def __init__(self, config=None, export_tabs=None, bulk_export=None,
crawl_yml: dict = None, descript_lang: dict = None):
try:
self.datum = '{:%d-%b-%Y}'.format(date.today())
self.maand_jaar = '{:%B-%Y}'.format(date.today())
try:
self.url = config['url']
self.domain = config['domain']
self.template_file = config['word_template']
self.search_console_url = config['search_console_url']
except KeyError as e:
raise Exception("Error getting config variables: {}".format(e))
self.start_path = os.path.dirname(os.path.realpath(__file__))
self.domain_folder = self.set_data_domain_path()
self.frog_data_folder = self.get_frog_folder()
self.graph_data_folder = self.get_graph_folder()
self.config_folder = self.get_config_folder()
self.export_tabs = export_tabs
self.bulk_export = bulk_export
self.crawl_yml = crawl_yml
self.descript_lang = descript_lang
self.ps = None
self.frog_files = {}
self.document_fields = None
self.doc = None
self.dp = None
self.data = {}
self.co_table_headers = None
self.co_readydata = None
self.template = None
self.dimensions_data = None
cf = readConfig()
self.config = cf.config
self.ps_api = self.config['google_page_speed_api']
self.template = self.get_doc_template()
self.word_output_file = self.get_doc_word_output()
self.get_frog_files()
self.create_crawl_data()
self.get_crawl_overview_data()
self.get_google_search_console_data()
self.ps_all_data = {}
# self.crawl_data = self.get_crawl_data()
self.prep_document()
self.merge_document()
self.write_document()
except Exception as e:
exc_type, exc_obj, exc_tb = sys.exc_info()
fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
logging.warning(str(e) + " | " + str(exc_type) +
" | " + str(fname) + " | " + str(exc_tb.tb_lineno))
return
def __init__(self):
self.cf = readConfig()
self.behandel_datum = ""
self.declaratie_file = None
self.backup_file = None
self.browser = None
self.get_behandel_datum()
self.get_declaratie_file()
if self.start_formulier():
self.backup_declaratie_file()
def __init__(self):
cf = readConfig()
self.config = cf.config
self.datum = '{:%d-%b-%Y}'.format(date.today())
dir_path = os.path.dirname(os.path.realpath(__file__))
folder = os.path.join(dir_path, "data")
data_file_name = "{}_weights.json".format(self.datum)
self.data_file = os.path.join(folder, data_file_name)
self.weight_data = {}
self.start_url = "https://cloud.vitadock.com/signin"
self.login_url = "https://cloud.vitadock.com/resources/j_spring_security_check"
self.weight_page = "https://cloud.vitadock.com/portal/target.php?lang=nl_NL"
self.weight_json = "https://cloud.vitadock.com/portal/server/target_server.php?lang=nl_NL&rnd=12345"
self.get_data()
def __init__(self,
user_agent=None,
workspace_id=None,
start_col=0,
start_row=0,
name=""):
if user_agent == workspace_id is None:
return None
cf = readConfig()
self.config = cf.config
self.start_col = start_col
self.start_row = start_row
self.normal_hours_day = 8
self.normal_work_hours = 7
self.months = [
"Unknown", "January", "Febuary", "March", "April", "May", "June",
"July", "August", "September", "October", "November", "December"
]
self.user_agent = user_agent
self.user_name = name
self.workspace_id = workspace_id
self.response = None
self.last_month_first = None
self.last_month_last = None
self.curr_year = None
self.filename = None
self.my_excel_data = []
self.excel_template = "excel/urenoverzicht-2020.xlsx"
self.excel_file = None
self.about_last_month()
self.get_data()
self.parse_data()
self.create_excel()
def __init__(self):
self.gitignore_start_file = os.path.join(
os.path.dirname(os.path.abspath(__file__)), 'start_files',
"gitignore.txt")
self.readme_start_file = os.path.join(
os.path.dirname(os.path.abspath(__file__)), 'start_files',
"readme.txt")
try:
config_file = os.path.join(
os.path.dirname(os.path.abspath(__file__)), 'config',
'config.yml')
cf = readConfig(config_file)
try:
self.GitHub_Token = cf.config['github_token']
self.projects_folder_name = cf.config['projects_folder_name']
self.license_template = cf.config['license_template']
self.twitter = cf.config['twitter']
self.email = cf.config['email']
except KeyError as e:
raise Exception(f"Config file broken {e}")
yn = ['y', 'n']
checkers = [None, ""]
correct = 1
self.repo = None
self.user = None
if self.GitHub_Token is None or self.GitHub_Token == '':
raise Exception("No GitHub Token")
home_folder = str(
Path.home()) # this is the users home folder on any OS
self.project_folder = os.path.join(home_folder,
self.projects_folder_name)
project_folder = Path(self.project_folder)
if not project_folder.exists():
raise Exception(
"Sorry, but your projects folder does not exists! {} ".
format(self.project_folder))
self.project_name = None
while self.project_name in checkers:
self.project_name = input(
"What is the name of your new project? ")
while correct not in yn and self.project_name not in checkers:
correct = input(
"Is this project name correct? {} - {} : ".format(
self.project_name, str(yn)))
if correct == "y":
break
self.private_repo = None
while self.private_repo not in yn:
self.private_repo = input(
"Do you want to create a public repository? {} : ".format(
str(yn)))
if self.private_repo == "y":
self.private_repo = True
break
elif self.private_repo == "n":
self.private_repo = False
break
self.auto_init = None
while self.auto_init in checkers:
self.auto_init = input(
"Do you want to create a readme file and initialize the repository? {} : "
"".format(str(yn)))
if self.auto_init == "y":
self.auto_init = True
break
elif self.auto_init == "n":
self.auto_init = False
break
self.description = None
while self.description in checkers:
self.description = input(
"Please provide a small repository description. (you can change it later) "
)
self.homepage = None
while self.homepage in checkers:
self.homepage = input(
"Please proivde a url with more information about your repository. "
"(you can change it later) ")
if self.create_git_repository():
if self.clone_git_repository():
self.create_extra_files()
except Exception as e:
logger.warning(e)
return
import gzip # For reading data
import pandas as pd # data handling
import colorsys # Generate color gradient.
import sys # Read command line arguments:
import argparse # Now command line arugments are properly set.
import pickle
# Importing custom functions:
from functions.helper_fun import *
from functions.color_fun import *
from functions.dataIntegrator import dataIntegrator
from functions.chromosome_plotter import chromosome_plotter
from functions.readConfig import readConfig
# reading parameters:
config = readConfig()
if __name__ == '__main__':
# Processing command line parameters:
parser = argparse.ArgumentParser(description='Script to plot genome chunks colored based on GC content and gene annotation. See github: https://github.com/DSuveges/GenomePlotter')
parser.add_argument('-c', '--chromosome', type = str, help='Selected chromosome to process', required = True)
parser.add_argument('-w', '--width', type = int, help='Number of chunks in one row.', default = 200)
parser.add_argument('-p', '--pixel', type = int, help='The size of a plotted chunk in pixels (default: 3).', default = 9)
parser.add_argument('-s', '--darkStart', type = float, help='Fraction of the width from where the colors start getting darker (default: 0.75).', default = 0.75)
parser.add_argument('-m', '--darkMax', type = float, help='How dark a pixel can get at the right end of the plot (default: 0.15).', default = 0.15)
parser.add_argument('-f', '--folder', type = str, help = 'The working directory (default is the current working directory)', default='.')
parser.add_argument('-t', '--test', type = int, help = 'The number of chunks to be read (by default the whole chromosome is processed.)', default = 0)
parser.add_argument('-d', '--dummy', type = bool, help = 'If instead of the chunks, a dummy is drawn with identical dimensions', default = False)
parser.add_argument('--config', type = str, help = 'Specifying json file containing custom configuration', default = 'config.json')
def write_document(self):
self.doc.save(self.word_output_file)
if __name__ == '__main__':
dir_path = os.path.dirname(os.path.realpath(__file__))
profiles = os.path.join(dir_path, "data")
word_output = os.path.join(dir_path, "word_output")
os.makedirs(word_output, exist_ok=True)
bulk_export = None
bulk_export_file = os.path.join(dir_path, 'config', 'bulk_exports.yml')
if os.path.isfile(bulk_export_file):
bulk_export = readConfig(bulk_export_file)
crawl_yml = None
crawl_overview_file = os.path.join(
dir_path, 'config', 'crawl_overview.yml')
if os.path.isfile(crawl_overview_file):
crawl_yml = readConfig(crawl_overview_file)
else:
print('No yml file')
descript_lang = None
descript_file = os.path.join(dir_path, 'config', 'crawl_overview_lang.yml')
if os.path.isfile(descript_file):
descript_lang = readConfig(descript_file)
export_tabs = None