diff apollo/ApolloInstance.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/apollo/ApolloInstance.py	Fri Feb 16 10:57:13 2018 -0500
@@ -0,0 +1,80 @@
+#!/usr/bin/env python
+import os
+import json
+import shutil
+import tempfile
+import logging
+import random
+import string
+from util import subtools
+from mako.lookup import TemplateLookup
+
+from ApolloOrganism import ApolloOrganism
+from ApolloUser import ApolloUser
+
+class ApolloInstance(object):
+    def __init__(self, apollo_host, apollo_admin, tool_directory):
+        self.apollo_host = apollo_host
+        self.tool_directory = tool_directory
+        self.logger = logging.getLogger(__name__)
+        self.apollo_admin =  apollo_admin
+        self.apolloTemplate = self._getApolloTemplate()
+        self._arrow_init()
+    
+    
+    def _arrow_init(self):
+        subtools.verify_user_login(self.apollo_admin['user_email'], self.apollo_admin['password'], self.apollo_host)
+        arrow_config = tempfile.NamedTemporaryFile(bufsize=0)
+        with open(arrow_config.name, 'w') as conf:
+            htmlMakoRendered = self.apolloTemplate.render(
+            apollo_host = self.apollo_host,
+            admin_user = self.apollo_admin['user_email'],
+            admin_pw = self.apollo_admin['password']
+        )
+            conf.write(htmlMakoRendered)
+
+        home_dir = os.path.expanduser('~')
+        arrow_config_dir = os.path.join(home_dir, '.apollo-arrow.yml')
+        shutil.copyfile(arrow_config.name, arrow_config_dir)
+        self.logger.debug("Initated arrow: apollo-arrow.yml= %s", arrow_config_dir)
+    
+    #TODO: Encode admin password
+    '''
+    def _generatePassword(self, length=8):
+        chars = string.digits + string.letters
+        pw = ''.join([random.choice(chars) for _ in range(length)])
+        return pw
+    '''
+
+    def _getApolloTemplate(self):
+        mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')],
+                                  output_encoding='utf-8', encoding_errors='replace')
+        apolloTemplate = mylookup.get_template("apollo-arrow.yml")
+        return apolloTemplate
+
+   
+    def manageApolloOrganism(self, organism_name, organism_dir, action):
+        organism = ApolloOrganism(organism_name, organism_dir) 
+        if action == "add":
+            organism.addOrganism()
+            self.logger.info("Successfully add a new organism (%s) to Apollo", organism_name)
+        elif action == "overwrite":
+            organism.overwriteOrganism()
+            self.logger.info("Successfully overwrite the organism %s", organism_name)
+        else:
+            self.logger.error("Invalid operation %s", action)
+            exit(-1)
+
+    def manageApolloUser(self, operations_dictionary = dict()):
+        for operation, users_list in operations_dictionary.items(): 
+            apollo_user = ApolloUser(users_list)
+            if operation == "create":
+                apollo_user.createApolloUser()
+            elif operation == "delete":
+                apollo_user.deleteApolloUser()
+            elif operation == "add":
+                apollo_user.addApolloUserToGroup()
+            elif operation == "remove":
+                apollo_user.removeApolloUserFromeGroup()
+
+