diff util/Reader.py @ 1:2ae1e96a8380 draft

planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a8c47ae0025953ef398bdc689dc5df5516edf686-dirty

--- a/util/Reader.py	Tue Oct 17 17:28:05 2017 -0400
+++ b/util/Reader.py	Tue Oct 24 18:24:40 2017 -0400
@@ -2,6 +2,7 @@
 import re
 import logging
 import codecs
+import socket
 from apollo.ApolloUser import ApolloUser
 from util import santitizer 
 
@@ -54,28 +55,33 @@
         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")
+        #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 getGenomeName(self):
-        jbrowse_hub = self.getJBrowseHubDir()
-        with open(jbrowse_hub, 'r') as f:
-            html = f.read()
-        m = re.search('The new Organism "(.+?)" is created on Apollo', html)
-        if m:
-            genome_name = m.group(1)
-        else:
-            print("Cannot find genome name in the jbrowse hub file!")
-            exit(1)
-        return genome_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")