diff util/Reader.py @ 0:ce4f91831680 draft default tip

planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 5367a00befb467f162d1870edb91f9face72e894

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/Reader.py	Fri Feb 16 10:57:13 2018 -0500
@@ -0,0 +1,92 @@
+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 getAction(self):
+        action = self.args.get("action")
+        return action
+
+    def getAdminUser(self):
+        apollo_admin = self.args.get("apollo_admin")
+        return apollo_admin    
+
+
+    def getOperationList(self):
+        l = self.args.get("operations")
+        return l
+
+    
\ No newline at end of file