Python Analysis.create方法代码示例

# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import create [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")

# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import create [as 别名]
    def test_create_nonqiita_portal(self):
        new_id = get_count("qiita.analysis") + 1
        qiita_config.portal = "EMP"
        Analysis.create(User("[email protected]"), "newAnalysis",
                        "A New Analysis")

        # make sure portal is associated
        obs = self.conn_handler.execute_fetchall(
            "SELECT * from qiita.analysis_portal WHERE analysis_id = %s",
            [new_id])
        self.assertEqual(obs, [[new_id, 2], [new_id, 1]])

# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import create [as 别名]
 def test_create_exists_return_existing(self):
     """Makes sure creation doesn't duplicate a job by returning existing"""
     Analysis.create(User("[email protected]"), "new", "desc")
     self.conn_handler.execute(
         "INSERT INTO qiita.analysis_sample (analysis_id, "
         "processed_data_id, sample_id) VALUES (3,1,'SKB8.640193'), "
         "(3,1,'SKD8.640184'), (3,1,'SKB7.640196'), (3,1,'SKM9.640192'),"
         "(3,1,'SKM4.640180')")
     new = Job.create("18S", "Beta Diversity",
                      {"--otu_table_fp": 1, "--mapping_fp": 1},
                      Analysis(3), return_existing=True)
     self.assertEqual(new.id, 2)

# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import create [as 别名]
 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'])

# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import create [as 别名]
 def test_set_step(self):
     new = Analysis.create(User("[email protected]"), "newAnalysis",
                           "A New Analysis", Analysis(1))
     new.step = 2
     sql = "SELECT * FROM qiita.analysis_workflow WHERE analysis_id = 3"
     obs = self.conn_handler.execute_fetchall(sql)
     self.assertEqual(obs, [[3, 2]])

# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import create [as 别名]
    def post(self):
        name = self.get_argument('name')
        desc = self.get_argument('description')
        analysis = Analysis.create(self.current_user, name, desc,
                                   from_default=True)

        self.redirect(u"%s/analysis/description/%s/"
                      % (qiita_config.portal_dir, analysis.id))

# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import create [as 别名]
 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]])

# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import create [as 别名]
 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)

# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import create [as 别名]
 def test_set_step_twice(self):
     new_id = get_count("qiita.analysis") + 1
     new = Analysis.create(User("[email protected]"), "newAnalysis",
                           "A New Analysis", Analysis(1))
     new.step = 2
     new.step = 4
     sql = "SELECT * FROM qiita.analysis_workflow WHERE analysis_id = %s"
     obs = self.conn_handler.execute_fetchall(sql, [new_id])
     self.assertEqual(obs, [[new_id, 4]])

# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import create [as 别名]
 def post(self):
     name = self.get_argument('name')
     desc = self.get_argument('description')
     analysis = Analysis.create(self.current_user, name, desc,
                                from_default=True)
     # set to third step since this page is third step in workflow
     analysis.step = SELECT_COMMANDS
     data_types = analysis.data_types
     commands = Command.get_commands_by_datatype()
     self.render('select_commands.html',
                 commands=commands, data_types=data_types, aid=analysis.id)

# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import create [as 别名]
    def post(self):
        name = self.get_argument('name')
        desc = self.get_argument('description')
        mdsi = self.get_argument('merge_duplicated_sample_ids', False)
        if mdsi in (b'on', 'on'):
            mdsi = True
        analysis = Analysis.create(
            self.current_user, name, desc, merge_duplicated_sample_ids=mdsi,
            from_default=True)

        self.redirect(u"%s/analysis/description/%s/"
                      % (qiita_config.portal_dir, analysis.id))

# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import create [as 别名]
 def test_create(self):
     sql = "SELECT EXTRACT(EPOCH FROM NOW())"
     time1 = float(self.conn_handler.execute_fetchall(sql)[0][0])
     new_id = get_count("qiita.analysis") + 1
     new = Analysis.create(User("[email protected]"), "newAnalysis",
                           "A New Analysis")
     self.assertEqual(new.id, new_id)
     sql = ("SELECT analysis_id, email, name, description, "
            "analysis_status_id, pmid, EXTRACT(EPOCH FROM timestamp) "
            "FROM qiita.analysis WHERE analysis_id = %s")
     obs = self.conn_handler.execute_fetchall(sql, [new_id])
     self.assertEqual(obs[0][:-1], [new_id, '[email protected]', 'newAnalysis',
                                    'A New Analysis', 1, None])
     self.assertTrue(time1 < float(obs[0][-1]))

# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import create [as 别名]
    def test_select_samples(self):
        newaid = Analysis.create(User("[email protected]"), "test1", "testdesc").id
        post_args = {
            'analysis-id': newaid,
            'action': 'select',
            'availstudies': "1#1",
            '1#1': 1,
            '1': 'SKD5.640186'}

        response = self.post('/analysis/2', post_args)

        # Make sure page response loaded sucessfully
        self.assertEqual(response.code, 200)
        # make sure sample added
        self.assertTrue("SKD5.640186" in str(response.body))

# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import create [as 别名]
    def post(self):
        name = self.get_argument('name')
        description = self.get_argument('description')
        user = self.get_current_user()
        # create list of studies
        study_ids = {s.id for s in Study.get_public()}
        userobj = User(user)
        [study_ids.add(x) for x in userobj.private_studies]
        [study_ids.add(x) for x in userobj.shared_studies]

        studies = [Study(i) for i in study_ids]
        analysis = Analysis.create(User(user), name, description)

        self.render('select_studies.html', user=user, aid=analysis.id,
                    studies=studies)

# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import create [as 别名]
    def test_get_analysis_jobs_handler(self):
        user = User('[email protected]')
        dflt_analysis = user.default_analysis
        dflt_analysis.add_samples(
            {4: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196',
                 '1.SKM9.640192', '1.SKM4.640180']})
        new = Analysis.create(user, "newAnalysis", "A New Analysis",
                              from_default=True)
        response = self.get('/analysis/description/%s/jobs/' % new.id)
        self.assertEqual(response.code, 200)

        # There is only one job
        job_id = new.jobs[0].id
        obs = loads(response.body)
        exp = {job_id: {'status': 'queued', 'step': None, 'error': ""}}
        self.assertEqual(obs, exp)