本文整理汇总了Python中qiita_db.analysis.Analysis._add_file方法的典型用法代码示例。如果您正苦于以下问题：Python Analysis._add_file方法的具体用法？Python Analysis._add_file怎么用？Python Analysis._add_file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.analysis.Analysis的用法示例。
在下文中一共展示了Analysis._add_file方法的2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: TestAnalysis
# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import _add_file [as 别名]
#.........这里部分代码省略.........
obs = self.analysis._get_samples()
exp = {1: ['1.SKB7.640196', '1.SKB8.640193', '1.SKD8.640184',
'1.SKM4.640180', '1.SKM9.640192']}
self.assertEqual(obs, exp)
def test_build_mapping_file(self):
samples = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196']}
self.analysis._build_mapping_file(samples,
conn_handler=self.conn_handler)
obs = self.analysis.mapping_file
self.assertEqual(obs, self.map_fp)
with open(self.map_fp) as f:
mapdata = f.readlines()
# check some columns for correctness
obs = [line.split('\t')[0] for line in mapdata]
exp = ['#SampleID', '1.SKB8.640193', '1.SKD8.640184',
'1.SKB7.640196']
self.assertEqual(obs, exp)
obs = [line.split('\t')[1] for line in mapdata]
exp = ['BarcodeSequence', 'AGCGCTCACATC', 'TGAGTGGTCTGT',
'CGGCCTAAGTTC']
self.assertEqual(obs, exp)
obs = [line.split('\t')[2] for line in mapdata]
exp = ['LinkerPrimerSequence', 'GTGCCAGCMGCCGCGGTAA',
'GTGCCAGCMGCCGCGGTAA', 'GTGCCAGCMGCCGCGGTAA']
self.assertEqual(obs, exp)
obs = [line.split('\t')[19] for line in mapdata]
exp = ['host_subject_id', '1001:M7', '1001:D9',
'1001:M8']
self.assertEqual(obs, exp)
obs = [line.split('\t')[47] for line in mapdata]
exp = ['tot_org_carb', '5.0', '4.32', '5.0']
self.assertEqual(obs, exp)
obs = [line.split('\t')[-1] for line in mapdata]
exp = ['Description\n'] + ['Cannabis Soil Microbiome\n'] * 3
self.assertEqual(obs, exp)
def test_build_mapping_file_duplicate_samples(self):
samples = {1: ['1.SKB8.640193', '1.SKB8.640193', '1.SKD8.640184']}
with self.assertRaises(ValueError):
self.analysis._build_mapping_file(samples,
conn_handler=self.conn_handler)
def test_build_biom_tables(self):
samples = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196']}
self.analysis._build_biom_tables(samples, 100,
conn_handler=self.conn_handler)
obs = self.analysis.biom_tables
self.assertEqual(obs, {'18S': self.biom_fp})
table = load_table(self.biom_fp)
obs = set(table.ids(axis='sample'))
exp = {'1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196'}
self.assertEqual(obs, exp)
obs = table.metadata('1.SKB8.640193')
exp = {'Study':
'Identification of the Microbiomes for Cannabis Soils',
'Processed_id': 1}
self.assertEqual(obs, exp)
def test_build_files(self):
self.analysis.build_files()
def test_build_files_raises_type_error(self):
with self.assertRaises(TypeError):
self.analysis.build_files('string')
with self.assertRaises(TypeError):
self.analysis.build_files(100.5)
def test_build_files_raises_value_error(self):
with self.assertRaises(ValueError):
self.analysis.build_files(0)
with self.assertRaises(ValueError):
self.analysis.build_files(-10)
def test_add_file(self):
fp = join(get_mountpoint('analysis')[0][1], 'testfile.txt')
with open(fp, 'w') as f:
f.write('testfile!')
self.analysis._add_file('testfile.txt', 'plain_text', '18S')
obs = self.conn_handler.execute_fetchall(
'SELECT * FROM qiita.filepath WHERE filepath_id = 19')
exp = [[19, 'testfile.txt', 9, '3675007573', 1, 1]]
self.assertEqual(obs, exp)
obs = self.conn_handler.execute_fetchall(
'SELECT * FROM qiita.analysis_filepath WHERE filepath_id = 19')
exp = [[1, 19, 2]]
self.assertEqual(obs, exp)示例2: TestAnalysis
# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import _add_file [as 别名]
#.........这里部分代码省略.........
def test_build_mapping_file(self):
new_id = get_count('qiita.filepath') + 1
samples = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196']}
self.analysis._build_mapping_file(samples)
obs = self.analysis.mapping_file
self.assertEqual(obs, self.map_fp)
base_dir = get_mountpoint('analysis')[0][1]
obs = pd.read_csv(obs, sep='\t', infer_datetime_format=True,
parse_dates=True, index_col=False, comment='\t')
exp = pd.read_csv(join(base_dir, '1_analysis_mapping_exp.txt'),
sep='\t', infer_datetime_format=True,
parse_dates=True, index_col=False, comment='\t')
assert_frame_equal(obs, exp)
sql = """SELECT * FROM qiita.filepath
WHERE filepath=%s ORDER BY filepath_id"""
obs = self.conn_handler.execute_fetchall(
sql, ("%d_analysis_mapping.txt" % self.analysis.id,))
exp = [[13, '1_analysis_mapping.txt', 9, '852952723', 1, 1],
[new_id, '1_analysis_mapping.txt', 9, '1606265094', 1, 1]]
self.assertEqual(obs, exp)
sql = """SELECT * FROM qiita.analysis_filepath
WHERE analysis_id=%s ORDER BY filepath_id"""
obs = self.conn_handler.execute_fetchall(sql, (self.analysis.id,))
exp = [[1L, 14L, 2L], [1L, 15L, None], [1L, new_id, None]]
def test_build_mapping_file_duplicate_samples(self):
samples = {1: ['1.SKB8.640193', '1.SKB8.640193', '1.SKD8.640184']}
with self.assertRaises(QiitaDBError):
self.analysis._build_mapping_file(samples)
def test_build_biom_tables(self):
new_id = get_count('qiita.filepath') + 1
samples = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196']}
self.analysis._build_biom_tables(samples, 100)
obs = self.analysis.biom_tables
self.assertEqual(obs, {'18S': self.biom_fp})
table = load_table(self.biom_fp)
obs = set(table.ids(axis='sample'))
exp = {'1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196'}
self.assertEqual(obs, exp)
obs = table.metadata('1.SKB8.640193')
exp = {'Study':
'Identification of the Microbiomes for Cannabis Soils',
'Processed_id': 1}
self.assertEqual(obs, exp)
sql = """SELECT EXISTS(SELECT * FROM qiita.filepath
WHERE filepath_id=%s)"""
obs = self.conn_handler.execute_fetchone(sql, (new_id,))[0]
self.assertTrue(obs)
sql = """SELECT * FROM qiita.analysis_filepath
WHERE analysis_id=%s ORDER BY filepath_id"""
obs = self.conn_handler.execute_fetchall(sql, (self.analysis.id,))
exp = [[1L, 14L, 2L], [1L, 15L, None], [1L, new_id, None]]
def test_build_files(self):
self.analysis.build_files()
def test_build_files_raises_type_error(self):
with self.assertRaises(TypeError):
self.analysis.build_files('string')
with self.assertRaises(TypeError):
self.analysis.build_files(100.5)
def test_build_files_raises_value_error(self):
with self.assertRaises(ValueError):
self.analysis.build_files(0)
with self.assertRaises(ValueError):
self.analysis.build_files(-10)
def test_add_file(self):
new_id = get_count('qiita.filepath') + 1
fp = join(get_mountpoint('analysis')[0][1], 'testfile.txt')
with open(fp, 'w') as f:
f.write('testfile!')
self.analysis._add_file('testfile.txt', 'plain_text', '18S')
obs = self.conn_handler.execute_fetchall(
'SELECT * FROM qiita.filepath WHERE filepath_id = %s',
(new_id,))
exp = [[new_id, 'testfile.txt', 9, '3675007573', 1, 1]]
self.assertEqual(obs, exp)
obs = self.conn_handler.execute_fetchall(
'SELECT * FROM qiita.analysis_filepath WHERE filepath_id = %s',
(new_id,))
exp = [[1, new_id, 2]]
self.assertEqual(obs, exp)