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Enhance the Tool Shed API to provide information about users that is public (i.e., public username) and to include a function for creating a new user. Add a Tool Shed API script that retrieves all of the pubic information about users from a Tool Shed, automatically generates test email accounts and test passwords, and creates the list of users in another Tool Shed. This script streamlines the process of populating a development Tool Shed with users, enabling import of a repository capsule exportied from the specified Tool Shed. This simplifies the process of developing new repository hierarchies in a local development Tool Shed.
This commit is contained in:
Greg Von Kuster
@@ -0,0 +1,128 @@
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import logging
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import os
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from galaxy import util
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from galaxy import web
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from galaxy.web.base.controller import BaseAPIController
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from galaxy.security.validate_user_input import validate_email
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from galaxy.security.validate_user_input import validate_publicname
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from galaxy.security.validate_user_input import validate_password
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import tool_shed.util.shed_util_common as suc
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log = logging.getLogger( __name__ )
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class UsersController( BaseAPIController ):
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"""RESTful controller for interactions with users in the Tool Shed."""
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@web.expose_api
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def create_user( self, trans, payload, **kwd ):
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"""
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POST /api/users/create_user
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Returns a dictionary of information about the created user.
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: param key: the current Galaxy admin user's API key
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The following parameters are included in the payload.
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:param username (required): the public username of the user
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"""
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user_dict = dict( message = '',
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status = 'ok' )
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# Make sure the current user's API key proves he is an admin user in this Tool Shed.
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if trans.user_is_admin():
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# Get the information about the user to be created from the payload.
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email = payload.get( 'email', '' )
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password = payload.get( 'password', '' )
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username = payload.get( 'username', '' )
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message = self.__validate( trans,
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email=email,
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password=password,
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confirm=password,
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username=username )
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if message:
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message = 'email: %s, username: %s - %s' % ( email, username, message )
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user_dict[ 'message' ] = message
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user_dict[ 'status' ] = 'error'
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else:
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# Create the user.
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user = self.__create_user( trans, email, username, password )
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user_dict = user.to_dict( view='element',
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value_mapper=self.__get_value_mapper( trans ) )
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user_dict[ 'message' ] = "User '%s' has been created." % str( user.username )
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user_dict[ 'url' ] = web.url_for( controller='users',
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action='show',
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id=trans.security.encode_id( user.id ) )
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else:
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user_dict[ 'message' ] = 'You are not authorized to create a user in this Tool Shed.'
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user_dict[ 'status' ] = 'error'
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return user_dict
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def __create_user( self, trans, email, username, password ):
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user = trans.app.model.User( email=email )
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user.set_password_cleartext( password )
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user.username = username
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if trans.app.config.user_activation_on:
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user.active = False
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else:
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user.active = True # Activation is off, every new user is active by default.
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trans.sa_session.add( user )
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trans.sa_session.flush()
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trans.app.security_agent.create_private_user_role( user )
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return user
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def __get_value_mapper( self, trans ):
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value_mapper = { 'id' : trans.security.encode_id }
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return value_mapper
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@web.expose_api_anonymous
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def index( self, trans, deleted=False, **kwd ):
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"""
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GET /api/users
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Returns a list of dictionaries that contain information about each user.
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"""
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# Example URL: http://localhost:9009/api/users
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user_dicts = []
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deleted = util.asbool( deleted )
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for user in trans.sa_session.query( trans.app.model.User ) \
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.filter( trans.app.model.User.table.c.deleted == deleted ) \
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.order_by( trans.app.model.User.table.c.username ):
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user_dict = user.to_dict( view='collection',
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value_mapper=self.__get_value_mapper( trans ) )
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user_dict[ 'url' ] = web.url_for( controller='users',
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action='show',
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id=trans.security.encode_id( user.id ) )
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user_dicts.append( user_dict )
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return user_dicts
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@web.expose_api_anonymous
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def show( self, trans, id, **kwd ):
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"""
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GET /api/users/{encoded_user_id}
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Returns a dictionary of information about a user.
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:param id: the encoded id of the User object.
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"""
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# Example URL: http://localhost:9009/api/users/f9cad7b01a472135
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user = suc.get_user( trans, id )
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if user is None:
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user_dict = dict( message = 'Unable to locate user record for id %s.' % ( str( id ) ),
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status = 'error' )
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return user_dict
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user_dict = user.to_dict( view='element',
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value_mapper=self.__get_value_mapper( trans ) )
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user_dict[ 'url' ] = web.url_for( controller='users',
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action='show',
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id=trans.security.encode_id( user.id ) )
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return user_dict
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def __validate( self, trans, email, password, confirm, username ):
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if not username:
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return "A public user name is required in the Tool Shed."
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if username in [ 'repos' ]:
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return "The term <b>%s</b> is a reserved word in the Tool Shed, so it cannot be used as a public user name." % username
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message = validate_email( trans, email )
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if not message:
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message = validate_password( trans, password, confirm )
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if not message and username:
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message = validate_publicname( trans, username )
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return message
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@@ -107,6 +107,13 @@ def app_factory( global_conf, **kwargs ):
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name_prefix='repository_revision_',
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path_prefix='/api',
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parent_resources=dict( member_name='repository_revision', collection_name='repository_revisions' ) )
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webapp.mapper.resource( 'user',
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'users',
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controller='users',
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name_prefix='user_',
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path_prefix='/api',
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new={ 'create_user' : 'POST' },
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parent_resources=dict( member_name='user', collection_name='users' ) )
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webapp.finalize_config()
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# Wrap the webapp in some useful middleware
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if kwargs.get( 'middleware', True ):
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@@ -20,8 +20,8 @@ class APIKeys( object ):
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class User( object, Dictifiable ):
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dict_collection_visible_keys = ( 'id', 'email' )
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dict_element_visible_keys = ( 'id', 'email', 'username' )
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dict_collection_visible_keys = ( 'id', 'username' )
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dict_element_visible_keys = ( 'id', 'username' )
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def __init__( self, email=None, password=None ):
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self.email = email
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@@ -9,10 +9,10 @@ will not be affected.
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This script is very useful for populating a new development Tool Shed with the set of categories that
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currently exist in either the test or main public Galaxy Tool Sheds. This will streamline building
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new repository hierarchies in the development Tool Shed and exportin gthem into a capsule that can be
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new repository hierarchies in the development Tool Shed and exporting them into a capsule that can be
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imported into one of the public Tool Sheds.
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Here is a working example of how to use this script to retrieve the current set of repositories that are
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Here is a working example of how to use this script to retrieve the current set of categories that are
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available in the test public Tool Shed and create each of them in a local development Tool Shed.
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./create_categories.py -a <api key> -f http://testtoolshed.g2.bx.psu.edu -t http://localhost:9009
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@@ -0,0 +1,60 @@
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#!/usr/bin/env python
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"""
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This script will retrieve a list of dictionaries (one for each user) from the Tool Shed defined
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by the --from_tool_shed parameter, which should be a base Tool Shed URL. It will retrieve the
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username from each dictionary and create a new user with that username in the Tool Shed defined
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by the --to_tool_shed parameter (a different base Tool Shed URL). An email and password value
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will automatically be provided for each user. Email addresses will be <username>@test.org and
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passwords will be testuser. Users that already exist with a specified username in the Tool Shed
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in which the users are being created will not be affected.
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This script is very useful for populating a new development Tool Shed with the set of users that
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currently exist in either the test or main public Galaxy Tool Sheds. This will streamline building
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new repository hierarchies in the development Tool Shed and exporting them into a capsule that can
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be imported into one of the public Tool Sheds.
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Here is a working example of how to use this script to retrieve the current set of users that
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are available in the test public Tool Shed and create each of them in a local development Tool Shed.
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./create_users.py -a <api key> -f http://testtoolshed.g2.bx.psu.edu -t http://localhost:9009
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"""
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import os
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import sys
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import argparse
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sys.path.insert( 0, os.path.dirname( __file__ ) )
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from common import get
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from common import submit
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def main( options ):
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api_key = options.api
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from_tool_shed = options.from_tool_shed.rstrip( '/' )
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to_tool_shed = options.to_tool_shed.rstrip( '/' )
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# Get the users from the specified Tool Shed.
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url = '%s/api/users' % from_tool_shed
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user_dicts = get( url )
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create_response_dicts = []
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for user_dict in user_dicts:
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username = user_dict.get( 'username', None )
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if username is not None:
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email = '%s@test.org' % username
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password = 'testuser'
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data = dict( email=email,
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password=password,
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username=username )
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url = '%s/api/users/new/create_user' % to_tool_shed
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try:
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response = submit( url, data, api_key )
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except Exception, e:
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response = str( e )
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log.exception( str( e ) )
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create_response_dict = dict( response=response )
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create_response_dicts.append( create_response_dict )
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if __name__ == '__main__':
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parser = argparse.ArgumentParser( description='Retrieve a list of users from a Tool Shed and create them in another Tool Shed.' )
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parser.add_argument( "-a", "--api", dest="api", required=True, help="API Key for Tool Shed in which users will be created" )
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parser.add_argument( "-f", "--from_tool_shed", dest="from_tool_shed", required=True, help="URL of Tool Shed from which to retrieve the users" )
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parser.add_argument( "-t", "--to_tool_shed", dest="to_tool_shed", required=True, help="URL of Tool Shed in which to create the users" )
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options = parser.parse_args()
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main( options )
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