diff util/Reader.py @ 3:6f262a92e8dc draft default tip

planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 91b46f7c891c2466bc5b6a063411cdae75964515-dirty

--- a/util/Reader.py	Wed Oct 25 12:41:34 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,101 +0,0 @@
-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
-
-    
\ No newline at end of file