本文整理汇总了Python中qiita_db.analysis.Analysis.add_samples方法的典型用法代码示例。如果您正苦于以下问题:Python Analysis.add_samples方法的具体用法?Python Analysis.add_samples怎么用?Python Analysis.add_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.add_samples方法的4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: test_remove_portal
# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import add_samples [as 别名]
def test_remove_portal(self):
Portal.create("NEWPORTAL", "SOMEDESC")
# Select some samples on a default analysis
qiita_config.portal = "NEWPORTAL"
a = Analysis(User("[email protected]").default_analysis)
a.add_samples({1: ['1.SKB8.640193', '1.SKD5.640186']})
Portal.delete("NEWPORTAL")
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.portal_type")
exp = [[1, 'QIITA', 'QIITA portal. Access to all data stored '
'in database.'],
[2, 'EMP', 'EMP portal']]
self.assertItemsEqual(obs, exp)
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.analysis_portal")
exp = [[1, 1], [2, 1], [3, 1], [4, 1], [5, 1], [6, 1], [7, 2], [8, 2],
[9, 2], [10, 2]]
self.assertItemsEqual(obs, exp)
with self.assertRaises(QiitaDBLookupError):
Portal.delete("NOEXISTPORTAL")
with self.assertRaises(QiitaDBError):
Portal.delete("QIITA")
Portal.create("NEWPORTAL2", "SOMEDESC")
# Add analysis to this new portal and make sure error raised
qiita_config.portal = "NEWPORTAL2"
Analysis.create(User("[email protected]"), "newportal analysis", "desc")
qiita_config.portal = "QIITA"
with self.assertRaises(QiitaDBError):
Portal.delete("NEWPORTAL2")
# Add study to this new portal and make sure error raised
info = {
"timeseries_type_id": 1,
"metadata_complete": True,
"mixs_compliant": True,
"number_samples_collected": 25,
"number_samples_promised": 28,
"study_alias": "FCM",
"study_description": "Microbiome of people who eat nothing but "
"fried chicken",
"study_abstract": "Exploring how a high fat diet changes the "
"gut microbiome",
"emp_person_id": StudyPerson(2),
"principal_investigator_id": StudyPerson(3),
"lab_person_id": StudyPerson(1)
}
Portal.create("NEWPORTAL3", "SOMEDESC")
qiita_config.portal = "NEWPORTAL3"
Study.create(User('[email protected]'), "Fried chicken microbiome",
[1], info)
qiita_config.portal = "QIITA"
with self.assertRaises(QiitaDBError):
Portal.delete("NEWPORTAL3")
示例2: 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 add_samples [as 别名]
def on_message(self, msg):
"""Selects samples on a message from the user
Parameters
----------
msg : JSON str
Message containing sample and prc_data information, in the form
{proc_data_id': [s1, s2, ...], ...]}
"""
msginfo = loads(msg)
default = Analysis(self.current_user.default_analysis)
default.add_samples(msginfo['sel'])
# Count total number of unique samples selected and return
self.write_message(dumps({
'sel': len(set(
chain.from_iterable(s for s in viewvalues(msginfo['sel']))))
}))
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 add_samples [as 别名]
def post(self):
analysis_id = self.get_argument('analysis-id')
study_args = self.get_arguments('studies')
split = [x.split("#") for x in study_args]
# build dictionary of studies and datatypes selected
# as well a set of unique datatypes selected
study_dts = defaultdict(list)
data_types = set()
for study_id, data_type in split:
study_dts[study_id].append(data_type)
data_types.add(data_type)
# sort the elements to have 16S be the first tho show on the tabs
data_types = sorted(list(data_types))
# FIXME: Pull out from the database, see #111
commands = {'16S': ['Beta Diversity', 'Summarize Taxa'],
'18S': ['Beta Diversity', 'Summarize Taxa'],
'Metabolomic': ['Beta Diversity'],
'Metagenomic': ['Beta Diversity']}
self.render('select_commands.html', user=self.get_current_user(),
commands=commands, data_types=data_types, aid=analysis_id)
analysis = Analysis(analysis_id)
for study_id in study_dts:
study = Study(study_id)
processed_data = {ProcessedData(pid).data_type: pid for pid in
study.processed_data}
sample_ids = SampleTemplate(study.id).keys()
for data_type in study_dts[study.id]:
samples = [(processed_data[data_type], sid) for sid in
sample_ids]
analysis.add_samples(samples)
示例4: post
# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import add_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"))