Python RawData.get_filepaths方法代码示例

# 需要导入模块: from qiita_db.data import RawData [as 别名]
# 或者: from qiita_db.data.RawData import get_filepaths [as 别名]
    def render(self, raw_data_id, prep_template, study, files):
        rd = RawData(raw_data_id)
        raw_data_files = [(basename(fp), fp_type[4:])
                          for _, fp, fp_type in rd.get_filepaths()]
        filetype = rd.filetype
        fp_types = fp_type_by_ft[filetype]
        raw_data_link_status = rd.link_filepaths_status

        show_buttons = rd.status(study) == 'sandbox'
        link_msg = ""
        if show_buttons:
            # Define the message for the link status
            if raw_data_link_status == 'linking':
                link_msg = "Linking files..."
                show_buttons = False
            elif raw_data_link_status == 'unlinking':
                link_msg = "Unlinking files..."
                show_buttons = False
            elif raw_data_link_status.startswith('failed'):
                link_msg = "Error (un)linking files: %s" % raw_data_link_status

        link_msg = convert_text_html(link_msg)
        return self.render_string(
            "study_description_templates/raw_data_info.html",
            rd_id=raw_data_id,
            rd_filetype=rd.filetype,
            raw_data_files=raw_data_files,
            prep_template_id=prep_template.id,
            files=files,
            filepath_types=fp_types,
            filetype=filetype,
            link_msg=link_msg,
            show_buttons=show_buttons)

# 需要导入模块: from qiita_db.data import RawData [as 别名]
# 或者: from qiita_db.data.RawData import get_filepaths [as 别名]
 def test_get_filepaths(self):
     """Correctly returns the filepaths to the raw files"""
     rd = RawData(1)
     obs = rd.get_filepaths()
     exp = [
         (join(self.db_test_raw_dir, '1_s_G1_L001_sequences.fastq.gz'), 1),
         (join(self.db_test_raw_dir,
               '1_s_G1_L001_sequences_barcodes.fastq.gz'), 2)]
     self.assertEqual(obs, exp)

# 需要导入模块: from qiita_db.data import RawData [as 别名]
# 或者: from qiita_db.data.RawData import get_filepaths [as 别名]
         WHERE raw_data_id NOT IN (
            SELECT DISTINCT raw_data_id FROM qiita.prep_template);"""
rd_ids = [x[0] for x in conn_handler.execute_fetchall(sql)]

# We will delete those RawData. However, if they have files attached, we should
# move them to the uploads folder of the study
sql_detach = """DELETE FROM qiita.study_raw_data
                WHERE raw_data_id = %s AND study_id = %s"""
sql_unlink = "DELETE FROM qiita.raw_filepath WHERE raw_data_id = %s"
sql_delete = "DELETE FROM qiita.raw_data WHERE raw_data_id = %s"
sql_studies = """SELECT study_id FROM qiita.study_raw_data
                 WHERE raw_data_id = %s"""
move_files = []
for rd_id in rd_ids:
    rd = RawData(rd_id)
    filepaths = rd.get_filepaths()
    studies = [s[0] for s in conn_handler.execute_fetchall(sql_studies,
                                                           (rd_id,))]
    if filepaths:
        # we need to move the files to a study. We chose the one with lower
        # study id. Currently there is no case in the live database in which a
        # RawData with no prep templates is attached to more than one study,
        # but I think it is better to normalize this just in case
        move_files.append((min(studies), filepaths))

    # To delete the RawData we first need to unlink all the files
    conn_handler.add_to_queue(queue, sql_unlink, (rd_id,))

    # Then, remove the raw data from all the studies
    for st_id in studies:
        conn_handler.add_to_queue(queue, sql_detach, (rd_id, st_id))