本文整理汇总了Python中qiita_db.metadata_template.PrepTemplate.get方法的典型用法代码示例。如果您正苦于以下问题：Python PrepTemplate.get方法的具体用法？Python PrepTemplate.get怎么用？Python PrepTemplate.get使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类qiita_db.metadata_template.PrepTemplate的用法示例。
在下文中一共展示了PrepTemplate.get方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: TestPrepTemplate
# 需要导入模块: from qiita_db.metadata_template import PrepTemplate [as 别名]
# 或者: from qiita_db.metadata_template.PrepTemplate import get [as 别名]
class TestPrepTemplate(TestCase):
"""Tests the PrepTemplate class"""
def setUp(self):
metadata_dict = {
'SKB8.640193': {'center_name': 'ANL',
'center_project_name': 'Test Project',
'ebi_submission_accession': None,
'EMP_status_id': 1,
'data_type_id': 2,
'str_column': 'Value for sample 1'},
'SKD8.640184': {'center_name': 'ANL',
'center_project_name': 'Test Project',
'ebi_submission_accession': None,
'EMP_status_id': 1,
'data_type_id': 2,
'str_column': 'Value for sample 2'},
'SKB7.640196': {'center_name': 'ANL',
'center_project_name': 'Test Project',
'ebi_submission_accession': None,
'EMP_status_id': 1,
'data_type_id': 2,
'str_column': 'Value for sample 3'}
}
self.metadata = pd.DataFrame.from_dict(metadata_dict, orient='index')
self.test_raw_data = RawData(1)
fd, seqs_fp = mkstemp(suffix='_seqs.fastq')
close(fd)
fd, barcodes_fp = mkstemp(suffix='_barcodes.fastq')
close(fd)
filepaths = [(seqs_fp, 1), (barcodes_fp, 2)]
with open(seqs_fp, "w") as f:
f.write("\n")
with open(barcodes_fp, "w") as f:
f.write("\n")
self.new_raw_data = RawData.create(2, filepaths, [Study(1)])
db_test_raw_dir = join(get_db_files_base_dir(), 'raw_data')
db_seqs_fp = join(db_test_raw_dir, "3_%s" % basename(seqs_fp))
db_barcodes_fp = join(db_test_raw_dir, "3_%s" % basename(barcodes_fp))
self._clean_up_files = [db_seqs_fp, db_barcodes_fp]
self.tester = PrepTemplate(1)
self.exp_sample_ids = {'SKB1.640202', 'SKB2.640194', 'SKB3.640195',
'SKB4.640189', 'SKB5.640181', 'SKB6.640176',
'SKB7.640196', 'SKB8.640193', 'SKB9.640200',
'SKD1.640179', 'SKD2.640178', 'SKD3.640198',
'SKD4.640185', 'SKD5.640186', 'SKD6.640190',
'SKD7.640191', 'SKD8.640184', 'SKD9.640182',
'SKM1.640183', 'SKM2.640199', 'SKM3.640197',
'SKM4.640180', 'SKM5.640177', 'SKM6.640187',
'SKM7.640188', 'SKM8.640201', 'SKM9.640192'}
def tearDown(self):
for f in self._clean_up_files:
remove(f)
def test_init_unknown_error(self):
"""Init raises an error if the id is not known"""
with self.assertRaises(QiitaDBUnknownIDError):
PrepTemplate(2)
def test_init(self):
"""Init successfully instantiates the object"""
st = PrepTemplate(1)
self.assertTrue(st.id, 1)
def test_table_name(self):
"""Table name return the correct string"""
obs = PrepTemplate._table_name(self.test_raw_data)
self.assertEqual(obs, "prep_1")
def test_create_duplicate(self):
"""Create raises an error when creating a duplicated PrepTemplate"""
with self.assertRaises(QiitaDBDuplicateError):
PrepTemplate.create(self.metadata, self.test_raw_data)
def test_create_duplicate_header(self):
"""Create raises an error when duplicate headers are present"""
self.metadata['STR_COLUMN'] = pd.Series(['', '', ''],
index=self.metadata.index)
with self.assertRaises(QiitaDBDuplicateHeaderError):
PrepTemplate.create(self.metadata, self.new_raw_data)
def test_create(self):
"""Creates a new PrepTemplate"""
pt = PrepTemplate.create(self.metadata, self.new_raw_data)
# The returned object has the correct id
self.assertEqual(pt.id, 3)
# The relevant rows to common_prep_info have been added.
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.common_prep_info WHERE raw_data_id=3")
# raw_data_id, sample_id, center_name, center_project_name,
# ebi_submission_accession, ebi_study_accession, emp_status_id,
# data_type_id
exp = [[3, 'SKB8.640193', 'ANL', 'Test Project', None, None, 1, 2],
[3, 'SKD8.640184', 'ANL', 'Test Project', None, None, 1, 2],
[3, 'SKB7.640196', 'ANL', 'Test Project', None, None, 1, 2]]
self.assertEqual(sorted(obs), sorted(exp))
#.........这里部分代码省略.........