def test_add_taxa_to_taxon_group(self):
taxonomy_1 = TaxonomyF.create()
taxonomy_2 = TaxonomyF.create()
BiologicalCollectionRecordF.create(taxonomy=taxonomy_1)
taxon_group_1 = TaxonGroupF.create()
add_taxa_to_taxon_group([taxonomy_1.id, taxonomy_2.id],
taxon_group_1.id)
self.assertEqual(
TaxonGroup.objects.get(
id=taxon_group_1.id).taxonomies.all().count(), 2)
self.assertTrue(
BiologicalCollectionRecord.objects.filter(
module_group=taxon_group_1).exists())
def test_get_module_summary(self):
view = ModuleSummary.as_view()
taxon_class_1 = TaxonomyF.create(scientific_name='Aves',
rank=TaxonomicRank.CLASS.name)
taxon_species_1 = TaxonomyF.create(scientific_name='Bird1',
rank=TaxonomicRank.SPECIES.name,
parent=taxon_class_1)
BiologicalCollectionRecordF.create(taxonomy=taxon_species_1,
validated=True,
site=self.location_site)
TaxonGroupF.create(name='fish',
category=TaxonomicGroupCategory.SPECIES_MODULE.name,
taxonomies=(taxon_class_1, ))
request = self.factory.get(reverse('module-summary'))
response = view(request)
self.assertTrue(len(response.data['fish']) > 0)
def setUp(self):
"""
Sets up before each test
"""
self.taxon = TaxonomyF.create(scientific_name='Aves',
rank=TaxonomicRank.CLASS.name)
self.permission = PermissionF.create(name='Can validate data',
codename='can_validate_data')
def test_merge_duplicated_taxa(self):
"""Test a function responsible for merging duplicated taxa"""
vernacular_name_1 = VernacularNameF.create(name='common_name_1')
vernacular_name_2 = VernacularNameF.create(name='common_name_2')
vernacular_name_3 = VernacularNameF.create(name='common_name_3')
taxa_1 = TaxonomyF.create(canonical_name='taxa_to_merged',
vernacular_names=(vernacular_name_1, ))
taxa_2 = TaxonomyF.create(canonical_name='verified_taxa',
vernacular_names=(vernacular_name_2, ))
taxa_3 = TaxonomyF.create(canonical_name='taxa_to_merged',
vernacular_names=(vernacular_name_3,
vernacular_name_1))
collection = BiologicalCollectionRecordF.create(taxonomy=taxa_1)
taxon_group = TaxonGroupF.create(name='test',
taxonomies=(taxa_1, taxa_3))
taxon_group_2 = TaxonGroupF.create(name='test_3',
taxonomies=(taxa_3, ))
self.assertTrue(taxon_group.taxonomies.filter(id=taxa_1.id).exists())
self.assertEqual(collection.taxonomy, taxa_1)
# Merge all taxa
merge_taxa_data(
excluded_taxon=Taxonomy.objects.get(
canonical_name='verified_taxa'),
taxa_list=Taxonomy.objects.filter(canonical_name='taxa_to_merged'))
# Collection should point to taxa_2
self.assertEqual(
BiologicalCollectionRecord.objects.get(id=collection.id).taxonomy,
taxa_2)
# Taxon group should have updated taxa member
self.assertFalse(
TaxonGroup.objects.filter(id=taxon_group.id,
taxonomies__id=taxa_1.id).exists())
self.assertTrue(
TaxonGroup.objects.filter(id=taxon_group.id,
taxonomies__id=taxa_2.id).exists())
self.assertTrue(
TaxonGroup.objects.filter(id=taxon_group_2.id,
taxonomies__id=taxa_2.id).exists())
# Vernacular names should be updated
self.assertEqual(
Taxonomy.objects.get(id=taxa_2.id).vernacular_names.all().count(),
3)
def test_Taxon_delete(self):
"""
Tests taxon model delete
"""
model = TaxonomyF.create()
model.delete()
# check if deleted
self.assertTrue(model.pk is None)
def setUp(self):
self.factory = APIRequestFactory()
self.location_site = LocationSiteF.create(
pk=1, location_context_document='""')
self.taxonomy_class_1 = TaxonomyF.create(scientific_name='Aves',
rank=TaxonomicRank.CLASS.name)
self.taxonomy_1 = TaxonomyF.create(scientific_name='Some aves name 1',
canonical_name='aves name 1',
rank=TaxonomicRank.SPECIES.name,
parent=self.taxonomy_class_1)
self.taxonomy_2 = TaxonomyF.create(scientific_name='Some aves name 2',
canonical_name='aves name 2',
rank=TaxonomicRank.SPECIES.name,
parent=self.taxonomy_class_1)
self.aves_collection_1 = BiologicalCollectionRecordF.create(
original_species_name=u'Aves collection 1',
site=self.location_site,
validated=True,
ready_for_validation=True,
taxonomy=self.taxonomy_1)
self.aves_collection_2 = BiologicalCollectionRecordF.create(
original_species_name=u'Aves collection 2',
site=self.location_site,
validated=True,
ready_for_validation=True,
taxonomy=self.taxonomy_2)
self.fish_collection_1 = BiologicalCollectionRecordF.create(
original_species_name=u'Test fish species name 1',
site=self.location_site,
validated=True)
self.fish_collection_2 = BiologicalCollectionRecordF.create(
original_species_name=u'Test fish species name 2',
site=self.location_site,
validated=True)
self.admin_user = UserF.create(is_superuser=True, is_staff=True)
self.rebuild_index()
def test_remove_taxa_from_taxon_group(self):
taxonomy_1 = TaxonomyF.create()
taxonomy_2 = TaxonomyF.create()
taxonomy_3 = TaxonomyF.create()
taxon_group_1 = TaxonGroupF.create(taxonomies=(taxonomy_1, taxonomy_2))
biological_1 = BiologicalCollectionRecordF.create(
taxonomy=taxonomy_1, module_group=taxon_group_1)
BiologicalCollectionRecordF.create(taxonomy=taxonomy_3,
module_group=taxon_group_1)
self.assertEqual(taxon_group_1.taxonomies.all().count(), 2)
self.assertEqual(biological_1.module_group, taxon_group_1)
remove_taxa_from_taxon_group([taxonomy_1.id], taxon_group_1.id)
# Removing taxon that doesn't exist in the group
remove_taxa_from_taxon_group([taxonomy_3.id], taxon_group_1.id)
self.assertEqual(
TaxonGroup.objects.get(
id=taxon_group_1.id).taxonomies.all().count(), 1)
self.assertEqual(
TaxonGroup.objects.get(
id=taxon_group_1.id).taxonomies.all().count(), 1)
self.assertFalse(
BiologicalCollectionRecord.objects.filter(
module_group=taxon_group_1).exists())
def test_Taxon_create(self):
"""
Tests taxon creation
"""
model = TaxonomyF.create()
# check if pk exists
self.assertTrue(model.pk is not None)
# check if iucn_status exists
self.assertTrue(model.iucn_status is not None)
# check if scientific name exists
self.assertTrue(model.scientific_name is not None)
def test_Taxon_read(self):
"""
Tests taxon model read
"""
iucn_status = IUCNStatusF.create(
category=u'custom iucn status',
sensitive=True,
)
model = TaxonomyF.create(iucn_status=iucn_status,
scientific_name=u'custom scientific name',
canonical_name=u'custom common name',
author=u'custom author')
self.assertTrue(model.iucn_status.category == 'custom iucn status')
self.assertTrue(model.scientific_name == 'custom scientific name')
self.assertTrue(model.canonical_name == 'custom common name')
self.assertTrue(model.author == 'custom author')
def test_get_taxon_by_id(self):
pk = 1
taxon = TaxonomyF.create(
pk=1,
scientific_name=u'Golden fish',
)
view = TaxonDetail.as_view()
request = self.factory.get('/api/taxon/' + str(pk))
response = view(request, str(pk))
self.assertEqual(taxon.scientific_name,
response.data['scientific_name'])
# def test_get_allowed_geometry_location_type_by_id(self):
view = LocationTypeAllowedGeometryDetail.as_view()
pk = '%s' % self.fish_collection_1.site.location_type.pk
request = self.factory.get('/api/location-type/%s/allowed-geometry/' %
pk)
response = view(request, pk)
self.assertEqual(response.data, 'POINT')
def test_Taxon_update(self):
"""
Tests taxon model update
"""
model = TaxonomyF.create()
iucn_status = IUCNStatusF.create(
category=u'custom iucn status',
sensitive=True,
)
new_data = {
'iucn_status': iucn_status,
'scientific_name': u'new scientific name',
'common_name': u'new common name',
'author': u'custom author',
}
model.__dict__.update(new_data)
model.save()
# check if updated
for key, val in new_data.items():
self.assertEqual(model.__dict__.get(key), val)
