diff apollo/ApolloInstance.py @ 0:bc00f5c4c59e draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/apollo/ApolloInstance.py	Tue Oct 17 17:28:05 2017 -0400
@@ -0,0 +1,71 @@
+#!/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()
+    
+    #TODO: Encode password
+    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")
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