# 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
},
"type": "container"
}
}
def run_build(build_dir,params,verbose=True, compress_image=False):
'''run_build takes a build directory and params dictionary, and does the following:
- downloads repo to a temporary directory
- changes branch or commit, if needed
- creates and bootstraps singularity image from Singularity file
- returns a dictionary with:
image (path), image_package (path), metadata (dict)
The following must be included in params:
spec_file, repo_url, branch, commit
Optional parameters
size
'''
# Download the repo and image
download_repo(repo_url=params['repo_url'],
destination=build_dir)
os.chdir(build_dir)
if params['branch'] != None:
bot.info('Checking out branch %s' %params['branch'])
os.system('git checkout %s' %(params['branch']))
else:
params['branch'] = "master"
# Commit
if params['commit'] not in [None,'']:
bot.info('Checking out commit %s' %params['commit'])
os.system('git checkout %s .' %(params['commit']))
# From here on out commit is used as a unique id, if we don't have one, we use current
else:
params['commit'] = os.popen('git log -n 1 --pretty=format:"%H"').read()
bot.warning("commit not specified, setting to current %s" %params['commit'])
# Dump some params for the builder, in case it fails after this
passing_params = "/tmp/params.pkl"
pickle.dump(params,open(passing_params,'wb'))
# Now look for spec file
if os.path.exists(params['spec_file']):
bot.info("Found spec file %s in repository" %params['spec_file'])
# If the user has a symbolic link
if os.path.islink(params['spec_file']):
bot.info("%s is a symbolic link." %params['spec_file'])
params['spec_file'] = os.path.realpath(params['spec_file'])
# START TIMING
start_time = datetime.now()
image = build_from_spec(spec_file=params['spec_file'], # default will package the image
build_dir=build_dir,
isolated=True,
sandbox=False,
debug=params['debug'])
# Save has for metadata (also is image name)
version = get_image_file_hash(image)
params['version'] = version
pickle.dump(params,open(passing_params,'wb'))
final_time = (datetime.now() - start_time).seconds
bot.info("Final time of build %s seconds." %final_time)
# Did the container build successfully?
test_result = test_container(image)
if test_result['return_code'] != 0:
bot.error("Image failed to build, cancelling.")
sys.exit(1)
# Get singularity version
singularity_version = get_singularity_version()
# Package the image metadata (files, folders, etc)
image_package = package(image_path=image,
spec_path=params['spec_file'],
output_folder=build_dir,
remove_image=True,
verbose=True)
# Derive software tags by subtracting similar OS
diff = get_diff(image_package=image_package)
# Inspect to get labels and other metadata
cli = Singularity(debug=params['debug'])
inspect = cli.inspect(image_path=image)
# Get information on apps
app_names = cli.apps(image_path=image)
apps = extract_apps(image_path=image, app_names=app_names)
# Count file types, and extensions
counts = dict()
counts['readme'] = file_counts(diff=diff)
counts['copyright'] = file_counts(diff=diff,patterns=['copyright'])
counts['authors-thanks-credit'] = file_counts(diff=diff,
patterns=['authors','thanks','credit','contributors'])
counts['todo'] = file_counts(diff=diff,patterns=['todo'])
extensions = extension_counts(diff=diff)
os_sims = estimate_os(image_package=image_package,return_top=False)
most_similar = os_sims['SCORE'].values.argmax()
most_similar = os_sims['SCORE'].index.tolist()[most_similar]
metrics = {'build_time_seconds':final_time,
'singularity_version':singularity_version,
'singularity_python_version':singularity_python_version,
'estimated_os': most_similar,
'os_sims':os_sims['SCORE'].to_dict(),
'file_counts':counts,
'file_ext':extensions,
'inspect':inspect,
'version': version,
'apps': apps}
# Compress Image
if compress_image is True:
compressed_image = "%s.gz" %image
os.system('gzip -c -9 %s > %s' %(image,compressed_image))
image = compressed_image
output = {'image':image,
'image_package':image_package,
'metadata':metrics,
'params':params }
return output
else:
# Tell the user what is actually there
present_files = glob("*")
bot.error("Build file %s not found in repository" %params['spec_file'])
bot.info("Found files are %s" %"\n".join(present_files))
# Params have been exported, will be found by log
sys.exit(1)
