本文整理汇总了Python中qiita_db.analysis.Analysis._build_biom_tables方法的典型用法代码示例。如果您正苦于以下问题：Python Analysis._build_biom_tables方法的具体用法？Python Analysis._build_biom_tables怎么用？Python Analysis._build_biom_tables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._build_biom_tables方法的3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 _build_biom_tables [as 别名]
#.........这里部分代码省略.........
'SKB7.640196': {'physical_specimen_location': 'location1',
'physical_specimen_remaining': True,
'dna_extracted': True,
'sample_type': 'type1',
'required_sample_info_status': 'received',
'collection_timestamp':
datetime(2014, 5, 29, 12, 24, 51),
'host_subject_id': 'NotIdentified',
'Description': 'Test Sample 3',
'str_column': 'Value for sample 3',
'latitude': 4.8,
'longitude': 4.41,
'taxon_id': 9606,
'scientific_name': 'homo sapiens'},
}
metadata = pd.DataFrame.from_dict(metadata_dict, orient='index')
Study.create(User("[email protected]"), "Test study 2", [1], info)
SampleTemplate.create(metadata, Study(2))
mp = get_mountpoint("processed_data")[0][1]
study_fp = join(mp, "2_study_1001_closed_reference_otu_table.biom")
ProcessedData.create("processed_params_uclust", 1, [(study_fp, 6)],
study=Study(2), data_type="16S")
self.conn_handler.execute(
"INSERT INTO qiita.analysis_sample (analysis_id, "
"processed_data_id, sample_id) VALUES "
"(1,2,'2.SKB8.640193'), (1,2,'2.SKD8.640184'), "
"(1,2,'2.SKB7.640196')")
samples = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196'],
2: ['2.SKB8.640193', '2.SKD8.640184']}
self.analysis._build_biom_tables(samples, 10000)
exp = {1: {'1.SKM4.640180', '1.SKM9.640192'},
2: {'2.SKB7.640196'}}
self.assertEqual(self.analysis.dropped_samples, exp)
def test_empty_analysis(self):
analysis = Analysis(2)
# These should be empty as the analysis hasn't started
self.assertEqual(analysis.biom_tables, {})
self.assertEqual(analysis.dropped_samples, {})
def test_retrieve_portal(self):
self.assertEqual(self.analysis._portals, ["QIITA"])
def test_retrieve_data_types(self):
exp = ['18S']
self.assertEqual(self.analysis.data_types, exp)
def test_retrieve_shared_with(self):
self.assertEqual(self.analysis.shared_with, ["[email protected]"])
def test_retrieve_biom_tables(self):
exp = {"18S": join(self.fp, "1_analysis_18S.biom")}
self.assertEqual(self.analysis.biom_tables, exp)
def test_all_associated_filepaths(self):
exp = {10, 11, 12, 13}
self.assertEqual(self.analysis.all_associated_filepath_ids, exp)
def test_retrieve_biom_tables_empty(self):
new = Analysis.create(User("[email protected]"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.biom_tables, {})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 _build_biom_tables [as 别名]
#.........这里部分代码省略.........
'latitude': 4.2,
'longitude': 1.1},
'SKB7.640196': {'physical_location': 'location1',
'has_physical_specimen': True,
'has_extracted_data': True,
'sample_type': 'type1',
'required_sample_info_status': 'received',
'collection_timestamp':
datetime(2014, 5, 29, 12, 24, 51),
'host_subject_id': 'NotIdentified',
'Description': 'Test Sample 3',
'str_column': 'Value for sample 3',
'latitude': 4.8,
'longitude': 4.41},
}
metadata = pd.DataFrame.from_dict(metadata_dict, orient='index')
Study.create(User("[email protected]"), "Test study 2", [1], info)
SampleTemplate.create(metadata, Study(2))
mp = get_mountpoint("processed_data")[0][1]
study_fp = join(mp, "2_study_1001_closed_reference_otu_table.biom")
ProcessedData.create("processed_params_uclust", 1, [(study_fp, 6)],
study=Study(2), data_type="16S")
self.conn_handler.execute(
"INSERT INTO qiita.analysis_sample (analysis_id, "
"processed_data_id, sample_id) VALUES "
"(1,2,'2.SKB8.640193'), (1,2,'2.SKD8.640184'), "
"(1,2,'2.SKB7.640196')")
samples = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196'],
2: ['2.SKB8.640193', '2.SKD8.640184']}
self.analysis._build_biom_tables(samples, 10000,
conn_handler=self.conn_handler)
exp = {1: {'1.SKM4.640180', '1.SKM9.640192'},
2: {'2.SKB7.640196'}}
self.assertEqual(self.analysis.dropped_samples, exp)
def test_retrieve_data_types(self):
exp = ['18S']
self.assertEqual(self.analysis.data_types, exp)
def test_retrieve_shared_with(self):
self.assertEqual(self.analysis.shared_with, ["[email protected]"])
def test_retrieve_biom_tables(self):
exp = {"18S": join(self.fp, "1_analysis_18S.biom")}
self.assertEqual(self.analysis.biom_tables, exp)
def test_all_associated_filepaths(self):
exp = {12, 13, 14, 15}
self.assertEqual(self.analysis.all_associated_filepath_ids, exp)
def test_retrieve_biom_tables_none(self):
new = Analysis.create(User("[email protected]"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.biom_tables, None)
def test_set_step(self):
new_id = get_count("qiita.analysis") + 1
new = Analysis.create(User("[email protected]"), "newAnalysis",
"A New Analysis", Analysis(1))
new.step = 2
sql = "SELECT * FROM qiita.analysis_workflow WHERE analysis_id = %s"
obs = self.conn_handler.execute_fetchall(sql, [new_id])示例3: TestAnalysis
# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import _build_biom_tables [as 别名]
class TestAnalysis(TestCase):
def setUp(self):
self.analysis = Analysis(1)
def test_lock_check(self):
for status in ["queued", "running", "public", "completed",
"error"]:
new = Analysis.create(User("[email protected]"), "newAnalysis",
"A New Analysis")
new.status = status
with self.assertRaises(QiitaDBStatusError):
new._lock_check(self.conn_handler)
def test_lock_check_ok(self):
self.analysis.status = "in_construction"
self.analysis._lock_check(self.conn_handler)
def test_status_setter_checks(self):
self.analysis.status = "public"
with self.assertRaises(QiitaDBStatusError):
self.analysis.status = "queued"
def test_get_public(self):
self.assertEqual(Analysis.get_public(), [])
self.analysis.status = "public"
self.assertEqual(Analysis.get_public(), [1])
def test_create(self):
sql = "SELECT EXTRACT(EPOCH FROM NOW())"
time1 = float(self.conn_handler.execute_fetchall(sql)[0][0])
new = Analysis.create(User("[email protected]"), "newAnalysis",
"A New Analysis")
self.assertEqual(new.id, 3)
sql = ("SELECT analysis_id, email, name, description, "
"analysis_status_id, pmid, EXTRACT(EPOCH FROM timestamp) "
"FROM qiita.analysis WHERE analysis_id = 3")
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(obs[0][:-1], [3, '[email protected]', 'newAnalysis',
'A New Analysis', 1, None])
self.assertTrue(time1 < float(obs[0][-1]))
def test_create_parent(self):
sql = "SELECT EXTRACT(EPOCH FROM NOW())"
time1 = float(self.conn_handler.execute_fetchall(sql)[0][0])
new = Analysis.create(User("[email protected]"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.id, 3)
sql = ("SELECT analysis_id, email, name, description, "
"analysis_status_id, pmid, EXTRACT(EPOCH FROM timestamp) "
"FROM qiita.analysis WHERE analysis_id = 3")
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(obs[0][:-1], [3, '[email protected]', 'newAnalysis',
'A New Analysis', 1, None])
self.assertTrue(time1 < float(obs[0][-1]))
sql = "SELECT * FROM qiita.analysis_chain WHERE child_id = 3"
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(obs, [[1, 3]])
def test_retrieve_owner(self):
self.assertEqual(self.analysis.owner, "[email protected]")
def test_retrieve_name(self):
self.assertEqual(self.analysis.name, "SomeAnalysis")
def test_retrieve_description(self):
self.assertEqual(self.analysis.description, "A test analysis")
def test_set_description(self):
self.analysis.description = "New description"
self.assertEqual(self.analysis.description, "New description")
def test_retrieve_samples(self):
exp = {1: ['SKB8.640193', 'SKD8.640184', 'SKB7.640196',
'SKM9.640192', 'SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_retrieve_dropped_samples(self):
biom_fp = join(get_db_files_base_dir(), "analysis",
"1_analysis_18S.biom")
try:
samples = {1: ['SKB8.640193', 'SKD8.640184', 'SKB7.640196']}
self.analysis._build_biom_tables(samples, 100,
conn_handler=self.conn_handler)
exp = {1: {'SKM4.640180', 'SKM9.640192'}}
self.assertEqual(self.analysis.dropped_samples, exp)
finally:
with open(biom_fp, 'w') as f:
f.write("")
def test_retrieve_data_types(self):
exp = ['18S']
self.assertEqual(self.analysis.data_types, exp)
def test_retrieve_shared_with(self):
self.assertEqual(self.analysis.shared_with, ["[email protected]"])
def test_retrieve_biom_tables(self):
#.........这里部分代码省略.........