def clean_up(files):
'''clean up will delete a list of files, only if they exist
'''
if not isinstance(files, list):
files = [files]
for f in files:
if os.path.exists(f):
bot.verbose3("Cleaning up %s" % f)
os.remove(f)
def extract_env(self):
'''extract the environment from the manifest, or return None.
Used by functions env_extract_image, and env_extract_tar
'''
environ = self._get_config('Env')
if environ is not None:
if not isinstance(environ, list):
environ = [environ]
lines = []
for line in environ:
line = re.findall("(?P<var_name>.+?)=(?P<var_value>.+)", line)
line = ['export %s="%s"' % (x[0], x[1]) for x in line]
lines = lines + line
environ = "\n".join(lines)
bot.verbose3("Found Docker container environment!")
return environ
def extract_runscript(self):
'''extract the runscript (EntryPoint) as first priority, unless the
user has specified to use the CMD. If Entrypoint is not defined,
we default to None:
1. IF SREGISTRY_DOCKERHUB_CMD is set, use Cmd
2. If not set, or Cmd is None/blank, try Entrypoint
3. If Entrypoint is not set, use default /bin/bash
'''
use_cmd = self._get_setting('SREGISTRY_DOCKER_CMD')
# Does the user want to use the CMD instead of ENTRYPOINT?
commands = ["Entrypoint", "Cmd"]
if use_cmd is not None:
commands.reverse()
# Parse through commands until we hit one
for command in commands:
cmd = self._get_config(command)
if cmd is not None:
break
# Only continue if command still isn't None
if cmd is not None:
bot.verbose3("Adding Docker %s as Singularity runscript..."
% command.upper())
# If the command is a list, join. (eg ['/usr/bin/python','hello.py']
bot.debug(cmd)
if not isinstance(cmd, list):
cmd = [cmd]
cmd = " ".join(['"%s"' % x for x in cmd])
cmd = 'exec %s "$@"' % cmd
cmd = "#!/bin/sh\n\n%s\n" % cmd
return cmd
bot.debug("CMD and ENTRYPOINT not found, skipping runscript.")
return cmd
def create_metadata_tar(self,
destination=None,
metadata_folder=".singularity.d"):
'''create a metadata tar (runscript and environment) to add to the
downloaded image. This function uses all functions in this section
to obtain key--> values from the manifest config, and write
to a .tar.gz
Parameters
==========
metadata_folder: the metadata folder in the singularity image.
default is .singularity.d
'''
tar_file = None
# We will add these files to it
files = []
# Extract and add environment
environ = self._extract_env()
if environ not in [None, ""]:
bot.verbose3('Adding Docker environment to metadata tar')
template = get_template('tarinfo')
template['name'] = './%s/env/10-docker.sh' % (metadata_folder)
template['content'] = environ
files.append(template)
# Extract and add labels
labels = self._extract_labels()
if labels is not None:
labels = print_json(labels)
bot.verbose3('Adding Docker labels to metadata tar')
template = get_template('tarinfo')
template['name'] = "./%s/labels.json" % metadata_folder
template['content'] = labels
files.append(template)
# Runscript
runscript = self._extract_runscript()
if runscript is not None:
bot.verbose3('Adding Docker runscript to metadata tar')
template = get_template('tarinfo')
template['name'] = "./%s/runscript" % metadata_folder
template['content'] = runscript
files.append(template)
if len(files) > 0:
dest = self._get_download_cache(destination, subfolder='metadata')
tar_file = create_tar(files, dest)
else:
bot.warning("No metadata will be included.")
return tar_file
