def test_generate_dataset(self):
lsid = 'urn:lsid:biodiversity.org.au:afd.taxon:31a9b8b8-4e8f-4343-a15f-2ed24e0bf1ae'
file_manager = MagicMock()
ala_job_dao = MagicMock()
ala_occurrence_dao = MagicMock()
ala_dataset_factory = MagicMock()
ala_service = ALAService(file_manager, ala_job_dao, ala_occurrence_dao, ala_dataset_factory)
ala_service._occurrence_url = "http://biocache.ala.org.au/ws/webportal/occurrences.gz?q=lsid:${lsid}&fq=geospatial_kosher:true&fl=raw_taxon_name,longitude,latitude&pageSize=999999999"
ala_service._metadata_url = "http://bie.ala.org.au/species/${lsid}.json"
ala_occurrence_dao.create_new = MagicMock()
ala_dataset_factory.generate_dataset = MagicMock()
temp_dir = tempfile.mkdtemp(suffix=__name__)
# Directory is empty
self.assertEqual(0, len(os.listdir(temp_dir)))
ala_service._file_manager.ala_file_manager = ALAFileManager(temp_dir)
result = ala_service.getOccurrenceByLSID(lsid)
self.assertTrue(result)
# ALA directory exists
ala_dir = os.path.join(temp_dir)
self.assertTrue(os.path.isdir(ala_dir))
# The file exists
occurrence_file = os.path.join(ala_dir, lsid + ".csv")
self.assertTrue(os.path.isfile(occurrence_file))
# The metadata file exists
metadata_file = os.path.join(ala_dir, lsid + ".json")
self.assertTrue(os.path.isfile(metadata_file))
ala_occurrence = ALAOccurrence(lsid, occurrence_file, metadata_file)
ala_dataset_factory = DatasetFactory()
ala_dataset_factory._occurrence_url = "http://biocache.ala.org.au/ws/webportal/occurrences.gz?q=lsid:${lsid}&fq=geospatial_kosher:true&fl=raw_taxon_name,longitude,latitude&pageSize=999999999"
ala_dataset = ala_dataset_factory.generate_dataset(ala_occurrence)
now = datetime.datetime.now()
expected_title = "Red Kangaroo (Macropus rufus) occurrences"
expected_description = "Observed occurrences for Red Kangaroo (Macropus rufus), imported from ALA on " + now.strftime('%d/%m/%Y')
expected_num_occurrences = 35136
expected_provenance_url = "http://biocache.ala.org.au/ws/webportal/occurrences.gz?q=lsid:urn:lsid:biodiversity.org.au:afd.taxon:31a9b8b8-4e8f-4343-a15f-2ed24e0bf1ae&fq=geospatial_kosher:true&fl=raw_taxon_name,longitude,latitude&pageSize=999999999"
self.assertEqual(expected_title, ala_dataset.title)
self.assertEqual(expected_description, ala_dataset.description)
self.assertEqual(expected_num_occurrences, ala_dataset.num_occurrences)
self.assertEqual(expected_provenance_url, ala_dataset.provenance.url)
self.assertEqual(path_to_url(occurrence_file), ala_dataset.files[0].url)
self.assertEqual(os.path.getsize(occurrence_file), ala_dataset.files[0].size)
self.assertEqual(path_to_url(metadata_file), ala_dataset.files[1].url)
self.assertEqual(os.path.getsize(metadata_file), ala_dataset.files[1].size)
shutil.rmtree(temp_dir)
def testAlaOccurrence(self):
lsid = 'urn:lsid:biodiversity.org.au:afd.taxon:31a9b8b8-4e8f-4343-a15f-2ed24e0bf1ae'
file_manager = MagicMock()
ala_job_dao = MagicMock()
ala_occurrence_dao = MagicMock()
ala_dataset_factory = MagicMock()
ala_service = ALAService(file_manager, ala_job_dao, ala_occurrence_dao, ala_dataset_factory)
ala_service._occurrence_url = "http://biocache.ala.org.au/ws/webportal/occurrences.gz?q=lsid:${lsid}&fq=geospatial_kosher:true&fl=raw_taxon_name,longitude,latitude&pageSize=999999999"
ala_service._metadata_url = "http://bie.ala.org.au/species/${lsid}.json"
ala_occurrence_dao.create_new = MagicMock()
temp_dir = tempfile.mkdtemp(suffix=__name__)
# Directory is empty
self.assertEqual(0, len(os.listdir(temp_dir)))
ala_service._file_manager.ala_file_manager = ALAFileManager(temp_dir)
result = ala_service.getOccurrenceByLSID(lsid)
self.assertTrue(result)
# ALA directory exists
ala_dir = os.path.join(temp_dir)
self.assertTrue(os.path.isdir(ala_dir))
# The file exists
occurrence_file = os.path.join(ala_dir, lsid + ".csv")
self.assertTrue(os.path.isfile(occurrence_file))
# The metadata file exists
metadata_file = os.path.join(ala_dir, lsid + ".json")
self.assertTrue(os.path.isfile(metadata_file))
# The occurrence file has been normalized
with io.open(occurrence_file, mode='r+') as f:
lines = f.readlines()
self.assertTrue(len(lines) > 1)
header = lines[0]
self.assertEqual(1, header.count('SPPCODE'))
self.assertEqual(1, header.count('LNGDEC'))
self.assertEqual(1, header.count('LATDEC'))
expected_occurrence_path = '%s/%s.csv' % (ala_dir, lsid)
expected_metadata_path = '%s/%s.json' % (ala_dir, lsid)
ala_service._ala_occurrence_dao.create_new.assert_called_with(lsid, expected_occurrence_path, expected_metadata_path)
# Remove temp dir
shutil.rmtree(temp_dir)
