本文整理汇总了Python中qiita_db.data.RawData.get_filepaths方法的典型用法代码示例。如果您正苦于以下问题:Python RawData.get_filepaths方法的具体用法?Python RawData.get_filepaths怎么用?Python RawData.get_filepaths使用的例子?那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类qiita_db.data.RawData
的用法示例。
在下文中一共展示了RawData.get_filepaths方法的3个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: render
# 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)
示例2: test_get_filepaths
# 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)
示例3: IN
# 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))