Include tags and attributes in csv file download (#4112)

bims/tasks/download_taxa_list.py

@@ -23,6 +23,8 @@ def __init__(self, get_data):
  # Get the taxa list based on request parameters
  taxa_list = TaxaList.get_taxa_by_parameters(request_get)
 
+ tag_titles = []
+
  # Define the header update function
  def update_headers(_headers):
  _updated_headers = []
@@ -34,7 +36,7 @@ def update_headers(_headers):
  elif header == 'common_name':
  header = 'Common Name'
  header = header.replace('_or_', '/')
- if not header.istitle():
+ if not header.istitle() and header not in tag_titles:
  header = header.replace('_', ' ').capitalize()
  if header == 'Sub species':
  header = 'SubSpecies'
@@ -44,6 +46,7 @@ def update_headers(_headers):
  # Serialize a single item to extract headers
  sample_item = next(taxa_list.iterator())
  sample_serializer = TaxaCSVSerializer(sample_item)
+ tag_titles = sample_serializer.context.get('tags', [])
  headers = list(sample_serializer.data.keys())
  updated_headers = update_headers(headers)
 

bims/tests/test_taxa.py

@@ -1,9 +1,12 @@
 from django.test import TestCase
+
+from bims.enums import TaxonomicGroupCategory
 from bims.tests.model_factories import (
  TaxonomyF, BiologicalCollectionRecordF, TaxonGroupF, VernacularNameF
 )
 from bims.utils.fetch_gbif import merge_taxa_data
-from bims.models import Taxonomy, BiologicalCollectionRecord, TaxonGroup
+from bims.models import Taxonomy, BiologicalCollectionRecord, TaxonGroup, IUCNStatus, TaxonExtraAttribute
+from bims.views.download_csv_taxa_list import TaxaCSVSerializer
 
 
 class TestTaxaHelpers(TestCase):
@@ -86,3 +89,68 @@ def test_merge_duplicated_taxa(self):
  Taxonomy.objects.get(id=taxa_2.id).vernacular_names.all().count(),
  3
  )
+
+
+class TaxaCSVSerializerTest(TestCase):
+ def setUp(self):
+ self.taxon_group = TaxonGroupF.create(
+ category=TaxonomicGroupCategory.SPECIES_MODULE.name)
+
+ self.vernacular_name = VernacularNameF(
+ name='Human',
+ language='en'
+ )
+ self.taxonomy = TaxonomyF.create(
+ rank='SPECIES',
+ canonical_name='Homo sapiens',
+ scientific_name='Homo sapiens Linnaeus',
+ endemism=None,
+ iucn_status=IUCNStatus.objects.create(category='LC'),
+ national_conservation_status=IUCNStatus.objects.create(category='NT'),
+ gbif_key='12345',
+ additional_data={'Growth form': 'Tree'},
+ vernacular_names=(self.vernacular_name,)
+ )
+ self.taxonomy.tags.add('freshwater', 'testing')
+ self.taxonomy.biographic_distributions.add('ANT', 'TEST (?)')
+
+ self.taxon_group.taxonomies.add(self.taxonomy)
+ self.taxon_extra_attribute = TaxonExtraAttribute.objects.create(
+ taxon_group=self.taxon_group,
+ name='Growth form'
+ )
+
+ def test_serializer_fields(self):
+ serializer = TaxaCSVSerializer(instance=self.taxonomy)
+ serialized_data = serializer.data
+
+ expected_fields = [
+ 'taxon_rank', 'kingdom', 'phylum', 'class_name', 'order', 'family', 'genus', 'species',
+ 'sub_species', 'taxon', 'scientific_name_and_authority', 'common_name', 'origin',
+ 'endemism', 'conservation_status_global', 'conservation_status_national', 'on_gbif', 'gbif_link',
+ 'Growth form', 'freshwater', 'testing', 'ANT'
+ ]
+
+ for field in expected_fields:
+ self.assertIn(field, serialized_data)
+
+ def test_serializer_values(self):
+ serializer = TaxaCSVSerializer(instance=self.taxonomy)
+ serialized_data = serializer.data
+
+ self.assertEqual(serialized_data['taxon_rank'], 'Species')
+ self.assertEqual(serialized_data['species'], 'Homo sapiens')
+ self.assertEqual(serialized_data['taxon'], 'Homo sapiens')
+ self.assertEqual(serialized_data['scientific_name_and_authority'], 'Homo sapiens Linnaeus')
+ self.assertEqual(serialized_data['common_name'], 'Human')
+ self.assertEqual(serialized_data['endemism'], 'Unknown')
+ self.assertEqual(serialized_data['conservation_status_global'], 'Least Concern')
+ self.assertEqual(serialized_data['conservation_status_national'], 'Near Threatened')
+ self.assertEqual(serialized_data['on_gbif'], 'Yes')
+ self.assertEqual(serialized_data['gbif_link'], 'https://www.gbif.org/species/12345')
+ self.assertEqual(serialized_data['Growth form'], 'Tree')
+ self.assertEqual(serialized_data['freshwater'], 'Y')
+ self.assertEqual(serialized_data['testing'], 'Y')
+ self.assertEqual(serialized_data['ANT'], 'Y')
+ self.assertEqual(serialized_data['TEST'], '?')
+ self.assertTrue(len(serializer.context.get('tags')) > 0)

bims/views/download_csv_taxa_list.py

@@ -83,7 +83,9 @@ def get_scientific_name_and_authority(self, obj):
 
  def get_common_name(self, obj):
  vernacular_names = list(
- obj.vernacular_names.filter(language__istartswith='en').values_list('name', flat=True))
+ obj.vernacular_names.filter(
+ language__istartswith='en'
+ ).values_list('name', flat=True))
  if len(vernacular_names) == 0:
  return ''
  else:
@@ -157,47 +159,49 @@ def __init__(self, *args, **kwargs):
  super(TaxaCSVSerializer, self).__init__(*args, **kwargs)
  self.context['headers'] = []
  self.context['additional_data'] = []
+ self.context['tags'] = []
 
- def to_representation(self, instance):
- result = super(
- TaxaCSVSerializer, self).to_representation(
- instance)
+ def _ensure_headers(self, keys):
  if 'headers' not in self.context:
- self.context['headers'] = list(result.keys())
+ self.context['headers'] = list(keys)
 
+ def _add_additional_attributes(self, instance, result):
  taxon_group = TaxonGroup.objects.filter(
  category=TaxonomicGroupCategory.SPECIES_MODULE.name,
- taxonomies__in=[instance]).first()
+ taxonomies__in=[instance]
+ ).first()
 
  if taxon_group:
  taxon_extra_attributes = TaxonExtraAttribute.objects.filter(
  taxon_group=taxon_group
  )
- if taxon_extra_attributes.exists():
- for taxon_extra_attribute in taxon_extra_attributes:
- taxon_attribute_name = taxon_extra_attribute.name
- if taxon_attribute_name not in self.context['headers']:
- self.context['headers'].append(taxon_attribute_name)
- try:
- if (
- taxon_attribute_name == 'Growth form'
- ):
- if (
- taxon_attribute_name not in
- instance.additional_data or
- instance.additional_data[
- taxon_attribute_name] == ''
- ):
- taxon_attribute_name = 'Growth Form'
- if taxon_attribute_name in instance.additional_data:
- result[taxon_attribute_name] = (
- instance.additional_data[taxon_attribute_name]
- )
- else:
- result[taxon_attribute_name] = ''
- except TypeError:
- result[taxon_attribute_name] = ''
+ for taxon_extra_attribute in taxon_extra_attributes:
+ attribute_name = taxon_extra_attribute.name
+ if attribute_name not in self.context['headers']:
+ self.context['headers'].append(attribute_name)
+ if instance.additional_data:
+ result[attribute_name] = (
+ instance.additional_data.get(attribute_name, '')
+ )
+
+ def _add_tags(self, instance, result):
+ all_tags = list(instance.tags.all()) + list(instance.biographic_distributions.all())
+ for tag in all_tags:
+ tag_name = tag.name.strip()
+ tag_value = 'Y'
+ if '(?)' in tag_name:
+ tag_value = '?'
+ tag_name = tag_name.replace('(?)', '').strip()
+ if tag_name not in self.context['headers']:
+ self.context['headers'].append(tag_name)
+ self.context['tags'].append(tag_name)
+ result[tag_name] = tag_value
 
+ def to_representation(self, instance):
+ result = super().to_representation(instance)
+ self._ensure_headers(result.keys())
+ self._add_additional_attributes(instance, result)
+ self._add_tags(instance, result)
  return result