From 0a47b4a8546782fbd030b5109c2509d63dd932fb Mon Sep 17 00:00:00 2001
From: Dimas Ciputra <dimas.ciputra@gmail.com>
Date: Tue, 13 Aug 2024 10:58:25 +0100
Subject: [PATCH] Update and improve csv generator (#4143)

---
 bims/api_views/checklist.py              | 10 ++++++++--
 bims/api_views/location_site_overview.py |  4 ++--
 bims/serializers/checklist_serializer.py | 15 +++++++++++----
 bims/tasks/email_csv.py                  |  2 +-
 4 files changed, 22 insertions(+), 9 deletions(-)

diff --git a/bims/api_views/checklist.py b/bims/api_views/checklist.py
index bc12a06d2..b8491d44b 100644
--- a/bims/api_views/checklist.py
+++ b/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'])
diff --git a/bims/api_views/location_site_overview.py b/bims/api_views/location_site_overview.py
index 747402be9..5defced56 100644
--- a/bims/api_views/location_site_overview.py
+++ b/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(
diff --git a/bims/serializers/checklist_serializer.py b/bims/serializers/checklist_serializer.py
index 01c9520c8..8a2a1a761 100644
--- a/bims/serializers/checklist_serializer.py
+++ b/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',
diff --git a/bims/tasks/email_csv.py b/bims/tasks/email_csv.py
index 647b12620..a092d6783 100644
--- a/bims/tasks/email_csv.py
+++ b/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}')