Python SampleTemplate.get_filepaths方法代碼示例

# 需要導入模塊: from qiita_db.metadata_template.sample_template import SampleTemplate [as 別名]
# 或者: from qiita_db.metadata_template.sample_template.SampleTemplate import get_filepaths [as 別名]
def sample_template_overview_handler_get_request(study_id, user):
    # Check if the current user has access to the sample template
    sample_template_checks(study_id, user)

    # Check if the sample template exists
    exists = SampleTemplate.exists(study_id)

    # The following information should always be provided:
    # The files that have been uploaded to the system and can be a
    # sample template file
    files = [f for _, f, _ in get_files_from_uploads_folders(study_id)
             if f.endswith(('txt', 'tsv', 'xlsx'))]
    # If there is a job associated with the sample information, the job id
    job = None
    job_info = r_client.get(SAMPLE_TEMPLATE_KEY_FORMAT % study_id)
    if job_info:
        job = loads(job_info)['job_id']

    # Specific information if it exists or not:
    data_types = []
    st_fp_id = None
    old_files = []
    num_samples = 0
    num_cols = 0
    if exists:
        # If it exists we need to provide:
        # The id of the sample template file so the user can download it and
        # the list of old filepaths
        st = SampleTemplate(study_id)
        all_st_files = st.get_filepaths()
        # The current sample template file is the first one in the list
        # (pop(0)) and we are interested only in the id ([0])
        st_fp_id = all_st_files.pop(0)[0]
        # For the old filepaths we are only interested in their basename
        old_files = [basename(fp) for _, fp in all_st_files]
        # The number of samples - this is a space efficient way of counting
        # the number of samples. Doing len(list(st.keys())) creates a list
        # that we are not using
        num_samples = sum(1 for _ in st.keys())
        # The number of columns
        num_cols = len(st.categories())
    else:
        # It doesn't exist, we also need to provide the data_types in case
        # the user uploads a QIIME mapping file
        data_types = sorted(data_types_get_req()['data_types'])

    return {'exists': exists,
            'uploaded_files': files,
            'data_types': data_types,
            'user_can_edit': Study(study_id).can_edit(user),
            'job': job,
            'download_id': st_fp_id,
            'old_files': old_files,
            'num_samples': num_samples,
            'num_columns': num_cols}

# 需要導入模塊: from qiita_db.metadata_template.sample_template import SampleTemplate [as 別名]
# 或者: from qiita_db.metadata_template.sample_template.SampleTemplate import get_filepaths [as 別名]
def sample_template_filepaths_get_req(study_id, user_id):
    """Returns all the filepaths attached to the sample template

    Parameters
    ----------
    study_id : int
        The current study object id
    user_id : str
        The current user object id

    Returns
    -------
    dict
        Filepaths in the form
        {'status': status,
         'message': msg,
         'filepaths': filepaths}
        status can be success, warning, or error depending on result
        message has the warnings or errors
        filepaths is a list of tuple of int and str
        All files in the sample template, as [(id, URL), ...]
    """
    exists = _check_sample_template_exists(int(study_id))
    if exists['status'] != 'success':
        return exists
    access_error = check_access(study_id, user_id)
    if access_error:
        return access_error

    try:
        template = SampleTemplate(int(study_id))
    except QiitaDBUnknownIDError as e:
        return {'status': 'error',
                'message': str(e)}

    return {'status': 'success',
            'message': '',
            'filepaths': template.get_filepaths()
            }