Mercurial > repos > yating-l > gonramp_apollo_tools

comparison apollo/ApolloInstance.py @ 0:ce4f91831680 draft default tip

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planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 5367a00befb467f162d1870edb91f9face72e894
author yating-l
date Fri, 16 Feb 2018 10:57:13 -0500
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-1:000000000000 0:ce4f91831680
1 #!/usr/bin/env python
2 import os
3 import json
4 import shutil
5 import tempfile
6 import logging
7 import random
8 import string
9 from util import subtools
10 from mako.lookup import TemplateLookup
11
12 from ApolloOrganism import ApolloOrganism
13 from ApolloUser import ApolloUser
14
15 class ApolloInstance(object):
16 def __init__(self, apollo_host, apollo_admin, tool_directory):
17 self.apollo_host = apollo_host
18 self.tool_directory = tool_directory
19 self.logger = logging.getLogger(__name__)
20 self.apollo_admin = apollo_admin
21 self.apolloTemplate = self._getApolloTemplate()
22 self._arrow_init()
23
24
25 def _arrow_init(self):
26 subtools.verify_user_login(self.apollo_admin['user_email'], self.apollo_admin['password'], self.apollo_host)
27 arrow_config = tempfile.NamedTemporaryFile(bufsize=0)
28 with open(arrow_config.name, 'w') as conf:
29 htmlMakoRendered = self.apolloTemplate.render(
30 apollo_host = self.apollo_host,
31 admin_user = self.apollo_admin['user_email'],
32 admin_pw = self.apollo_admin['password']
33 )
34 conf.write(htmlMakoRendered)
35
36 home_dir = os.path.expanduser('~')
37 arrow_config_dir = os.path.join(home_dir, '.apollo-arrow.yml')
38 shutil.copyfile(arrow_config.name, arrow_config_dir)
39 self.logger.debug("Initated arrow: apollo-arrow.yml= %s", arrow_config_dir)
40
41 #TODO: Encode admin password
42 '''
43 def _generatePassword(self, length=8):
44 chars = string.digits + string.letters
45 pw = ''.join([random.choice(chars) for _ in range(length)])
46 return pw
47 '''
48
49 def _getApolloTemplate(self):
50 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')],
51 output_encoding='utf-8', encoding_errors='replace')
52 apolloTemplate = mylookup.get_template("apollo-arrow.yml")
53 return apolloTemplate
54
55
56 def manageApolloOrganism(self, organism_name, organism_dir, action):
57 organism = ApolloOrganism(organism_name, organism_dir)
58 if action == "add":
59 organism.addOrganism()
60 self.logger.info("Successfully add a new organism (%s) to Apollo", organism_name)
61 elif action == "overwrite":
62 organism.overwriteOrganism()
63 self.logger.info("Successfully overwrite the organism %s", organism_name)
64 else:
65 self.logger.error("Invalid operation %s", action)
66 exit(-1)
67
68 def manageApolloUser(self, operations_dictionary = dict()):
69 for operation, users_list in operations_dictionary.items():
70 apollo_user = ApolloUser(users_list)
71 if operation == "create":
72 apollo_user.createApolloUser()
73 elif operation == "delete":
74 apollo_user.deleteApolloUser()
75 elif operation == "add":
76 apollo_user.addApolloUserToGroup()
77 elif operation == "remove":
78 apollo_user.removeApolloUserFromeGroup()
79
80