Mercurial > repos > yating-l > jbrowsehubtoapollo
view util/Reader.py @ 1:2ae1e96a8380 draft
planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a8c47ae0025953ef398bdc689dc5df5516edf686-dirty
author | yating-l |
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date | Tue, 24 Oct 2017 18:24:40 -0400 |
parents | bc00f5c4c59e |
children |
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import json import re import logging import codecs import socket from apollo.ApolloUser import ApolloUser from util import santitizer class Reader(object): def __init__(self, input_json_file): self.inputFile = input_json_file self.args = self.loadJson() def loadJson(self): try: data_file = codecs.open(self.inputFile, 'r', 'utf-8') return json.load(data_file) except IOError: print "Cannot find JSON file\n" exit(1) def getJBrowseHubDir(self): try: return self.args["jbrowse_hub"] except KeyError: print ("jbrowse_hub is not defined in the input file!") exit(1) def getToolDir(self): try: return self.args["tool_directory"] except KeyError: print ("tool_directory is not defined in the input file!") exit(1) def getExtFilesPath(self): try: return self.args["extra_files_path"] except KeyError: print ("extra_files_path is not defined in the input file!") exit(1) def getUserEmail(self): try: return self.args["user_email"] except KeyError: print ("user_email is not defined in the input file!") exit(1) def getDebugMode(self): try: return self.args["debug_mode"] except KeyError: print ("debug_mode is not defined in the input file!") exit(1) def getPortNum(self): try: return self.args["port"] except KeyError: print ("port is not defined in the input file!") exit(1) def getApolloHost(self): #apollo_host = self.args.get("apollo_host") hostname = socket.gethostname() ip = socket.gethostbyname(hostname) protocol = socket.getprotobyname(hostname) apollo_host = str(protocol) + str(ip) return apollo_host def getSpeciesName(self): species_name = santitizer.sanitize_name_input(self.args["species_name"]) return species_name def getAdminUser(self): admin_info = self.args.get("apollo_admin") user_email = admin_info['user_email'] password = admin_info['password'] apollo_admin = ApolloUser(user_email, password) return apollo_admin def getApolloUser(self): user_info = self.args.get("apollo_user") if not user_info: firstname = "demo" lastname = "user" password = "gonramp" user_email = self.getUserEmail() else: firstname = user_info['firstname'] lastname = user_info['lastname'] user_email = user_info['user_email'] password = user_info['password'] apollo_user = ApolloUser(user_email, firstname, lastname, password) return apollo_user