def copy_scans_tsv_file_to_loris_bids_dir(self, bids_sub_id,
loris_bids_root_dir, data_dir):
file = self.scans_tsv_file
copy = loris_bids_root_dir + '/sub-' + bids_sub_id + '/' + os.path.basename(
self.scans_tsv_file)
utilities.copy_file(file, copy, self.verbose)
# determine the relative path and return it
relative_path = copy.replace(data_dir, "")
return relative_path
def extract_iso_images(path):
"""Extract ISO images into webserver directory
Args:
path (str): Directory path containing ISOs
Returns:
list: Paths to extracted ISO images
"""
return_list = []
if not path.endswith('/'):
path += '/'
# Extract ISO into web directory for access over http
for _file in os.listdir(path):
if _file.endswith('.iso'):
name = os.path.splitext(_file)[0]
dest_dir = HTML_DIR + name
# If dest dir already exists continue to next file
if not os.path.isdir(dest_dir):
os.mkdir(dest_dir)
util.bash_cmd('xorriso -osirrox on -indev %s -extract / %s' %
((path + _file), dest_dir))
util.bash_cmd('chmod 755 $(find %s -type d)' % dest_dir)
# Do not return paths to "mini" isos
if not _file.endswith('mini.iso'):
return_list.append(dest_dir)
# Ubuntu ppc64el before 16.04.2 requires files from netboot mini iso
for _file in os.listdir(path):
if _file.endswith('mini.iso'):
src_dir = (HTML_DIR + _file[:-4] + '/install/')
dest_dir = (HTML_DIR + _file[:-9] +
'/install/netboot/ubuntu-installer/ppc64el/')
if not os.path.isdir(dest_dir):
os.makedirs(dest_dir)
for netboot_file in os.listdir(src_dir):
util.copy_file(src_dir + netboot_file, dest_dir)
return return_list
def setup_image_config_files(path, html_dir):
"""Setup image config files
Args:
path (str): Directory path image config files
html_dir (str): Path to root http directory
"""
if not path.endswith('/'):
path += '/'
# Update preseed configurations with default user id
# Copy preseed & kickstart files to cobbler kickstart directory
for _file in os.listdir(path):
if _file.endswith('.ks') or _file.endswith('.seed'):
util.copy_file(path + _file, KICKSTARTS_DIR)
# Copy custom snippets to cobbler snippets directory
snippets_src_dir = path + 'snippets/'
for _file in os.listdir(snippets_src_dir):
util.copy_file(snippets_src_dir + _file, SNIPPETS_DIR)
# Copy apt source lists to web repo directory
if not os.path.isdir(html_dir + 'ubuntu_sources'):
os.makedirs(html_dir + 'ubuntu_sources')
for _file in os.listdir(path):
if _file.endswith('.list'):
util.copy_file(path + _file, html_dir + 'ubuntu_sources')
def copy_file_to_loris_bids_dir(self, file, derivatives_path=None):
"""
Wrapper around the utilities.copy_file function that copies the file
to the LORIS BIDS import directory and returns the relative path of the
file (without the data_dir part).
:param file: full path to the original file
:type file: str
:param derivatives_path: path to the derivative folder
:type derivatives_path: str
:return: relative path to the copied file
:rtype: str
"""
# determine the path of the copied file
copy_file = self.loris_bids_eeg_rel_dir
if self.bids_ses_id:
copy_file += os.path.basename(file)
else:
# make sure the ses- is included in the new filename if using
# default visit label from the LORIS config
copy_file += str.replace(
os.path.basename(file), "sub-" + self.bids_sub_id,
"sub-" + self.bids_sub_id + "_ses-" + self.default_vl)
if derivatives_path:
# create derivative subject/vl/modality directory
lib.utilities.create_dir(
derivatives_path + self.loris_bids_eeg_rel_dir, self.verbose)
copy_file = derivatives_path + copy_file
else:
copy_file = self.loris_bids_root_dir + copy_file
# copy the file
utilities.copy_file(file, copy_file, self.verbose)
# determine the relative path and return it
relative_path = copy_file.replace(self.data_dir, "")
return relative_path