Update and improve csv generator (#4143)

bims/api_views/checklist.py

@@ -2,7 +2,6 @@
 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
@@ -14,6 +13,7 @@
 from rest_framework.views import APIView
 
 from bims.api_views.search import CollectionSearch
+from bims.enums import TaxonomicRank
 from bims.models.taxonomy import Taxonomy
 from bims.utils.domain import get_current_domain
 from bims.models.download_request import DownloadRequest
@@ -140,7 +140,13 @@ def generate_pdf_checklist(download_request, module_name, collection_records, ba
  unique_taxonomy_ids = set(record_taxonomy_ids) - written_taxa_ids
 
  if unique_taxonomy_ids:
- taxa = Taxonomy.objects.filter(id__in=unique_taxonomy_ids)
+ taxa = Taxonomy.objects.filter(
+ id__in=unique_taxonomy_ids
+ ).filter(
+ rank__in=[
+ TaxonomicRank.SPECIES.name,
+ TaxonomicRank.SUBSPECIES.name]
+ )
  taxon_serializer = ChecklistPDFSerializer(taxa, many=True)
  for taxon in taxon_serializer.data:
  written_taxa_ids.add(taxon['id'])

bims/api_views/location_site_overview.py

@@ -67,9 +67,9 @@ def biodiversity_data(self):
  collection_results = collection_results.select_related(
  'taxonomy', 'taxonomy__endemism', 'taxonomy__iucn_status', 'site_visit'
  )
- location_site_ids = set()
- taxonomy_ids = set()
  for group in groups:
+ location_site_ids = set()
+ taxonomy_ids = set()
  group_data = {}
  try:
  group_data[self.GROUP_ICON] = get_thumbnail(

bims/serializers/checklist_serializer.py

@@ -46,10 +46,7 @@ def get_common_name(self, obj: Taxonomy):
  if len(vernacular_names) == 0:
  return ''
  else:
- return ', '.join(
- list(
- set([name.capitalize() for name in vernacular_names]))
- )
+ return vernacular_names[0]
 
  def get_threat_status(self, obj: Taxonomy):
  if obj.iucn_status:
@@ -232,6 +229,15 @@ def get_sources(self, obj: Taxonomy):
 
  # TODO
  def get_confidence(self, obj: Taxonomy):
+ bio = self.get_bio_data(obj)
+ if not bio.exists():
+ return ''
+ if bio.exclude(certainty_of_identification='').exists():
+ return (
+ bio.exclude(
+ certainty_of_identification=''
+ ).first().certainty_of_identification
+ )
  return ''
 
  def get_park_or_mpa_name(self, obj: Taxonomy):
@@ -303,6 +309,7 @@ class Meta:
  'family',
  'scientific_name',
  'synonyms',
+ 'rank',
  'common_name',
  'most_recent_record',
  'origin',

bims/tasks/email_csv.py

@@ -111,7 +111,7 @@ def send_csv_via_email(
  zip_folder = os.path.join(
  settings.MEDIA_ROOT, settings.PROCESSED_CSV_PATH, user.username)
  if not os.path.exists(zip_folder):
- os.mkdir(zip_folder)
+ os.makedirs(zip_folder)
  zip_file = os.path.join(zip_folder, '{}.zip'.format(file_name))
  with zipfile.ZipFile(zip_file, 'w', zipfile.ZIP_DEFLATED) as zf:
  zf.write(download_file_path, f'{file_name}.{extension}')