Python Analysis.add_samples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 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")

# 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']))))
        }))

# 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)

# 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"))