def create_token(self):
import getpass
import github3
# Asks user for username/password
user = input("Please enter your GitHub username: "******"Please enter your GitHub password: "******"/!\\ WARNING /!\\ Bad GitHub credentials.")
print(
"Cannot access disease packages. Please contact %s for assistance."
.format(self.SUPPORT_EMAIL))
sys.stdout.flush()
raise self.AuthorizationError()
# Write the info to disk
# Update the (local) mysql db with the token
from simtools.DataAccess.DataStore import DataStore
DataStore.save_setting(
DataStore.create_setting(key=self.auth_token_field,
value=auth.token))
return auth.token
def check_overseer():
"""
Ensure that the overseer thread is running.
The thread pid is retrieved from the settings and then we test if it corresponds to a python thread.
If not, just start it.
"""
logger.debug("Checking Overseer state")
setting = DataStore.get_setting('overseer_pid')
overseer_pid = int(setting.value) if setting else None
# Launch the Overseer if needed
if is_running(overseer_pid, name_part='python'):
logger.debug("A valid Overseer was detected, pid: %d" %
overseer_pid)
else:
logger.debug(
"A valid Overseer was not detected for stored pid %s." %
overseer_pid)
current_dir = os.path.dirname(os.path.realpath(__file__))
runner_path = os.path.abspath(
os.path.join(current_dir, '..', 'Overseer.py'))
if LocalOS.name == LocalOS.WINDOWS:
p = subprocess.Popen([sys.executable, runner_path],
shell=False,
creationflags=512)
else:
p = subprocess.Popen([sys.executable, runner_path],
shell=False)
# Save the pid in the settings
DataStore.save_setting(
DataStore.create_setting(key='overseer_pid', value=str(p.pid)))
def LogCleaner():
# Get the last time a cleanup happened
last_cleanup = DataStore.get_setting('last_log_cleanup')
if not last_cleanup or (datetime.today() - datetime.strptime(last_cleanup.value.split(' ')[0],'%Y-%m-%d')).days > 1:
# Do the cleanup
from simtools.DataAccess.LoggingDataStore import LoggingDataStore
LoggingDataStore.log_cleanup()
DataStore.save_setting(DataStore.create_setting(key='last_log_cleanup', value=datetime.today()))
def get_package(args, unknownArgs):
import pip
import tempfile
import zipfile
is_test = args.is_test if hasattr(
args, 'is_test') else None # test == no pip install
# overwrite any existing package by the same name (any version) with the specified version
release_dir = None
try:
package_name = args.package_name
github = DTKGitHub(disease=package_name)
if args.package_version.upper() == GitHub.HEAD:
version = GitHub.HEAD
elif args.package_version.lower() == 'latest':
version = github.get_latest_version(
) # if no versions exist, returns None
elif github.version_exists(version=args.package_version):
version = args.package_version
else:
version = None
if version is None:
print(
"Requested version: %s for package: %s does not exist. No changes made."
% (args.package_version, package_name))
return
tempdir = tempfile.mkdtemp()
zip_filename = github.get_zip(version=version, destination=tempdir)
# Unzip the obtained zip
zip_ref = zipfile.ZipFile(zip_filename, 'r')
zip_ref.extractall(tempdir)
zip_ref.close()
os.remove(zip_filename)
# Identify the unziped source directory
source_dir_candidates = [
f for f in os.listdir(tempdir)
if 'InstituteforDiseaseModeling-%s' %
DTKGitHub.PACKAGE_LIST[package_name] in f
]
if len(source_dir_candidates) != 1:
raise Exception('Failure to identify package to install')
else:
source_dir = source_dir_candidates[0]
release_dir = os.path.join(os.path.dirname(zip_filename), source_dir)
# edit source dir setup file for the correct version
setup_file = os.path.join(release_dir, 'setup.py')
with open(setup_file, 'r') as file:
text = file.read()
text = text.replace('$VERSION$', str(version))
with open(setup_file, 'w') as file:
file.write(text)
# install
if not is_test:
pip.main([
'install', '--no-dependencies', '--ignore-installed',
release_dir
])
# update the local DB with the version
db_key = github.disease_package_db_key
DataStore.save_setting(
DataStore.create_setting(key=db_key, value=str(version)))
shutil.rmtree(tempdir)
except GitHub.AuthorizationError:
pass
return release_dir
