def test_create_csv_other_delimitation(self):
cleaned_data = self.cleaned_data
cleaned_data['field_delimitor'] = 'other symbol'
table = VoucherTable(cleaned_data)
expected = '-,646,-'
response = table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)
def test_create_csv_number_bases_by_default(self):
cleaned_data = self.cleaned_data
cleaned_data['gene_info'] = ''
table = VoucherTable(cleaned_data)
expected = '515,669,1227,412'
response = table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)
def test_create_csv_tab_delimited(self):
cleaned_data = self.cleaned_data
cleaned_data['field_delimitor'] = 'TAB'
table = VoucherTable(cleaned_data)
expected = '-\t646\t-'
response = table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)
def test_create_csv_exist_or_empty(self):
cleaned_data = self.cleaned_data
cleaned_data['gene_info'] = 'EXIST OR EMPTY'
table = VoucherTable(cleaned_data)
expected = '-,X,-,-'
response = table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)
def test_create_csv_accession_number(self):
cleaned_data = self.cleaned_data
cleaned_data['gene_info'] = 'ACCESSION NUMBER'
table = VoucherTable(cleaned_data)
expected = 'AY218254,X'
response = table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)
def test_create_csv_other_delimitation(self):
cleaned_data = self.cleaned_data
cleaned_data['field_delimitor'] = 'other symbol'
table = VoucherTable(cleaned_data)
expected = 'Wahlberg,646,-'
response = table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)
def test_create_csv_missing_voucher(self):
cleaned_data = self.cleaned_data
cleaned_data['voucher_codes'] = 'CP1000-1000'
table = VoucherTable(cleaned_data)
table.create_csv_file()
expected = 'We don\'t have voucher CP1000-1000 in our database.'
result = table.warnings
self.assertTrue(expected in result)
def test_create_csv_exist_or_empty(self):
cleaned_data = self.cleaned_data
cleaned_data['gene_info'] = 'EXIST OR EMPTY'
table = VoucherTable(cleaned_data)
expected = ',X,-,-'
response = table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)
def test_create_csv_tab_delimited(self):
cleaned_data = self.cleaned_data
cleaned_data['field_delimitor'] = 'TAB'
table = VoucherTable(cleaned_data)
expected = 'Wahlberg\t646\t-'
response = table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)
def test_create_csv_accession_number(self):
cleaned_data = self.cleaned_data
cleaned_data['gene_info'] = 'ACCESSION NUMBER'
table = VoucherTable(cleaned_data)
expected = 'AY218269,AY218260'
response = table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)
def test_create_csv_number_bases_by_default(self):
cleaned_data = self.cleaned_data
cleaned_data['gene_info'] = ''
table = VoucherTable(cleaned_data)
expected = ',669,1227,412'
response = table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)
def test_create_csv_missing_voucher(self):
cleaned_data = self.cleaned_data
cleaned_data['voucher_codes'] = 'CP1000-1000'
table = VoucherTable(cleaned_data)
table.create_csv_file()
expected = 'We don\'t have voucher CP1000-1000 in our database.'
result = table.warnings
self.assertTrue(expected in result)
def setUp(self):
args = []
opts = {'dumpfile': 'test_db_dump.xml', 'verbosity': 0}
cmd = 'migrate_db'
call_command(cmd, *args, **opts)
taxonset = TaxonSets.objects.all()[0]
geneset = GeneSets.objects.all()[0]
self.cleaned_data = {
'collector_info': ['country', 'specific_locality', 'collector'],
'gene_codes': [],
'gene_info': 'NUMBER OF BASES',
'voucher_info': ['code', 'genus', 'species'],
'field_delimitor': 'COMMA',
'taxonset': taxonset,
'voucher_codes': '',
'geneset': geneset,
}
self.table = VoucherTable(self.cleaned_data)
self.maxDiff = None
def setUp(self):
args = []
opts = {'dumpfile': 'test_db_dump.xml', 'verbosity': 0}
cmd = 'migrate_db'
call_command(cmd, *args, **opts)
taxonset = TaxonSets.objects.all()[0]
geneset = GeneSets.objects.all()[0]
self.cleaned_data = {
'collector_info': ['country', 'specificLocality', 'collector'],
'gene_codes': [],
'gene_info': 'NUMBER OF BASES',
'voucher_info': ['code', 'genus', 'species'],
'field_delimitor': 'COMMA',
'taxonset': taxonset,
'voucher_codes': '',
'geneset': geneset,
}
self.table = VoucherTable(self.cleaned_data)
self.maxDiff = None
class TestVoucherTable(TestCase):
def setUp(self):
args = []
opts = {'dumpfile': 'test_db_dump.xml', 'verbosity': 0}
cmd = 'migrate_db'
call_command(cmd, *args, **opts)
taxonset = TaxonSets.objects.all()[0]
geneset = GeneSets.objects.all()[0]
self.cleaned_data = {
'collector_info': ['country', 'specificLocality', 'collector'],
'gene_codes': [],
'gene_info': 'NUMBER OF BASES',
'voucher_info': ['code', 'genus', 'species'],
'field_delimitor': 'COMMA',
'taxonset': taxonset,
'voucher_codes': '',
'geneset': geneset,
}
self.table = VoucherTable(self.cleaned_data)
self.maxDiff = None
def test_header_csv_file(self):
expected = ('Code', 'Genus', 'Species', 'Country', 'Specific Locality', 'Collector', '16S',
'COI', 'EF1a', 'wingless')
result = self.table.get_headers()
self.assertEqual(expected, result)
def test_create_csv_file_taxa(self):
expected = 'CP100-10,Melitaea,diamina'
response = self.table.create_csv_file()
result = response.content
self.assertTrue(expected in result.decode('utf-8'))
def test_create_csv_file_genes(self):
expected = '515,669,1227,412'
response = self.table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)
def test_create_csv_missing_voucher(self):
cleaned_data = self.cleaned_data
cleaned_data['voucher_codes'] = 'CP1000-1000'
table = VoucherTable(cleaned_data)
table.create_csv_file()
expected = 'We don\'t have voucher CP1000-1000 in our database.'
result = table.warnings
self.assertTrue(expected in result)
def test_create_csv_missing_sequence(self):
self.table.create_csv_file()
expected = "We don't have sequences for 16S and CP100-11"
self.assertTrue(expected in self.table.warnings)
def test_create_csv_number_bases_by_default(self):
cleaned_data = self.cleaned_data
cleaned_data['gene_info'] = ''
table = VoucherTable(cleaned_data)
expected = '515,669,1227,412'
response = table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)
def test_create_csv_accession_number(self):
cleaned_data = self.cleaned_data
cleaned_data['gene_info'] = 'ACCESSION NUMBER'
table = VoucherTable(cleaned_data)
expected = 'AY218254,X'
response = table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)
def test_create_csv_exist_or_empty(self):
cleaned_data = self.cleaned_data
cleaned_data['gene_info'] = 'EXIST OR EMPTY'
table = VoucherTable(cleaned_data)
expected = '-,X,-,-'
response = table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)
def test_create_csv_tab_delimited(self):
cleaned_data = self.cleaned_data
cleaned_data['field_delimitor'] = 'TAB'
table = VoucherTable(cleaned_data)
expected = '-\t646\t-'
response = table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)
def test_create_csv_other_delimitation(self):
cleaned_data = self.cleaned_data
cleaned_data['field_delimitor'] = 'other symbol'
table = VoucherTable(cleaned_data)
expected = '-,646,-'
response = table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)
class TestVoucherTable(TestCase):
def setUp(self):
args = []
opts = {'dumpfile': 'test_db_dump.xml', 'verbosity': 0}
cmd = 'migrate_db'
call_command(cmd, *args, **opts)
taxonset = TaxonSets.objects.all()[0]
geneset = GeneSets.objects.all()[0]
self.cleaned_data = {
'collector_info': ['country', 'specific_locality', 'collector'],
'gene_codes': [],
'gene_info': 'NUMBER OF BASES',
'voucher_info': ['code', 'genus', 'species'],
'field_delimitor': 'COMMA',
'taxonset': taxonset,
'voucher_codes': '',
'geneset': geneset,
}
self.table = VoucherTable(self.cleaned_data)
self.maxDiff = None
def test_header_csv_file(self):
expected = ('Code', 'Genus', 'Species', 'Country', 'Specific Locality',
'Collector', 'COI', 'EF1a', 'wingless')
result = self.table.get_headers()
self.assertEqual(expected, result)
def test_create_csv_file_taxa(self):
expected = 'CP100-10,Melitaea,diamina'
response = self.table.create_csv_file()
result = response.content
self.assertTrue(expected in result.decode('utf-8'))
def test_create_csv_file_genes(self):
expected = ',669,1227,412'
response = self.table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)
def test_create_csv_missing_voucher(self):
cleaned_data = self.cleaned_data
cleaned_data['voucher_codes'] = 'CP1000-1000'
table = VoucherTable(cleaned_data)
table.create_csv_file()
expected = 'We don\'t have voucher CP1000-1000 in our database.'
result = table.warnings
self.assertTrue(expected in result)
def test_create_csv_missing_sequence(self):
self.table.create_csv_file()
expected = "We don't have sequences for EF1a and CP100-11"
self.assertTrue(expected in self.table.warnings)
def test_create_csv_number_bases_by_default(self):
cleaned_data = self.cleaned_data
cleaned_data['gene_info'] = ''
table = VoucherTable(cleaned_data)
expected = ',669,1227,412'
response = table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)
def test_create_csv_accession_number(self):
cleaned_data = self.cleaned_data
cleaned_data['gene_info'] = 'ACCESSION NUMBER'
table = VoucherTable(cleaned_data)
expected = 'AY218269,AY218260'
response = table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)
def test_create_csv_exist_or_empty(self):
cleaned_data = self.cleaned_data
cleaned_data['gene_info'] = 'EXIST OR EMPTY'
table = VoucherTable(cleaned_data)
expected = ',X,-,-'
response = table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)
def test_create_csv_tab_delimited(self):
cleaned_data = self.cleaned_data
cleaned_data['field_delimitor'] = 'TAB'
table = VoucherTable(cleaned_data)
expected = 'Wahlberg\t646\t-'
response = table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)
def test_create_csv_other_delimitation(self):
cleaned_data = self.cleaned_data
cleaned_data['field_delimitor'] = 'other symbol'
table = VoucherTable(cleaned_data)
expected = 'Wahlberg,646,-'
response = table.create_csv_file()
result = response.content.decode('utf-8')
self.assertTrue(expected in result)