class TestAnalysisCompare(unittest.TestCase):
def setUp(self):
self.tmpdir = tempfile.mkdtemp()
self.cli = Singularity()
self.container = self.cli.pull('docker://ubuntu:16.04',
pull_folder=self.tmpdir)
self.comparator = self.cli.pull('docker://ubuntu:12.04',
pull_folder=self.tmpdir)
def tearDown(self):
os.remove(self.container)
os.remove(self.comparator)
shutil.rmtree(self.tmpdir)
def test_container_similarity(self):
print(
"Testing singularity.analysis.compare.container_similarity_vector")
import pandas
from singularity.analysis.compare import container_similarity_vector
from singularity.package import get_packages
packages_set = get_packages('docker-os')[0:2]
vector = container_similarity_vector(container1=self.container,
custom_set=packages_set)
self.assertTrue('files.txt' in vector)
self.assertTrue(isinstance(vector['files.txt'], pandas.DataFrame))
print(
"Testing singularity.analysis.compare.compare_singularity_images")
from singularity.analysis.compare import compare_singularity_images
sim = compare_singularity_images(self.container, self.comparator)
self.assertTrue(isinstance(sim, pandas.DataFrame))
self.assertTrue(sim.loc[self.container, self.comparator] -
0.4803262269280298 < 0.01)
print("Testitng singularity.analysis.compare.compare_containers")
from singularity.analysis.compare import compare_containers
comparison = compare_containers(self.container, self.comparator)
self.assertTrue('files.txt' in comparison)
for key in ['total1', 'total2', 'intersect', 'unique2', 'unique1']:
self.assertTrue(key in comparison['files.txt'])
print("Testing singularity.analysis.compare.calculate_similarity")
from singularity.analysis.compare import calculate_similarity
sim = calculate_similarity(self.container, self.comparator)
self.assertTrue(sim['files.txt'] - 0.4921837537163134 < 0.01)
def test_information_coefficient(self):
print("Testing singularity.analysis.metrics.information_coefficient")
from singularity.analysis.metrics import information_coefficient
self.assertEqual(information_coefficient(100, 100, range(0, 50)), 0.5)
self.assertEqual(information_coefficient(100, 100, range(0, 100)), 1.0)
def main(args, parser, subparser):
# We can only continue if singularity is installed
if check_install() is not True:
bot.error("Cannot find Singularity! Is it installed?")
sys.exit(1)
# Output folder will be pwd if not specified
output_folder = os.getcwd()
if args.outfolder is not None:
output_folder = os.getcwd()
# If we are given an image, ensure full path
if args.image is not None:
image = args.image
if not os.path.exists(image):
cli = Singularity(debug=args.debug)
image = cli.pull(image)
if image is None:
bot.error("Cannot find image. Exiting.")
sys.exit(1)
remove_image = not args.include_image
package(image_path=image,
output_folder=output_folder,
remove_image=remove_image)
else:
print("Please specify an image to package with --image")
subparser.print_help()
def main(args, parser, subparser):
# We can only continue if singularity is installed
if check_install() is not True:
bot.error("Cannot find Singularity! Is it installed?")
sys.exit(1)
# Output folder will be pwd if not specified
output_folder = os.getcwd()
if args.outfolder is not None:
output_folder = os.getcwd()
# If we are given an image, ensure full path
if args.image is not None:
if not os.path.exists(args.image):
cli = Singularity(debug=args.debug)
image = cli.pull(args.image)
if image is None:
bot.error("Cannot find image. Exiting.")
sys.exit(1)
# the user wants to make a tree
if args.tree is True:
from singularity.cli.app import make_tree
make_tree(image)
clean_up(image, existed)
else:
print("Please specify an image to inspect with --image")
subparser.print_help()
class TestClient(unittest.TestCase):
def setUp(self):
self.pwd = get_installdir()
self.cli = Singularity()
self.tmpdir = tempfile.mkdtemp()
def tearDown(self):
shutil.rmtree(self.tmpdir)
def test_commands(self):
print('Testing client.create command')
container = "%s/container.img" % (self.tmpdir)
created_container = self.cli.create(container)
self.assertEqual(created_container, container)
self.assertTrue(os.path.exists(created_container))
os.remove(container)
print("Testing client.pull command")
print("...Case 1: Testing naming pull by image name")
image = self.cli.pull("shub://vsoch/singularity-images",
pull_folder=self.tmpdir)
self.assertTrue(os.path.exists(image))
self.assertTrue('vsoch-singularity-images-master' in image)
print(image)
os.remove(image)
print("...Case 3: Testing docker pull")
container = self.cli.pull("docker://ubuntu:14.04",
pull_folder=self.tmpdir)
self.assertTrue("ubuntu:14.04" in container)
print(container)
self.assertTrue(os.path.exists(container))
print('Testing client.execute command')
result = self.cli.execute(container, 'ls /')
print(result)
self.assertTrue('bin\nboot\ndev' in result)
print("Testing client.inspect command")
result = self.cli.inspect(container, quiet=True)
labels = json.loads(result)
self.assertTrue('data' in labels)
os.remove(container)
def main(args, parser, subparser):
# We can only continue if singularity is installed
if check_install() is not True:
bot.error("Cannot find Singularity! Is it installed?")
sys.exit(1)
# Output folder will be pwd if not specified
output_folder = os.getcwd()
if args.outfolder is not None:
output_folder = os.getcwd()
# If we are given an image, ensure full path
image = args.image
if image is not None:
existed = True
if not os.path.exists(image):
cli = Singularity(debug=args.debug)
image = cli.pull(image)
existed = False
if image is None:
bot.error("Cannot find image. Exiting.")
sys.exit(1)
# The user wants to estimate the os
if args.os is True:
from singularity.analysis.classify import estimate_os
estimated_os = estimate_os(container=image)
print(estimated_os)
# The user wants to get a list of all os
elif args.oscalc is True:
from singularity.analysis.classify import estimate_os
estimated_os = estimate_os(container=image, return_top=False)
print(estimated_os["SCORE"].to_dict())
# The user wants to get a list of tags
elif args.tags is True:
from singularity.analysis.classify import get_tags
tags = get_tags(container=image)
print(tags)
# The user wants to plot image vs. the docker os
elif args.osplot is True:
from singularity.app import plot_os_sims
plot_os_sims(image)
clean_up(image, existed)
else:
print("Please specify an image to analyze with --image")
subparser.print_help()
def main(args, parser, subparser):
# We can only continue if singularity is installed
if check_install() is not True:
bot.error("Cannot find Singularity! Is it installed?")
sys.exit(1)
# Output folder will be pwd if not specified
output_folder = os.getcwd()
if args.outfolder is not None:
output_folder = os.getcwd()
if args.images is not None:
image1, image2 = args.images.split(',')
bot.debug("Image1: %s" % image1)
bot.debug("Image2: %s" % image2)
images = dict()
cli = Singularity(debug=args.debug)
for image in [image1, image2]:
existed = True
if not os.path.exists(image):
image = cli.pull(image)
existed = False
images[image] = existed
# Just for clarity
image1, image2 = list(images.keys())
# the user wants to make a similarity tree
if args.simtree is True:
from singularity.cli.app import make_sim_tree
make_sim_tree(image1, image2)
# the user wants to make a difference tree
elif args.subtract is True:
from singularity.cli.app import make_diff_tree
make_diff_tree(image1, image2)
else: # If none specified, just print score
from singularity.analysis.compare import calculate_similarity
score = calculate_similarity(image1, image2, by="files.txt")
print(score["files.txt"])
for image, existed in images.items():
clean_up(image, existed)
else:
print("Please specify images to compare with --images")
subparser.print_help()
class TestClient(unittest.TestCase):
def setUp(self):
self.pwd = get_installdir()
self.cli = Singularity()
self.tmpdir = tempfile.mkdtemp()
self.image1 = "%s/tests/data/busybox-2016-02-16.img" % (self.pwd)
self.image2 = "%s/tests/data/cirros-2016-01-04.img" % (self.pwd)
def tearDown(self):
shutil.rmtree(self.tmpdir)
def test_create(self):
print('Testing client.create command')
container = "%s/container.img" % (self.tmpdir)
created_container = create_container(container)
self.assertEqual(created_container, container)
self.assertTrue(os.path.exists(container))
def test_import(self):
from singularity.build.utils import test_container
print("Testing client.import command")
container = create_container()
# Container should not be valid
print("Case 1: Before import, container is not valid")
result = test_container(container)
self.assertEqual(result['return_code'], 255)
print("Case 2: After import, container is valid")
self.cli.importcmd(container, 'docker://ubuntu')
result = test_container(container)
self.assertEqual(result['return_code'], 0)
def test_run(self):
print("Testing client.run command")
container = create_container(do_import=True)
result = self.cli.run(container)
self.assertEqual(result, '')
def test_exec(self):
print('Testing client.execute command')
container = create_container(do_import=True)
result = self.cli.execute(container, 'ls /')
print(result)
#if isinstance(result,bytes):
# result = result.decode('utf-8')
#self.assertTrue(len(result)>0)
def test_pull(self):
print("Testing client.pull command")
print("Case 1: Testing naming pull by image name")
image = self.cli.pull("shub://vsoch/singularity-images")
print(image)
print("Case 2: Testing naming pull by image commit")
image = self.cli.pull("shub://vsoch/singularity-images",
name_by="commit")
print(image)
print("Case 3: Testing naming pull by image hash")
image = self.cli.pull("shub://vsoch/singularity-images",
name_by="hash")
print(image)
def test_get_image(self):
print("Testing singularity.cli.get_image")
from singularity.cli import get_image
from singularity.build.utils import test_container
tmpimg = get_image('docker://ubuntu')
self.assertTrue(os.path.exists(tmpimg))
result = test_container(tmpimg)
self.assertEqual(result['return_code'], 0)
def pull_image(self,image_url):
"""Pull the singularity image to specified image path."""
image_path = self.get_image_path()
s = Singularity()
container_path = s.pull(image_url[0],image_name=image_path[0])
return Unicode(container_path)