def package(image_path,output_folder=None,runscript=True,software=True,remove_image=False,verbose=False):
'''package will take an image and generate a zip (including the image
to a user specified output_folder.
:param image_path: full path to singularity image file
:param runscript: if True, will extract runscript to include in package as runscript
:param software: if True, will extract files.txt and folders.txt to package
:param remove_image: if True, will not include original image in package (default,False)
:param verbose: be verbose when using singularity --export (default,False)
'''
S = Singularity(verbose=verbose)
tmptar = S.export(image_path=image_path,pipe=False)
tar = tarfile.open(tmptar)
members = tar.getmembers()
image_name = os.path.basename(image_path)
zip_name = "%s.zip" %(image_name.replace(" ","_"))
# Include the image in the package?
if remove_image:
to_package = dict()
else:
to_package = {image_name:image_path}
# Package the image with an md5 sum as VERSION
version = get_image_hash(image_path)
to_package["VERSION"] = version
# Look for runscript
if runscript == True:
try:
runscript_member = tar.getmember("./singularity")
runscript_file = tar.extractfile("./singularity")
runscript = runscript_file.read()
to_package["runscript"] = runscript
print("Found runscript!")
# Try to extract input args, only python supported, will return None otherwise
params_json = get_runscript_parameters(runscript=runscript,
name=image_name,
version=version)
if params_json != None:
print('Extracted runscript params!')
to_package['%s.json' %(image_name)] = params_json
except KeyError:
print("No runscript found in image!")
if software == True:
print("Adding software list to package!")
files = [x.path for x in members if x.isfile()]
folders = [x.path for x in members if x.isdir()]
to_package["files.txt"] = files
to_package["folders.txt"] = folders
# Do zip up here - let's start with basic structures
zipfile = zip_up(to_package,zip_name=zip_name,output_folder=output_folder)
print("Package created at %s" %(zipfile))
# return package to user
return zipfile
def get_memory_tar(image_path):
'''get an in memory tar of an image (does not require sudo!)'''
cli = Singularity()
if "pancakes" in os.environ:
del os.environ['pancakes']
byte_array = cli.export(image_path)
file_object = io.BytesIO(byte_array)
tar = tarfile.open(mode="r|*", fileobj=file_object)
return (file_object, tar)
def get_memory_tar(image_path):
'''get an in memory tar of an image. Use carefully, not as reliable
as get_image_tar
'''
cli = Singularity()
byte_array = cli.export(image_path)
file_object = io.BytesIO(byte_array)
tar = tarfile.open(mode="r|*", fileobj=file_object)
return (file_object, tar)
def get_image_tar(image_path, S=None):
'''get an image tar, either written in memory or to
the file system. file_obj will either be the file object,
or the file itself.
'''
bot.debug('Generate file system tar...')
if S is None:
S = Singularity()
file_obj = S.export(image_path=image_path)
if file_obj is None:
bot.error("Error generating tar, exiting.")
sys.exit(1)
tar = tarfile.open(file_obj)
return file_obj, tar
# Get general help:
S.help()
# These are the defaults, which can be specified
S = Singularity(sudo=True,verbose=False)
# Let's define a path to an image
# wget http://www.vbmis.com/bmi/project/singularity/package_image/ubuntu:latest-2016-04-06.img
image_path = 'ubuntu:latest-2016-04-06.img'
# Run singularity --exec
S.execute(image_path=image_path,command='ls')
# $'docker2singularity.sh\nget_docker_container_id.sh\nget_docker_meta.py\nmakeBases.py\nsingularity\nubuntu:latest-2016-04-06.img\n'
# These are the defaults, which can be specified
# For any function you can get the docs:
S.help(command="exec")
# or return as string
help = S.help(command="exec",stdout=False)
# export an image, default export_type="tar" , pipe=False , output_file = None will produce file in tmp
tmptar = S.export(image_path=image_path)
# create an empty image
S.create(image_path='test.img')
# import a docker image - no need to specify the file, the image name works
# still under development
docker_image = S.docker2singularity("ubuntu:latest")
# (Deprecated) create an image and import into it
image = S.create('myimage.simg')
S.importcmd(image, 'docker://ubuntu:latest')
# Execute command to container
result = S.execute(image, command='cat /singularity')
print(result)
'''
'#!/bin/sh\n\nexec "/bin/bash"\n'
'''
# For any function you can get the docs:
S.help(command="exec")
# export an image to tar
tar = S.export(image)
# Show apps and inspect
S.apps(image)
S.inspect(image)
'''
{
"data": {
"attributes": {
"deffile": null,
"help": null,
"labels": null,
"environment": "# Custom environment shell code should follow\n\n",
"runscript": "#!/bin/sh\n\nexec \"/bin/bash\"\n",
"test": null
},
image = S.create('myimage.img')
# Import into it
S.importcmd(image, 'docker://*****:*****@"
elif test -x /bin/sh; then
exec /bin/sh "$@"
else
echo "ERROR: No valid shell within container"
exit 255
fi
'''
# For any function you can get the docs:
S.help(command="exec")
# export an image as a byte array
byte_array = S.export(image)
# Get an in memory tar
from singularity.reproduce import get_memory_tar
tar = get_memory_tar(image)
def package(image_path,
spec_path=None,
output_folder=None,
runscript=True,
software=True,
remove_image=False,
verbose=False,
S=None,
sudopw=None,
old_version=False):
'''package will take an image and generate a zip (including the image
to a user specified output_folder.
:param image_path: full path to singularity image file
:param runscript: if True, will extract runscript to include in package as runscript
:param software: if True, will extract files.txt and folders.txt to package
:param remove_image: if True, will not include original image in package (default,False)
:param verbose: be verbose when using singularity --export (default,False)
:param S: the Singularity object (optional) will be created if not required.
'''
# Run create image and bootstrap with Singularity command line tool.
if S == None:
if sudopw != None:
S = Singularity(sudopw=sudopw, debug=verbose)
else:
S = Singularity(
debug=verbose) # This command will ask the user for sudo
# Singularity < version 2.3
if old_version == False:
file_obj, tar = get_memory_tar(image_path)
# Singularity 2.3 and up
else:
tmptar = S.export(image_path=image_path, old_version=True)
tar = tarfile.open(tmptar)
members = tar.getmembers()
image_name = os.path.basename(image_path)
zip_name = "%s.zip" % (image_name.replace(" ", "_"))
# Include the image in the package?
if remove_image:
to_package = dict()
else:
to_package = {"files": [image_path]}
# If the specfile is provided, it should also be packaged
if spec_path is not None:
singularity_spec = "".join(read_file(spec_path))
to_package['Singularity'] = singularity_spec
# Package the image with an sha1, identical standard, as VERSION
if old_version == False:
hashes = get_image_hashes(image_path)
to_package["HASHES"] = hashes
to_package["VERSION"] = hashes['IDENTICAL']
else:
to_package["VERSION"] = get_image_file_hash(image_path)
# Look for runscript
if runscript is True:
try:
to_package["runscript"] = extract_content(image_path,
'./singularity',
cli=S)
bot.logger.debug("Found runscript.")
except KeyError:
bot.logger.warning("No runscript found")
if software == True:
bot.logger.info("Adding software list to package.")
files = [x.path for x in members if x.isfile()]
folders = [x.path for x in members if x.isdir()]
to_package["files.txt"] = files
to_package["folders.txt"] = folders
# Do zip up here - let's start with basic structures
zipfile = zip_up(to_package,
zip_name=zip_name,
output_folder=output_folder)
bot.logger.debug("Package created at %s" % (zipfile))
if old_version == False:
file_obj.close()
# return package to user
return zipfile