Mercurial > repos > yating-l > gonramp_apollo

annotate apollo/ApolloInstance.py @ 0:cb8439d64ed3 draft default tip

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planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
author yating-l
date Mon, 27 Nov 2017 14:40:53 -0500
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0
cb8439d64ed3 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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1 #!/usr/bin/env python
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2 import os
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3 import json
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4 import shutil
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5 import tempfile
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6 import logging
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7 import random
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8 import string
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9 from util import subtools
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10 from mako.lookup import TemplateLookup
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11
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12 from ApolloOrganism import ApolloOrganism
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13 from ApolloUser import ApolloUser
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15 class ApolloInstance(object):
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16 def __init__(self, apollo_host, apollo_admin, tool_directory):
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17 self.apollo_host = apollo_host
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18 self.tool_directory = tool_directory
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19 self.logger = logging.getLogger(__name__)
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20 self.apollo_admin = apollo_admin
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21 self.apolloTemplate = self._getApolloTemplate()
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22 self._arrow_init()
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23
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25 def _arrow_init(self):
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26 subtools.verify_user_login(self.apollo_admin['user_email'], self.apollo_admin['password'], self.apollo_host)
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27 arrow_config = tempfile.NamedTemporaryFile(bufsize=0)
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28 with open(arrow_config.name, 'w') as conf:
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29 htmlMakoRendered = self.apolloTemplate.render(
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30 apollo_host = self.apollo_host,
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31 admin_user = self.apollo_admin['user_email'],
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32 admin_pw = self.apollo_admin['password']
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33 )
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34 conf.write(htmlMakoRendered)
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35
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36 home_dir = os.path.expanduser('~')
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37 arrow_config_dir = os.path.join(home_dir, '.apollo-arrow.yml')
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38 shutil.copyfile(arrow_config.name, arrow_config_dir)
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39 self.logger.debug("Initated arrow: apollo-arrow.yml= %s", arrow_config_dir)
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40
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41 #TODO: Encode admin password
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42 '''
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43 def _generatePassword(self, length=8):
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44 chars = string.digits + string.letters
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45 pw = ''.join([random.choice(chars) for _ in range(length)])
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46 return pw
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47 '''
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48
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49 def _getApolloTemplate(self):
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50 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')],
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51 output_encoding='utf-8', encoding_errors='replace')
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52 apolloTemplate = mylookup.get_template("apollo-arrow.yml")
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53 return apolloTemplate
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54
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55
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56 def manageApolloOrganism(self, organism_name, organism_dir, action):
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57 organism = ApolloOrganism(organism_name, organism_dir)
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58 if action == "add":
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59 organism.addOrganism()
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60 self.logger.info("Successfully add a new organism (%s) to Apollo", organism_name)
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61 elif action == "overwrite":
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62 organism.overwriteOrganism()
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63 self.logger.info("Successfully overwrite the organism %s", organism_name)
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64 else:
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65 self.logger.error("Invalid operation %s", action)
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66 exit(-1)
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67
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68 def manageApolloUser(self, operations_dictionary = dict()):
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69 for operation, users_list in operations_dictionary.items():
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70 apollo_user = ApolloUser(users_list)
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71 if operation == "create":
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72 apollo_user.createApolloUser()
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73 elif operation == "delete":
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74 apollo_user.deleteApolloUser()
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75 elif operation == "add":
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76 apollo_user.addApolloUserToGroup()
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77 elif operation == "delete":
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78 apollo_user.removeApolloUserFromeGroup()
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79
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80