Python Study.prep_templates方法代码示例

# 需要导入模块: from qiita_db.study import Study [as 别名]
# 或者: from qiita_db.study.Study import prep_templates [as 别名]

#.........这里部分代码省略.........
        exp = ['123456', '7891011']
        self.assertEqual(self.study.pmids, exp)

        new_values = ['654321', '1101987']
        self.study.pmids = new_values
        self.assertEqual(self.study.pmids, new_values)

    def test_pmids_setter_typeerror(self):
        with self.assertRaises(TypeError):
            self.study.pmids = '123456'

    def test_retrieve_investigation(self):
        self.assertEqual(self.study.investigation, 1)

    def test_retrieve_investigation_empty(self):
        new = Study.create(User('[email protected]'), 'NOT Identification of the '
                           'Microbiomes for Cannabis Soils', [1], self.info)
        self.assertEqual(new.investigation, None)

    def test_retrieve_sample_template(self):
        self.assertEqual(self.study.sample_template, 1)

    def test_retrieve_data_types(self):
        self.assertEqual(self.study.data_types, ['18S'])

    def test_retrieve_data_types_none(self):
        new = Study.create(User('[email protected]'), 'NOT Identification of the '
                           'Microbiomes for Cannabis Soils', [1], self.info)
        self.assertEqual(new.data_types, [])

    def test_retrieve_raw_data(self):
        self.assertEqual(self.study.raw_data(), [1])

    def test_retrieve_raw_data_none(self):
        new = Study.create(User('[email protected]'), 'NOT Identification of the '
                           'Microbiomes for Cannabis Soils', [1], self.info)
        self.assertEqual(new.raw_data(), [])

    def test_retrieve_prep_templates(self):
        self.assertEqual(self.study.prep_templates(), [1])

    def test_retrieve_prep_templates_none(self):
        new = Study.create(User('[email protected]'), 'NOT Identification of the '
                           'Microbiomes for Cannabis Soils', [1], self.info)
        self.assertEqual(new.prep_templates(), [])

    def test_retrieve_preprocessed_data(self):
        self.assertEqual(self.study.preprocessed_data(), [1, 2])

    def test_retrieve_preprocessed_data_none(self):
        new = Study.create(User('[email protected]'), 'NOT Identification of the '
                           'Microbiomes for Cannabis Soils', [1], self.info)
        self.assertEqual(new.preprocessed_data(), [])

    def test_retrieve_processed_data(self):
        self.assertEqual(self.study.processed_data(), [1])

    def test_retrieve_processed_data_none(self):
        new = Study.create(User('[email protected]'), 'NOT Identification of the '
                           'Microbiomes for Cannabis Soils', [1], self.info)
        self.assertEqual(new.processed_data(), [])

    def test_add_pmid(self):
        self._change_processed_data_status('sandbox')
        self.study.add_pmid('4544444')
        exp = ['123456', '7891011', '4544444']
        self.assertEqual(self.study.pmids, exp)

    def test_environmental_packages(self):
        obs = self.study.environmental_packages
        exp = ['soil', 'plant-associated']
        self.assertEqual(sorted(obs), sorted(exp))

    def test_environmental_packages_setter(self):
        new = Study.create(User('[email protected]'), 'NOT Identification of the '
                           'Microbiomes for Cannabis Soils', [1], self.info)
        obs = new.environmental_packages
        exp = []
        self.assertEqual(obs, exp)

        new_values = ['air', 'human-oral']
        new.environmental_packages = new_values
        obs = new.environmental_packages
        self.assertEqual(sorted(obs), sorted(new_values))

    def test_environmental_packages_setter_typeerror(self):
        new = Study.create(User('[email protected]'), 'NOT Identification of the '
                           'Microbiomes for Cannabis Soils', [1], self.info)
        with self.assertRaises(TypeError):
            new.environmental_packages = 'air'

    def test_environmental_packages_setter_valueerror(self):
        new = Study.create(User('[email protected]'), 'NOT Identification of the '
                           'Microbiomes for Cannabis Soils', [1], self.info)
        with self.assertRaises(ValueError):
            new.environmental_packages = ['air', 'not a package']

    def test_environmental_packages_sandboxed(self):
        with self.assertRaises(QiitaDBStatusError):
            self.study.environmental_packages = ['air']

# 需要导入模块: from qiita_db.study import Study [as 别名]
# 或者: from qiita_db.study.Study import prep_templates [as 别名]
def study_get_req(study_id, user_id):
    """Returns information available for the given study

    Parameters
    ----------
    study_id : int
        Study id to get prep template info for
    user_id : str
        User requesting the info

    Returns
    -------
    dict
        Data types information in the form
        {'status': status,
         'message': message,
         'info': dict of objects
        status can be success, warning, or error depending on result
        message has the warnings or errors
        info contains study information seperated by data type, in the form
        {col_name: value, ...} with value being a string, int, or list of
        strings or ints
    """
    access_error = check_access(study_id, user_id)
    if access_error:
        return access_error
    # Can only pass ids over API, so need to instantiate object
    study = Study(study_id)
    study_info = study.info
    # Add needed info that is not part of the initial info pull
    study_info['publication_doi'] = []
    study_info['publication_pid'] = []
    for pub, is_doi in study.publications:
        if is_doi:
            study_info['publication_doi'].append(pub)
        else:
            study_info['publication_pid'].append(pub)
    study_info['study_id'] = study.id
    study_info['study_title'] = study.title
    study_info['shared_with'] = [s.id for s in study.shared_with]
    study_info['status'] = study.status
    study_info['ebi_study_accession'] = study.ebi_study_accession
    study_info['ebi_submission_status'] = study.ebi_submission_status

    # Clean up StudyPerson objects to string for display
    pi = study_info['principal_investigator']
    study_info['principal_investigator'] = {
        'name': pi.name,
        'email': pi.email,
        'affiliation': pi.affiliation}

    lab_person = study_info['lab_person']
    if lab_person:
        study_info['lab_person'] = {
            'name': lab_person.name,
            'email': lab_person.email,
            'affiliation': lab_person.affiliation}

    samples = study.sample_template
    study_info['num_samples'] = 0 if samples is None else len(list(samples))
    study_info['owner'] = study.owner.id
    # Study.has_access no_public=True, will return True only if the user_id is
    # the owner of the study or if the study is shared with the user_id
    study_info['has_access_to_raw_data'] = study.has_access(
        User(user_id), True)

    study_info['show_biom_download_button'] = 'BIOM' in [
        a.artifact_type for a in study.artifacts()]
    study_info['show_raw_download_button'] = any([
        True for pt in study.prep_templates() if pt.artifact is not None])

    # getting study processing status from redis
    processing = False
    study_info['level'] = ''
    study_info['message'] = ''
    job_info = r_client.get(STUDY_KEY_FORMAT % study_id)
    if job_info:
        job_info = defaultdict(lambda: '', loads(job_info))
        job_id = job_info['job_id']
        job = ProcessingJob(job_id)
        job_status = job.status
        processing = job_status not in ('success', 'error')
        if processing:
            study_info['level'] = 'info'
            study_info['message'] = 'This study is currently being processed'
        elif job_status == 'error':
            study_info['level'] = 'danger'
            study_info['message'] = job.log.msg.replace('\n', '</br>')
        else:
            study_info['level'] = job_info['alert_type']
            study_info['message'] = job_info['alert_msg'].replace(
                '\n', '</br>')

    return {'status': 'success',
            'message': '',
            'study_info': study_info,
            'editable': study.can_edit(User(user_id))}