def get_environment_tar(self):
'''return the environment.tar generated with the Singularity software.
We first try the Linux Filesystem expected location in /usr/libexec
If not found, we detect the system archicture
dirname $(singularity selftest 2>&1 | grep 'lib' | awk '{print $4}' | sed -e 's@\(.*/singularity\).*@\1@')
'''
from sregistry.utils import ( which, run_command )
# First attempt - look at File System Hierarchy Standard (FHS)
res = which('singularity')['message']
libexec = res.replace('/bin/singularity','')
envtar = '%s/libexec/singularity/bootstrap-scripts/environment.tar' %libexec
if os.path.exists(envtar):
return envtar
# Second attempt, debian distribution will identify folder
try:
res = which('dpkg-architecture')['message']
if res is not None:
cmd = ['dpkg-architecture', '-qDEB_HOST_MULTIARCH']
triplet = run_command(cmd)['message'].strip('\n')
envtar = '/usr/lib/%s/singularity/bootstrap-scripts/environment.tar' %triplet
if os.path.exists(envtar):
return envtar
except:
pass
# Final, return environment.tar provided in package
return "%s/environment.tar" %os.path.abspath(os.path.dirname(__file__))
def test_which():
print("Testing utils.which")
from sregistry.utils import which
result = which('echo')
assert result['message'].endswith('echo')
assert result['return_code'] == 0
result = which('singularityaaaa')
assert result['message'] == ''
assert result['return_code'] == 1
def test_which():
print("Testing utils.which")
from sregistry.utils import which
result = which("echo")
assert result["message"].endswith("echo")
assert result["return_code"] == 0
result = which("singularityaaaa")
assert result["message"] == ""
assert result["return_code"] == 1
def get_metadata(self, image_file, names=None):
'''extract metadata using Singularity inspect, if the executable is found.
If not, return a reasonable default (the parsed image name)
Parameters
==========
image_file: the full path to a Singularity image
names: optional, an extracted or otherwise created dictionary of
variables for the image, likely from utils.parse_image_name
'''
if names is None:
names = {}
metadata = {}
# We can't return anything without image_file or names
if image_file:
if not os.path.exists(image_file):
bot.error('Cannot find %s.' % image_file)
return names or metadata
# The user provided a file, but no names
if not names:
names = parse_image_name(remove_uri(image_file))
# Look for the Singularity Executable
singularity = which('singularity')['message']
# Inspect the image, or return names only
if os.path.exists(singularity) and image_file:
from spython.main import Client as Singularity
# Store the original quiet setting
is_quiet = Singularity.quiet
# We try and inspect, but not required (wont work within Docker)
try:
Singularity.quiet = True
updates = Singularity.inspect(image=image_file)
except:
bot.warning(
'Inspect command not supported, metadata not included.')
updates = None
# Restore the original quiet setting
Singularity.quiet = is_quiet
# Try loading the metadata
if updates is not None:
try:
updates = json.loads(updates)
metadata.update(updates)
except:
pass
metadata.update(names)
return metadata
def get_metadata(self, image_file, names={}):
'''extract metadata using Singularity inspect, if the executable is found.
If not, return a reasonable default (the parsed image name)
Parameters
==========
image_file: the full path to a Singularity image
names: optional, an extracted or otherwise created dictionary of
variables for the image, likely from utils.parse_image_name
'''
metadata = dict()
# We can't return anything without image_file or names
if image_file is not None:
if not os.path.exists(image_file):
bot.error('Cannot find %s.' % image_file)
return names
# The user provided a file, but no names
if not names:
names = parse_image_name(remove_uri(image_file))
# Look for the Singularity Executable
singularity = which('singularity')['message']
# Inspect the image, or return names only
if os.path.exists(singularity) and image_file is not None:
from sregistry.client import Singularity
cli = Singularity()
updates = cli.inspect(image_path=image_file, quiet=True)
# Try loading the metadata
if updates is not None:
try:
updates = json.loads(updates)
metadata.update(updates)
except:
pass
metadata.update(names)
return metadata
def get_metadata(self, image_file, names=None):
"""extract metadata using Singularity inspect, if the executable is found.
If not, return a reasonable default (the parsed image name)
Parameters
==========
image_file: the full path to a Singularity image
names: optional, an extracted or otherwise created dictionary of
variables for the image, likely from utils.parse_image_name
"""
if names is None:
names = {}
metadata = {}
# We can't return anything without image_file or names
if image_file:
if not os.path.exists(image_file):
bot.error("Cannot find %s." % image_file)
return names or metadata
# The user provided a file, but no names
if not names:
names = parse_image_name(remove_uri(image_file))
# Look for the Singularity Executable
singularity = which("singularity")["message"]
# Inspect the image, or return names only
if os.path.exists(singularity) and image_file:
from spython.main import Client as Singularity
# Store the original quiet setting
is_quiet = Singularity.quiet
# We try and inspect, but not required (wont work within Docker)
try:
Singularity.quiet = True
updates = Singularity.inspect(image=image_file)
except:
bot.warning(
"Inspect command not supported, metadata not included.")
updates = None
# Restore the original quiet setting
Singularity.quiet = is_quiet
# Try loading the metadata
if updates is not None:
try:
updates = json.loads(updates)
# Singularity 3.x bug with missing top level
if "data" in updates:
updates = updates["data"]
metadata.update(updates)
# Flatten labels
if "attributes" in metadata:
if "labels" in metadata["attributes"]:
metadata.update(metadata["attributes"]["labels"])
del metadata["attributes"]
except:
pass
metadata.update(names)
# Add the type to the container
metadata["type"] = "container"
return metadata