(download_request, collection_records, batch_size):
+    pdf_file_path = os.path.join(
+        settings.MEDIA_ROOT,
+        'checklists',
+        f'checklist_{download_request.id}.pdf')
+    os.makedirs(os.path.dirname(pdf_file_path), exist_ok=True)
+
+    written_taxa_ids = set()
+    all_taxa = []
+
+    for start in range(0, collection_records.count(), batch_size):
+        batch = collection_records[start:start + batch_size]
+        record_taxonomy_ids = batch.values_list('taxonomy_id', flat=True)
+        unique_taxonomy_ids = set(record_taxonomy_ids) - written_taxa_ids
+
+        if unique_taxonomy_ids:
+            taxa = Taxonomy.objects.filter(id__in=unique_taxonomy_ids)
+            taxon_serializer = ChecklistPDFSerializer(taxa, many=True)
+            for taxon in taxon_serializer.data:
+                written_taxa_ids.add(taxon['id'])
+                del taxon['id']
+                all_taxa.append([
+                    Paragraph(taxon['scientific_name'], getSampleStyleSheet()['Normal']),
+                    Paragraph(taxon['common_name'], getSampleStyleSheet()['Normal']),
+                    Paragraph(taxon['threat_status'], getSampleStyleSheet()['Normal']),
+                    Paragraph(taxon['sources'], getSampleStyleSheet()['Normal'])
+                ])
+
+    # Generate the PDF
+    doc = SimpleDocTemplate(
+        pdf_file_path,
+        pagesize=landscape(A4), topMargin=0.5 * cm, bottomMargin=0.35 * cm)
+    elements = []
+
+    # Define table style
+    style_table = TableStyle([
+        ('BACKGROUND', (0, 0), (-1, 0), '#0D3511'),
+        ('TEXTCOLOR', (0, 0), (-1, 0), colors.white),
+        ('ALIGN', (0, 0), (-1, -1), 'LEFT'),
+        ('VALIGN', (0, 0), (-1, -1), 'TOP'),
+        ('FONTNAME', (0, 0), (-1, 0), 'Helvetica-Bold'),
+        ('FONTSIZE', (0, 0), (-1, 0), 11),
+        ('BOTTOMPADDING', (0, 0), (-1, 0), 5),
+        ('BACKGROUND', (0, 1), (-1, -1), colors.white),
+        ('GRID', (0, 0), (-1, -1), 1, colors.black),
+        ('LEFTPADDING', (0, 0), (-1, -1), 2),
+        ('RIGHTPADDING', (0, 0), (-1, -1), 2),
+        ('TOPPADDING', (0, 0), (-1, -1), 2),
+        ('BOTTOMPADDING', (0, 0), (-1, -1), 2),
+    ])
+
+    data = [['Scientific Name', 'Common Name', 'Threat Status', 'Sources']] + all_taxa
+    table_width = doc.width
+    col_widths = [table_width * 0.35, table_width * 0.30, table_width * 0.15, table_width * 0.30]
+
+    table = Table(data, colWidths=col_widths)
+    table.setStyle(style_table)
+
+    elements.append(table)
+    doc.build(elements)
+
+    download_request.processing = False
+    download_request.request_file = pdf_file_path
+    download_request.save()
+
+    return True
+
+
 def process_batch(batch, writer, written_taxa_ids):
     """
     Process a batch of collection records and write unique taxa to the CSV file.

bims/api_views/module_summary.py

@@ -1,5 +1,7 @@
 from django.contrib.sites.models import Site
 import threading
+
+from django.db.models.functions import Coalesce
 from rest_framework.views import APIView
 from rest_framework.response import Response
 from allauth.utils import get_user_model
@@ -13,7 +15,7 @@
 )
 from bims.models.taxonomy import Taxonomy
 from bims.enums.taxonomic_group_category import TaxonomicGroupCategory
-from bims.cache import get_cache, LANDING_PAGE_MODULE_SUMMARY_CACHE, set_cache
+from bims.cache import get_cache, LANDING_PAGE_MODULE_SUMMARY_CACHE, set_cache, delete_cache
 from sass.models.site_visit_taxon import SiteVisitTaxon
 from sass.models.site_visit import SiteVisit
 
@@ -90,17 +92,26 @@ def get_origin_summary(self, collections):
         """
         Returns origin summary data from the provided collections
         """
-        origin_data = dict(
-            collections.exclude(taxonomy__origin__exact='').values(
-                'taxonomy__origin').annotate(
-                count=Count('taxonomy__origin')
-            ).values_list('taxonomy__origin', 'count'))
+        origin_data = collections.annotate(
+            origin_value=Coalesce(
+                Case(
+                    When(taxonomy__origin='', then=Value('Unknown')),
+                    default=F('taxonomy__origin')
+                ),
+                Value('Unknown')
+            )
+        ).values('origin_value').annotate(
+            count=Count('origin_value')
+        ).values_list('origin_value', 'count')
+
+        origin_data_dict = dict(origin_data)
         updated_origin_data = {}
         origin_category = dict(Taxonomy.CATEGORY_CHOICES)
-        for key in origin_data.keys():
-            updated_origin_data[origin_category[key]] = (
-                origin_data[key]
-            )
+
+        for key, count in origin_data_dict.items():
+            category_name = origin_category.get(key, 'Unknown')
+            updated_origin_data[category_name] = count
+
         return updated_origin_data
 
     def get_endemism_summary(self, collections):
@@ -148,16 +159,29 @@ def get_conservation_status_summary(self, collections):
             collections.annotate(
                 value=Case(When(taxonomy__iucn_status__isnull=False,
                                 then=F('taxonomy__iucn_status__category')),
-                           default=Value('Not evaluated'))
+                           default=Value('NE'))
             ).values('value').annotate(
                 count=Count('value')
             ).values_list('value', 'count')
         )
         iucn_category = dict(IUCNStatus.CATEGORY_CHOICES)
-        updated_summary = {}
+        iucn_status = IUCNStatus.objects.filter(
+            national=False
+        )
+        updated_summary = {
+            'chart_data': {},
+            'colors': []
+        }
         for key in summary_temp.keys():
             if key in iucn_category:
-                updated_summary[iucn_category[key]] = summary_temp[key]
+                updated_summary['chart_data'][iucn_category[key]] = summary_temp[key]
+                try:
+                    updated_summary['colors'].append(
+                        iucn_status.filter(category=key).first().colour
+                    )
+                except AttributeError:
+                    updated_summary['colors'].append('#000000')
+
         return updated_summary
 
     def general_summary_data(self):
@@ -221,6 +245,7 @@ def summary_data(self):
         return module_summary
 
     def call_summary_data_in_background(self):
+        delete_cache(self._cache_key())
         background_thread = threading.Thread(
             target=self.summary_data,
         )

bims/api_views/remove_occurrences.py

@@ -4,12 +4,8 @@
 from preferences import preferences
 from bims.models import (
     TaxonGroup,
-    Taxonomy,
-    BiologicalCollectionRecord,
-    Survey,
-    LocationSite,
-    LocationContext
 )
+from bims.tasks.taxon_group import delete_occurrences_by_taxon_group
 
 
 class RemoveOccurrencesApiView(UserPassesTestMixin, APIView):
@@ -29,74 +25,6 @@ def get(self, request, *args):
             except TaxonGroup.DoesNotExist:
                 return JsonResponse({'error': 'Taxon group does not exist'})
 
-        messages = {
-            'success': 'OK'
-        }
-        if taxon_group:
-            collections = (
-                BiologicalCollectionRecord.objects.filter(
-                    module_group=taxon_group
-                )
-            )
-            total_collections = collections.count()
+        task = delete_occurrences_by_taxon_group.delay(taxon_module_id)
 
-            # -- Survey
-            survey_ids = list(
-                collections.values_list(
-                    'survey_id', flat=True).distinct('survey')
-            )
-            surveys = Survey.objects.filter(id__in=survey_ids)
-            total_surveys = surveys.count()
-
-            # -- Taxonomy
-            taxa_ids = list(taxon_group.taxonomies.all().values_list(
-                'id', flat=True
-            ))
-            taxa = Taxonomy.objects.filter(id__in=taxa_ids)
-            total_taxa = taxa.count()
-
-            # -- Sites
-            site_ids = list(
-                collections.values_list('site_id', flat=True).distinct('site'))
-            sites = LocationSite.objects.filter(
-                id__in=site_ids
-            )
-            total_sites = sites.count()
-
-            # -- Location Context
-            location_contexts = LocationContext.objects.filter(
-                site__in=sites
-            )
-
-            if collections.exists():
-                collections._raw_delete(collections.db)
-                messages['Collections deleted'] = total_collections
-
-            if surveys.exists():
-                surveys._raw_delete(surveys.db)
-                messages['Survey deleted'] = total_surveys
-
-            if taxa.exists():
-                taxon_group.taxonomies.clear()
-                taxa = taxa.filter(
-                    biologicalcollectionrecord__isnull=True
-                )
-                taxa_with_vernacular = taxa.filter(
-                    vernacular_names__isnull=False)
-                for taxon_with_vernacular in taxa_with_vernacular:
-                    taxon_with_vernacular.vernacular_names.clear()
-                taxa._raw_delete(taxa.db)
-                messages['Taxa deleted'] = total_taxa
-
-            if sites.exists():
-                location_contexts._raw_delete(location_contexts.db)
-                sites = sites.filter(
-                    survey__isnull=True,
-                    biological_collection_record__isnull=True
-                )
-                sites._raw_delete(sites.db)
-                messages['Sites deleted'] = total_sites
-
-            taxon_group.delete()
-
-        return JsonResponse(messages)
+        return JsonResponse({'status': 'Task initiated', 'task_id': task.id})

bims/api_views/taxon_group.py

@@ -83,7 +83,12 @@ def add_taxa_to_taxon_group(taxa_ids, taxon_group_id):
                     legacy_canonical_name=taxonomy.legacy_canonical_name,
                     taxon_group_under_review=taxon_group
                 )
-        taxon_group.taxonomies.add(taxonomy)
+        taxon_group.taxonomies.add(
+            taxonomy,
+            through_defaults={
+                'is_validated': False
+            }
+        )
 
 
 class TaxaUpdateMixin(UserPassesTestMixin, APIView):