Mercurial > repos > yating-l > jbrowsearchivecreator

annotate apollo/ApolloInstance.py @ 31:127037c49bc8 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
author yating-l
date Mon, 16 Oct 2017 18:03:58 -0400
parents 2191bd0798a9
children
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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 from util import subtools
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8 from mako.lookup import TemplateLookup
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9
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11 class ApolloInstance(object):
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12 def __init__(self, apollo_host, tool_directory, user_email):
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13 self.apollo_host = apollo_host
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14 self.tool_directory = tool_directory
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15 self.default_user = user_email
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16 self.logger = logging.getLogger(__name__)
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17 self.apolloTemplate = self._getApolloTemplate()
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18 self._arrow_init()
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20 def _arrow_init(self):
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21 arrow_config = tempfile.NamedTemporaryFile(bufsize=0)
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22 with open(arrow_config.name, 'w') as conf:
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23 htmlMakoRendered = self.apolloTemplate.render(
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24 apollo_host = self.apollo_host,
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25 admin_user = self.default_user,
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26 admin_pw = '1234'
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27 )
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28 conf.write(htmlMakoRendered)
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30 home_dir = os.path.expanduser('~')
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31 arrow_config_dir = os.path.join(home_dir, '.apollo-arrow.yml')
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32 shutil.copyfile(arrow_config.name, arrow_config_dir)
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33 self.logger.debug("Initated arrow: apollo-arrow.yml= %s", arrow_config_dir)
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36 def _getApolloTemplate(self):
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37 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')],
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38 output_encoding='utf-8', encoding_errors='replace')
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39 apolloTemplate = mylookup.get_template("apollo-arrow.yml")
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40 return apolloTemplate
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42 def getHost(self):
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43 return self.apollo_host
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45 def createApolloUser(self, apollo_user, admin=None):
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46 p = subtools.arrow_create_user(apollo_user.user_email, apollo_user.firstname, apollo_user.lastname, apollo_user.password, admin)
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47 user_info = json.loads(p)
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48 user_id = user_info.get('userId')
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49 if not user_id:
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50 self.logger.debug("Cannot create new user: %s; The user may already exist", apollo_user.user_email)
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51 user_id = subtools.arrow_get_users(apollo_user.user_email)
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52 self.logger.debug("Got user_id for new or existing user: user_id = %s", str(user_id))
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53 return user_id
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55 def grantPermission(self, user_id, organism_id, **user_permissions):
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56 subtools.arrow_update_organism_permissions(user_id, organism_id, **user_permissions)
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57 self.logger.debug("Grant user %s permissions to organism %s, permissions = %s", str(user_id), str(organism_id), ','.join(user_permissions))
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59 def addOrganism(self, organism_name, organism_dir):
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60 p = subtools.arrow_add_organism(organism_name, organism_dir)
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61 organism = json.loads(p)
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62 organism_id = organism['id']
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63 self.logger.debug("Added new organism to Apollo instance, %s", p)
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64 return organism_id
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66 def loadHubToApollo(self, apollo_user, organism_name, organism_dir, admin_user=False, **user_permissions):
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67 user_id = self.createApolloUser(apollo_user, admin_user)
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68 organism_id = self.addOrganism(organism_name, organism_dir)
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69 self.grantPermission(user_id, organism_id, **user_permissions)
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70 self.logger.debug("Successfully load the hub to Apollo")