def main():
try:
path = sys.argv[1]
except:
path = "server_config.json"
config = read_config(path)
server = Server(config)
server.loop()
def main():
try:
path = sys.argv[1]
except:
path = "client_config.json"
config = read_config(path)
client = Client(config)
client.loop()
from utility import open_url, read_config
open_url(read_config('base_url'))
import logging
import os
import traceback
from datetime import datetime
import base64
from google.api_core import retry
from google.cloud import bigquery
from google.cloud import firestore
from google.cloud import pubsub_v1
from google.cloud import storage
import pytz
from utility import read_config
config = read_config()
PROJECT_ID = config[r'devshell_project_id']
BQ_DATASET = config[r'dataset']
BQ_TABLE = 'dc'
ERROR_TOPIC = 'projects/%s/topics/%s' % (PROJECT_ID, config[r'streaming_error_topic'])
SUCCESS_TOPIC = 'projects/%s/topics/%s' % (PROJECT_ID, config[r'streaming_success_topic'])
DB = firestore.Client()
CS = storage.Client()
PS = pubsub_v1.PublisherClient()
BQ = bigquery.Client()
def move_file(data, context):
'''This function is triggered by a Cloud Pub/Sub'''
message = base64.b64decode(data['data']).decode('utf-8')
logging.info("move_file receive the message {}".format(message))
file_name = data['attributes']['file_name']
from selenium import webdriver
from utility import read_config
driver = webdriver.Chrome(read_config('driver'))
import globals as gl
import time
from utility import read_config, clear_previous_results, check_pathway_update_history, load_last_csv, create_zip
from draw import draw_json_run
from analysis import run_analysis
# --------------- INITIAL START TIME --------------
start_time = time.time()
# -------------- INITIAL MAIN --------------
print("----- INITIAL SHELL PARAMETERS -----")
read_config()
if gl.mode_input == 0:
print("----- CLEAN PREVIOUS RESULTS -----")
clear_previous_results()
starting_depth = 1
else:
print("----- LOAD LAST RESULTS (CSV) SAVED -----")
starting_depth = load_last_csv()
print("----- CHECK UPDATED PATHWAYS -----")
check_pathway_update_history('https://www.genome.jp/kegg/docs/upd_map.html')
print("----- START ANALYSIS -----")
run_analysis(starting_depth)
print("----- END ANALYSIS -----")
print("----- START GENERATE OUTPUT -----")
draw_json_run()
print("----- END GENERATE OUTPUT -----")
parser = argparse.ArgumentParser()
parser.add_argument('-r', '--report',type=str, required=True, help="Name of the report which you want to generate.")
args = parser.parse_args()
REPORT_DIR = os.path.join(CURRENT_DIR, 'reports', args.report)
TARGET_DIR = os.path.join(CURRENT_DIR, 'results')
TARGET_REPORT = os.path.join(TARGET_DIR, '%s.html' % args.report)
TEMP_DIR = os.path.join(CURRENT_DIR, 'temp')
GLOBAL_MAPPINGS_PATH = os.path.join(CURRENT_DIR, 'global.conf')
assert os.path.exists(REPORT_DIR)
MAPPINGS_PATH, REPORT_TEMPLATE_PATH, SETTINGS_PATH = map(lambda n: os.path.join(REPORT_DIR, n),['mappings.json', 'report_template.html', 'settings.conf'])
assert all(map(os.path.exists, [MAPPINGS_PATH, REPORT_TEMPLATE_PATH, SETTINGS_PATH]))
with open(MAPPINGS_PATH, 'rb') as f:
REPORT_MAPPING = json.load(f)
CONNECTION_STR = utility.read_config(SETTINGS_PATH, 'database', 'connection_string')
REPORT_NAME = utility.read_config(SETTINGS_PATH, 'global', 'report_name')
FROM_EMAIL = utility.read_config(GLOBAL_MAPPINGS_PATH, 'email', 'from')
TO_EMAIL = utility.read_config(GLOBAL_MAPPINGS_PATH, 'email', 'to')
SMTP = utility.read_config(GLOBAL_MAPPINGS_PATH, 'email', 'smtp')
USER = utility.read_config(GLOBAL_MAPPINGS_PATH, 'email', 'username')
PWD = utility.read_config(GLOBAL_MAPPINGS_PATH, 'email', 'password')
def generate_x_data(chart_data):
x = chart_data["xAxis"]["categories"]["data"]
x_col = chart_data["xAxis"]["categories"]["name"]
chart_data["xAxis"]["categories"] = [xItem.__dict__[x_col] for xItem in report_data[x]]
def generate_y_data(chart_data):
series = []
for series_info in chart_data["series"]: