def copy_static(self):
"""Copy template statics files to output dir.
Files under each path specifed by :py:attr:`static_roots`
will be copied to folder :file:`static` below :py:attr:`report_root`.
"""
if is_pathlike(self.static_roots):
_static_roots = [self.static_roots]
else:
_static_roots = self.static_roots
merged_copytree(_static_roots, self.report_root / 'static')
def __init__(self, job_info, report_root):
"""Initiate a Stage object.
Here NGS result info and path to gerenerate report is passed.
.. py:attribute:: job_info
:annotation: = job_info
:py:class:`~ngcloud.info.JobInfo` object.
.. py:attribute:: report_root
:annotation: = report_root
:py:class:`~pathlib.Path` object.
.. py:attribute:: result_info
:annotation: = dict()
A :class:`!dict` object to store NGS result info. See :meth:`parse`
for more information.
.. note:: Key names should follow Python argument naming rule.
.. py:attribute:: result_root
:annotation: = join_info.root_path + result_foldername
:class:`~pathlib.Path` object to the stage result root folder.
This attribute is automatically set by finding the matched
foldername based on :attr:`result_foldername`
"""
logger.info("Initating new stage {}".format(type(self).__name__))
self._setup_jinja2()
if is_pathlike(self.template_entrances):
tpls = [self.template_entrances]
else:
tpls = self.template_entrances
self._templates = {tpl: self._env.get_template(tpl) for tpl in tpls}
self.job_info = job_info
self.report_root = report_root
self.result_info = dict()
logger.debug("... Loacate result folder path")
self.result_root = self._locate_result_folder()
logger.debug("... stage initiated".format(type(self).__name__))
