diff apollo/ApolloInstance.py @ 3:6f262a92e8dc draft default tip

planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 91b46f7c891c2466bc5b6a063411cdae75964515-dirty

--- a/apollo/ApolloInstance.py	Wed Oct 25 12:41:34 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-#!/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, self.apollo_host)
-        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, self.apollo_host)
-            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")
\ No newline at end of file