Mercurial > repos > yating-l > jbrowsehubtoapollo
view apollo/ApolloInstance.py @ 1:2ae1e96a8380 draft
planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a8c47ae0025953ef398bdc689dc5df5516edf686-dirty
author | yating-l |
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date | Tue, 24 Oct 2017 18:24:40 -0400 |
parents | bc00f5c4c59e |
children | 8ff4b84d709f |
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#!/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 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) 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 createApolloUser(self, apollo_user, admin=None): p = subtools.arrow_create_user(apollo_user.user_email, apollo_user.firstname, apollo_user.lastname, apollo_user.password, admin) user_info = json.loads(p) user_id = user_info.get('userId') if not user_id: self.logger.debug("Cannot create new user: %s; The user may already exist", apollo_user.user_email) subtools.verify_user_login(apollo_user.user_email, apollo_user.password) user_id = subtools.arrow_get_users(apollo_user.user_email) self.logger.debug("Got user_id for new or existing user: user_id = %s", str(user_id)) return user_id def grantPermission(self, user_id, organism_id, **user_permissions): subtools.arrow_update_organism_permissions(user_id, organism_id, **user_permissions) self.logger.debug("Grant user %s permissions to organism %s, permissions = %s", str(user_id), str(organism_id), ','.join(user_permissions)) def addOrganism(self, organism_name, organism_dir): p = subtools.arrow_add_organism(organism_name, organism_dir) if not p: self.logger.error("The user is not authorized to add organism") exit(-1) organism = json.loads(p) organism_id = organism['id'] self.logger.debug("Added new organism to Apollo instance, %s", p) return organism_id def loadHubToApollo(self, apollo_user, organism_name, organism_dir, admin_user=False, **user_permissions): #user_id = self.createApolloUser(apollo_user, admin_user) organism_id = self.addOrganism(organism_name, organism_dir) #self.grantPermission(user_id, organism_id, **user_permissions) self.logger.debug("Successfully load the hub to Apollo")