class BiolomicsLiteratureClientTest(unittest.TestCase):
def setUp(self):
self.client = BiolomicsMirriClient(SERVER_URL, VERSION, CLIENT_ID,
SECRET_ID, USERNAME, PASSWORD)
def test_retrieve_biblio_by_id(self):
record_id = 100
record_name = "Miscellaneous notes on Mucoraceae"
biblio = self.client.retrieve_by_id(BIBLIOGRAPHY_WS, record_id)
self.assertEqual(biblio.record_id, record_id)
self.assertEqual(biblio.record_name, record_name)
def test_retrieve_media_by_id(self):
record_id = 100
record_name = "Miscellaneous notes on Mucoraceae"
biblio = self.client.retrieve_by_name(BIBLIOGRAPHY_WS, record_name)
self.assertEqual(biblio.record_id, record_id)
self.assertEqual(biblio.record_name, record_name)
self.assertEqual(biblio.year, 1994)
def test_create_biblio(self):
pub = Publication()
pub.pubmed_id = 'PM18192'
pub.journal = 'my_journal'
pub.title = 'awesome title'
pub.authors = 'pasdas, aposjdasd, alsalsfda'
record_id = None
try:
new_pub = self.client.create(BIBLIOGRAPHY_WS, pub)
record_id = new_pub.record_id
self.assertEqual(new_pub.title, pub.title)
finally:
if record_id is not None:
self.client.delete_by_id(BIBLIOGRAPHY_WS, record_id)
def get_or_create_sequence(client: BiolomicsMirriClient,
sequence: GenomicSequenceBiolomics):
seq = client.retrieve_by_name(sequence.marker_id)
if seq is not None:
return seq, False
new_seq = client.create(SEQUENCE_WS, sequence)
return new_seq, True
def get_or_create_strain(client: BiolomicsMirriClient, strain: StrainMirri):
new_strain = retrieve_strain_by_accession_number(client,
strain.id.strain_id)
if new_strain:
return new_strain, False
created_ids = OrderedDict()
try:
for pub in strain.publications:
new_pub, created = get_or_create_publication(client, pub)
if created:
if BIBLIOGRAPHY_WS not in created_ids:
created_ids[BIBLIOGRAPHY_WS] = []
created_ids[BIBLIOGRAPHY_WS].append(new_pub.record_id)
for marker in strain.genetics.markers:
new_marker, created = get_or_create_sequence(client, marker)
if created:
if SEQUENCE_WS not in created_ids:
created_ids[SEQUENCE_WS] = []
created_ids[SEQUENCE_WS].append(new_marker.record_id)
new_strain = client.create(STRAIN_WS, strain)
created_ids[STRAIN_WS] = [new_strain.record_id]
return new_strain, True
except Exception:
client.rollback(created_ids)
raise
class BiolomicsClientGrowthMediaTest(unittest.TestCase):
def setUp(self):
self.client = BiolomicsMirriClient(SERVER_URL, VERSION, CLIENT_ID,
SECRET_ID, USERNAME, PASSWORD)
def xtest_growth_media_by_name(self):
gm = self.client.retrieve('growth_media', 'AAA')
self.assertEqual(gm['Record Id'], 1)
class BiolomicsSequenceClientTest(unittest.TestCase):
def setUp(self):
self.client = BiolomicsMirriClient(SERVER_URL, VERSION, CLIENT_ID,
SECRET_ID, USERNAME, PASSWORD)
def test_retrieve_media_by_id(self):
record_id = 101
growth_medium = self.client.retrieve_by_id('growth_medium', record_id)
self.assertEqual(growth_medium.record_id, record_id)
self.assertEqual(growth_medium.record_name, 'MA2PH6')
def test_retrieve_media_by_id(self):
record_name = 'MA2PH6'
record_id = 101
growth_medium = self.client.retrieve_by_name('growth_medium', record_name)
self.assertEqual(growth_medium.record_id, record_id)
self.assertEqual(growth_medium.record_name, record_name)
def test_serialize_to_biolomics_remote(self):
client = BiolomicsMirriClient(SERVER_URL, VERSION, CLIENT_ID,
SECRET_ID, USERNAME, PASSWORD)
strain = create_full_data_strain()
ws_strain = strain_to_biolomics(strain, client=client)
self.assertEqual(
strain.collect.habitat_ontobiotope, ws_strain['RecordDetails']
['Ontobiotope']['Value'][0]['Name']['Value'])
self.assertEqual(
pycountry.countries.get(
alpha_3=strain.collect.location.country).name,
ws_strain['RecordDetails']['Country']['Value'][0]['Name']['Value'])
self.assertEqual(
strain.publications[0].title, ws_strain['RecordDetails']
['Literature']['Value'][0]['Name']['Value'])
class BiolomicsSequenceClientTest(unittest.TestCase):
def setUp(self) -> None:
self.client = BiolomicsMirriClient(SERVER_URL, VERSION, CLIENT_ID,
SECRET_ID, USERNAME, PASSWORD)
def test_retrieve_seq_by_id(self):
record_id = 101
sequence = self.client.retrieve_by_id('sequence', record_id)
self.assertEqual(sequence.record_id, record_id)
self.assertEqual(sequence.record_name, 'MUM 02.54 - CaM')
self.assertEqual(sequence.marker_type, 'CaM')
def test_retrieve_seq_by_name(self):
record_name = 'MUM 02.54 - CaM'
sequence = self.client.retrieve_by_name('sequence', record_name)
self.assertEqual(sequence.record_id, 101)
self.assertEqual(sequence.record_name, record_name)
self.assertEqual(sequence.marker_type, 'CaM')
def test_create_delete_sequence(self):
marker = GenomicSequenceBiolomics()
marker.marker_id = 'GGAAUUA'
marker.marker_seq = 'aattgacgat'
marker.marker_type = 'CaM'
marker.record_name = 'peioMarker'
new_marker = self.client.create('sequence', marker)
self.assertEqual(new_marker.marker_id, 'GGAAUUA')
self.assertEqual(new_marker.marker_seq, 'aattgacgat')
self.assertEqual(new_marker.marker_type, 'CaM')
self.assertEqual(new_marker.record_name, 'peioMarker')
self.assertTrue(new_marker.record_id)
self.client.delete_by_id('sequence', new_marker.record_id)
def setUp(self):
self.client = BiolomicsMirriClient(SERVER_URL, VERSION, CLIENT_ID,
SECRET_ID, USERNAME, PASSWORD)
def get_or_create_publication(client: BiolomicsMirriClient, pub: Publication):
pub = client.retrieve_by_name(pub.title)
if pub is not None:
return pub, False
new_pub = client.create(BIBLIOGRAPHY_WS, pub)
return new_pub, True
class BiolomicsSequenceClientTest(unittest.TestCase):
def setUp(self):
self.client = BiolomicsMirriClient(SERVER_URL, VERSION, CLIENT_ID,
SECRET_ID, USERNAME, PASSWORD)
def test_retrieve_strain_by_id(self):
record_id = 148038
strain = self.client.retrieve_by_id('strain', record_id)
self.assertEqual(strain.record_id, record_id)
def test_retrieve_strain_by_name(self):
record_id = 148038
record_name = 'MIRRI 2240561'
strain = self.client.retrieve_by_name('strain', record_name)
self.assertEqual(strain.record_name, record_name)
self.assertEqual(strain.record_id, record_id)
def test_search_strain(self):
accession_number = "BEA 0014B"
query = {
"Query": [{
"Index": 0,
"FieldName": "Collection accession number",
"Operation": "TextExactMatch",
"Value": accession_number
}],
"Expression":
"Q0",
"DisplayStart":
0,
"DisplayLength":
10
}
search_response = self.client.search('strain', query)
self.assertEqual(search_response['total'], 1)
self.assertEqual(search_response['records'][0].id.strain_id,
accession_number)
def test_search_strain4(self):
accession_number = "TESTCC 1"
query = {
"Query": [{
"Index": 0,
"FieldName": "Collection accession number",
"Operation": "TextExactMatch",
"Value": accession_number
}],
"Expression":
"Q0",
"DisplayStart":
0,
"DisplayLength":
10
}
search_response = self.client.search('strain', query)
for strain in search_response['records']:
print(strain)
self.client.delete_by_id('strain', strain.record_id)
def test_search_strain_no_found(self):
accession_number = "BEA 0014B_"
query = {
"Query": [{
"Index": 0,
"FieldName": "Collection accession number",
"Operation": "TextExactMatch",
"Value": accession_number
}],
"Expression":
"Q0",
"DisplayStart":
0,
"DisplayLength":
10
}
search_response = self.client.search('strain', query)
self.assertEqual(search_response['total'], 0)
self.assertFalse(search_response['records'])
def test_create_strain(self):
strain = create_full_data_strain()
record_id = None
try:
new_strain = self.client.create('strain', strain)
record_id = new_strain.record_id
self.assertEqual(new_strain.growth.recommended_media, ['AAA'])
self.assertEqual(new_strain.id.strain_id, strain.id.strain_id)
finally:
if record_id is not None:
self.client.delete_by_id('strain', record_id)
def test_update_strain(self):
strain = create_full_data_strain()
strain.growth.recommended_media.append('ahgfsdha')
record_id = None
try:
new_strain = self.client.create('strain', strain)
record_id = new_strain.record_id
self.assertEqual(new_strain.id.strain_id, strain.id.strain_id)
new_strain.id.number = '2'
updated_strain = self.client.update(STRAIN_WS, new_strain)
self.assertEqual(updated_strain.id.strain_id,
new_strain.id.strain_id)
retrieved_strain = self.client.retrieve_by_id(STRAIN_WS, record_id)
self.assertEqual(retrieved_strain.id.strain_id,
new_strain.id.strain_id)
finally:
if record_id is not None:
print('deleting')
self.client.delete_by_id('strain', record_id)
def test_search_by_accession_number(self):
accession_number = "BEA 0014B"
strain = retrieve_strain_by_accession_number(self.client,
accession_number)
self.assertEqual(strain.id.strain_id, accession_number)
def test_search_by_accession_number(self):
accession_number = "BEA 0014B_"
strain = retrieve_strain_by_accession_number(self.client,
accession_number)
self.assertFalse(strain)