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

planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty

#!/usr/bin/env python
import os
import json
import shutil
import tempfile
import logging
from util import subtools
from mako.lookup import TemplateLookup


class ApolloInstance(object):
    def __init__(self, apollo_host, tool_directory, user_email):
        self.apollo_host = apollo_host
        self.tool_directory = tool_directory
        self.default_user = user_email
        self.logger = logging.getLogger(__name__)
        self.apolloTemplate = self._getApolloTemplate()
        self._arrow_init()
    
    def _arrow_init(self):
        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.default_user,
            admin_pw = '1234'
        )
            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)


    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 getHost(self):
        return self.apollo_host

    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)
            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)
        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")