本文整理汇总了Python中qiita_db.analysis.Analysis.remove_samples方法的典型用法代码示例。如果您正苦于以下问题:Python Analysis.remove_samples方法的具体用法?Python Analysis.remove_samples怎么用?Python Analysis.remove_samples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.remove_samples方法的6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: on_message
# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import remove_samples [as 别名]
def on_message(self, msg):
# When the websocket receives a message from the javascript client,
# parse into JSON
msginfo = loads(msg)
default = Analysis(self.current_user.default_analysis)
if 'remove_sample' in msginfo:
data = msginfo['remove_sample']
default.remove_samples([data['proc_data']], data['samples'])
elif 'remove_pd' in msginfo:
data = msginfo['remove_pd']
default.remove_samples([data['proc_data']])
elif 'clear' in msginfo:
data = msginfo['clear']
default.remove_samples(data['pids'])
self.write_message(msg)
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 remove_samples [as 别名]
#.........这里部分代码省略.........
def test_retrieve_mapping_file(self):
exp = join(self.fp, "1_analysis_mapping.txt")
obs = self.analysis.mapping_file
self.assertEqual(obs, exp)
self.assertTrue(exists(exp))
def test_retrieve_mapping_file_none(self):
new = Analysis.create(User("[email protected]"), "newAnalysis",
"A New Analysis", Analysis(1))
obs = new.mapping_file
self.assertEqual(obs, None)
# def test_get_parent(self):
# raise NotImplementedError()
# def test_get_children(self):
# raise NotImplementedError()
def test_summary_data(self):
obs = self.analysis.summary_data()
exp = {'studies': 1,
'processed_data': 1,
'samples': 5}
self.assertEqual(obs, exp)
def test_add_samples(self):
new = Analysis.create(User("[email protected]"), "newAnalysis",
"A New Analysis")
new.add_samples({1: ['1.SKB8.640193', '1.SKD5.640186']})
obs = new.samples
self.assertEqual(obs.keys(), [1])
self.assertItemsEqual(obs[1], ['1.SKB8.640193', '1.SKD5.640186'])
def test_remove_samples_both(self):
self.analysis.remove_samples(proc_data=(1, ),
samples=('1.SKB8.640193', ))
exp = {1: ['1.SKD8.640184', '1.SKB7.640196', '1.SKM9.640192',
'1.SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_remove_samples_samples(self):
self.analysis.remove_samples(samples=('1.SKD8.640184', ))
exp = {1: ['1.SKB8.640193', '1.SKB7.640196', '1.SKM9.640192',
'1.SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_remove_samples_processed_data(self):
self.analysis.remove_samples(proc_data=(1, ))
exp = {}
self.assertEqual(self.analysis.samples, exp)
def test_share(self):
self.analysis.share(User("[email protected]"))
self.assertEqual(self.analysis.shared_with, ["[email protected]",
"[email protected]"])
def test_unshare(self):
self.analysis.unshare(User("[email protected]"))
self.assertEqual(self.analysis.shared_with, [])
def test_get_samples(self):
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)
示例3: post
# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import remove_samples [as 别名]
def post(self):
user = self.current_user
action = self.get_argument("action")
# set required template variables
results = {}
meta_headers = []
counts = {}
fullcounts = {}
query = ""
searchmsg = ""
selsamples = {}
selproc_data = {}
# get analysis and selected samples if exists, or create if necessary
if action == "create":
name = self.get_argument('name')
description = self.get_argument('description')
analysis = Analysis.create(user, name, description)
analysis_id = analysis.id
# set to second step since this page is second step in workflow
analysis.step = SELECT_SAMPLES
# fill example studies by running query for specific studies
search = QiitaStudySearch()
def_query = 'study_id = 1 OR study_id = 2 OR study_id = 3'
results, meta_headers = search(def_query, user)
results, counts, fullcounts = self._parse_search_results(
results, selsamples, meta_headers)
else:
analysis_id = int(self.get_argument("analysis-id"))
analysis = Analysis(analysis_id)
check_analysis_access(user, analysis)
selproc_data, selsamples = self._selected_parser(analysis)
# run through action requested
if action == "search":
search = QiitaStudySearch()
query = str(self.get_argument("query"))
try:
results, meta_headers = search(query, user)
except ParseException:
searchmsg = "Malformed search query, please read search help."
except QiitaDBIncompatibleDatatypeError as e:
searchmsg = ''.join(e)
if not results and not searchmsg:
searchmsg = "No results found."
else:
results, counts, fullcounts = self._parse_search_results(
results, selsamples, meta_headers)
elif action == "select":
analysis.add_samples(self._parse_form_select())
# rebuild the selected from database to reflect changes
selproc_data, selsamples = self._selected_parser(analysis)
elif action == "deselect":
proc_data, samples = self._parse_form_deselect()
if proc_data:
analysis.remove_samples(proc_data=proc_data)
if samples:
analysis.remove_samples(samples=samples)
if not proc_data and not samples:
searchmsg = "Must select samples to remove from analysis!"
# rebuild the selected from database to reflect changes
selproc_data, selsamples = self._selected_parser(analysis)
self.render('search_studies.html', user=user, aid=analysis_id,
results=results, meta_headers=meta_headers,
selsamples=selsamples, selproc_data=selproc_data,
counts=counts, fullcounts=fullcounts, searchmsg=searchmsg,
query=query, availmeta=SampleTemplate.metadata_headers() +
get_table_cols("study"))
示例4: TestAnalysis
# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import remove_samples [as 别名]
#.........这里部分代码省略.........
def test_retrieve_mapping_file(self):
exp = join(self.fp, "1_analysis_mapping.txt")
obs = self.analysis.mapping_file
self.assertEqual(obs, exp)
self.assertTrue(exists(exp))
def test_retrieve_mapping_file_none(self):
new = Analysis.create(User("[email protected]"), "newAnalysis",
"A New Analysis", Analysis(1))
obs = new.mapping_file
self.assertEqual(obs, None)
# def test_get_parent(self):
# raise NotImplementedError()
# def test_get_children(self):
# raise NotImplementedError()
def test_summary_data(self):
obs = self.analysis.summary_data()
exp = {'studies': 1,
'processed_data': 1,
'samples': 5}
self.assertEqual(obs, exp)
def test_add_samples(self):
new = Analysis.create(User("[email protected]"), "newAnalysis",
"A New Analysis")
new.add_samples({1: ['1.SKB8.640193', '1.SKD5.640186']})
obs = new.samples
self.assertEqual(obs.keys(), [1])
self.assertItemsEqual(obs[1], ['1.SKB8.640193', '1.SKD5.640186'])
def test_remove_samples_both(self):
self.analysis.remove_samples(proc_data=(1, ),
samples=('1.SKB8.640193', ))
exp = {1: ['1.SKD8.640184', '1.SKB7.640196', '1.SKM9.640192',
'1.SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_remove_samples_samples(self):
self.analysis.remove_samples(samples=('1.SKD8.640184', ))
exp = {1: ['1.SKB8.640193', '1.SKB7.640196', '1.SKM9.640192',
'1.SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_remove_samples_processed_data(self):
self.analysis.remove_samples(proc_data=(1, ))
exp = {}
self.assertEqual(self.analysis.samples, exp)
def test_share(self):
self.analysis.share(User("[email protected]"))
self.assertEqual(self.analysis.shared_with, ["[email protected]",
"[email protected]"])
def test_unshare(self):
self.analysis.unshare(User("[email protected]"))
self.assertEqual(self.analysis.shared_with, [])
def test_get_samples(self):
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)
示例5: TestAnalysis
# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import remove_samples [as 别名]
#.........这里部分代码省略.........
"A New Analysis", Analysis(1))
self.assertEqual(new.pmid, None)
def test_set_pmid(self):
self.analysis.pmid = "11211221212213"
self.assertEqual(self.analysis.pmid, "11211221212213")
def test_retrieve_mapping_file(self):
exp = join(get_db_files_base_dir(), "analysis",
"1_analysis_mapping.txt")
obs = self.analysis.mapping_file
self.assertEqual(obs, exp)
self.assertTrue(exists(exp))
def test_retrieve_mapping_file_none(self):
new = Analysis.create(User("[email protected]"), "newAnalysis",
"A New Analysis", Analysis(1))
obs = new.mapping_file
self.assertEqual(obs, None)
# def test_get_parent(self):
# raise NotImplementedError()
# def test_get_children(self):
# raise NotImplementedError()
def test_add_samples(self):
new = Analysis.create(User("[email protected]"), "newAnalysis",
"A New Analysis")
new.add_samples([(1, 'SKB8.640193'), (1, 'SKD5.640186')])
exp = {1: ['SKB8.640193', 'SKD5.640186']}
self.assertEqual(new.samples, exp)
def test_remove_samples_both(self):
self.analysis.remove_samples(proc_data=(1, ),
samples=('SKB8.640193', ))
exp = {1: ['SKD8.640184', 'SKB7.640196', 'SKM9.640192', 'SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_remove_samples_samples(self):
self.analysis.remove_samples(samples=('SKD8.640184', ))
exp = {1: ['SKB8.640193', 'SKB7.640196', 'SKM9.640192', 'SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_remove_samples_processed_data(self):
self.analysis.remove_samples(proc_data=(1, ))
exp = {}
self.assertEqual(self.analysis.samples, exp)
def test_share(self):
self.analysis.share(User("[email protected]"))
self.assertEqual(self.analysis.shared_with, ["[email protected]",
"[email protected]"])
def test_unshare(self):
self.analysis.unshare(User("[email protected]"))
self.assertEqual(self.analysis.shared_with, [])
def test_get_samples(self):
obs = self.analysis._get_samples()
exp = {1: ['SKB7.640196', 'SKB8.640193', 'SKD8.640184', 'SKM4.640180',
'SKM9.640192']}
self.assertEqual(obs, exp)
def test_build_mapping_file(self):
map_fp = join(get_db_files_base_dir(), "analysis",
示例6: TestAnalysis
# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import remove_samples [as 别名]
class TestAnalysis(TestCase):
def setUp(self):
self.analysis = Analysis(1)
def test_lock_check(self):
self.analysis.status = "public"
with self.assertRaises(QiitaDBStatusError):
self.analysis._lock_check(self.conn_handler)
def test_lock_check_ok(self):
self.analysis.status = "queued"
self.analysis._lock_check(self.conn_handler)
def test_create(self):
new = Analysis.create(User("[email protected]"), "newAnalysis",
"A New Analysis")
self.assertEqual(new.id, 3)
sql = "SELECT * FROM qiita.analysis WHERE analysis_id = 3"
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(obs, [[3, '[email protected]', 'newAnalysis',
'A New Analysis', 1, None]])
def test_create_parent(self):
new = Analysis.create(User("[email protected]"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.id, 3)
sql = "SELECT * FROM qiita.analysis WHERE analysis_id = 3"
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(obs, [[3, '[email protected]', 'newAnalysis',
'A New Analysis', 1, None]])
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_shared_with(self):
self.assertEqual(self.analysis.shared_with, ["[email protected]"])
def test_retrieve_biom_tables(self):
self.assertEqual(self.analysis.biom_tables, [7])
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_retrieve_jobs(self):
self.assertEqual(self.analysis.jobs, [1, 2])
def test_retrieve_jobs_none(self):
new = Analysis.create(User("[email protected]"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.jobs, None)
def test_retrieve_pmid(self):
self.assertEqual(self.analysis.pmid, "121112")
def test_retrieve_pmid_none(self):
new = Analysis.create(User("[email protected]"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.pmid, None)
def test_set_pmid(self):
self.analysis.pmid = "11211221212213"
self.assertEqual(self.analysis.pmid, "11211221212213")
# def test_get_parent(self):
# raise NotImplementedError()
# def test_get_children(self):
# raise NotImplementedError()
def test_add_samples(self):
new = Analysis.create(User("[email protected]"), "newAnalysis",
"A New Analysis")
new.add_samples([(1, 'SKB8.640193')])
def test_remove_samples(self):
self.analysis.remove_samples([(1, 'SKB8.640193'), (1, 'SKD8.640184')])
def test_add_biom_tables(self):
new = Analysis.create(User("[email protected]"), "newAnalysis",
#.........这里部分代码省略.........