def _main():
"""Entry point."""
cli_args = args.parse_args()
# Build the base image first
docker.build("-t", "py-deploy-base-image", "-f", BASE_DOCKERFILE_PATH,
SCRIPT_DIR)
# Extend with specific image
docker.build("-t", cli_args.image, "-f", cli_args.dockerfile,
cli_args.workdir)
# Run the container
docker.run("--name", cli_args.container, cli_args.image)
# Copy artifacts if required
if cli_args.cp:
docker.cp("{}:{}".format(cli_args.container, cli_args.cp),
cli_args.workdir)
# Clean up
docker.rm(cli_args.container)
def main():
args = parse_args()
s = requests.session()
s.verify = False if args.notlscheck else True
atexit.register(lambda: s.close())
r = s.get(
f'{args.prometheus}/api/v1/query_range?query={args.query}&start={args.start}Z&end={args.end}&step=1s'
)
r.raise_for_status()
over = 0
under = 0
total_nonnull = 0
run_time = 0
min_tstp = sys.maxsize
max_tstp = -sys.maxsize
for pod in r.json()['data']['result']:
for v in pod['values']:
# Time bound detection
if v[0] < min_tstp:
min_tstp = v[0]
if v[0] > max_tstp:
max_tstp = v[0]
m = float(v[1]) # Value
if m > args.value:
over += (m - args.value)
elif (m < args.value) and (m != 0):
under += (args.value - m)
if m != 0:
total_nonnull += 1
run_time += 1
user_time_duration = max_tstp - min_tstp
print("Average pods running: %.3f" % (run_time / user_time_duration))
print("Overusage: %d%%" % (over * 100 / total_nonnull))
print("Underusage: %d%%" % (under * 100 / total_nonnull))
Description: Search through KEGG KGML Pathway map files for a given substring
"""
from src.biodata import *
from src.config import load_configuration
from src import arguments, error
from sys import stdout, exit
from lib.pygrep import grep
from lib.args import parse_args
from os.path import isfile
import threading
# Argument handling
args = parse_args("search",
[('o', 'search by organism', [str, str], arguments.organism),
('m', 'search by map file', [str, str], arguments.mapfile),
('l', 'list organisms', [], arguments.listOrganisms)])
def organism_file_path(organism):
"Construct path to organism file"
return config['map_file_directory'] + "/" + organism + '*'
def map_file_path(mapfile):
"Construct path to map file"
return config['map_file_directory'] + "/" + mapfile
def print_results(lines):
if len(lines) > 0:
from src.config import load_configuration
from src import error
from sys import stdout, exit
from lib.args import parse_args
from os.path import isfile
import threading
import sys
sys.path.append(sys.path[0]+'/pkg')
# Argument handling
args = parse_args("download",
[('o', 'download organism', [str], "Download all files for a given organism"),
('u', 'update', [], "Update any existing map files"),
('r', 'retry', [], "Retry any previously failed map file url's"),
('a', 'download all', [], "Download all available map files for every organism"),
('l', 'list organisms', [], "List all organism codes")])
def remote_resource_previously_failed(url):
if isfile(config['failed_list']):
return url in open(config['failed_list'], 'r').read()
return False
def multi_thread_download(links, forceOverwrite):
def dl(l, o):
download(l, o, forceOverwrite)
for item in links:
# Need to add ability to skip
