1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/f337aefda5c6/ Changeset: f337aefda5c6 User: greg Date: 2014-05-01 22:07:48 Summary: 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. Affected #: 5 files

diff -r f6561aae5484240c8b76cc32a7b4b1f501b0e660 -r f337aefda5c6c709760c51019df777c083b036bb lib/galaxy/webapps/tool_shed/api/users.py --- /dev/null +++ b/lib/galaxy/webapps/tool_shed/api/users.py @@ -0,0 +1,128 @@ +import logging +import os + +from galaxy import util +from galaxy import web +from galaxy.web.base.controller import BaseAPIController +from galaxy.security.validate_user_input import validate_email +from galaxy.security.validate_user_input import validate_publicname +from galaxy.security.validate_user_input import validate_password +import tool_shed.util.shed_util_common as suc + +log = logging.getLogger( __name__ ) + + +class UsersController( BaseAPIController ): + """RESTful controller for interactions with users in the Tool Shed.""" + + @web.expose_api + def create_user( self, trans, payload, **kwd ): + """ + POST /api/users/create_user + Returns a dictionary of information about the created user. + +: param key: the current Galaxy admin user's API key + + The following parameters are included in the payload. + :param username (required): the public username of the user + """ + user_dict = dict( message = '', + status = 'ok' ) + # Make sure the current user's API key proves he is an admin user in this Tool Shed. + if trans.user_is_admin(): + # Get the information about the user to be created from the payload. + email = payload.get( 'email', '' ) + password = payload.get( 'password', '' ) + username = payload.get( 'username', '' ) + message = self.__validate( trans, + email=email, + password=password, + confirm=password, + username=username ) + if message: + message = 'email: %s, username: %s - %s' % ( email, username, message ) + user_dict[ 'message' ] = message + user_dict[ 'status' ] = 'error' + else: + # Create the user. + user = self.__create_user( trans, email, username, password ) + user_dict = user.to_dict( view='element', + value_mapper=self.__get_value_mapper( trans ) ) + user_dict[ 'message' ] = "User '%s' has been created." % str( user.username ) + user_dict[ 'url' ] = web.url_for( controller='users', + action='show', + id=trans.security.encode_id( user.id ) ) + else: + user_dict[ 'message' ] = 'You are not authorized to create a user in this Tool Shed.' + user_dict[ 'status' ] = 'error' + return user_dict + + def __create_user( self, trans, email, username, password ): + user = trans.app.model.User( email=email ) + user.set_password_cleartext( password ) + user.username = username + if trans.app.config.user_activation_on: + user.active = False + else: + user.active = True # Activation is off, every new user is active by default. + trans.sa_session.add( user ) + trans.sa_session.flush() + trans.app.security_agent.create_private_user_role( user ) + return user + + def __get_value_mapper( self, trans ): + value_mapper = { 'id' : trans.security.encode_id } + return value_mapper + + @web.expose_api_anonymous + def index( self, trans, deleted=False, **kwd ): + """ + GET /api/users + Returns a list of dictionaries that contain information about each user. + """ + # Example URL: http://localhost:9009/api/users + user_dicts = [] + deleted = util.asbool( deleted ) + for user in trans.sa_session.query( trans.app.model.User ) \ + .filter( trans.app.model.User.table.c.deleted == deleted ) \ + .order_by( trans.app.model.User.table.c.username ): + user_dict = user.to_dict( view='collection', + value_mapper=self.__get_value_mapper( trans ) ) + user_dict[ 'url' ] = web.url_for( controller='users', + action='show', + id=trans.security.encode_id( user.id ) ) + user_dicts.append( user_dict ) + return user_dicts + + @web.expose_api_anonymous + def show( self, trans, id, **kwd ): + """ + GET /api/users/{encoded_user_id} + Returns a dictionary of information about a user. + + :param id: the encoded id of the User object. + """ + # Example URL: http://localhost:9009/api/users/f9cad7b01a472135 + user = suc.get_user( trans, id ) + if user is None: + user_dict = dict( message = 'Unable to locate user record for id %s.' % ( str( id ) ), + status = 'error' ) + return user_dict + user_dict = user.to_dict( view='element', + value_mapper=self.__get_value_mapper( trans ) ) + user_dict[ 'url' ] = web.url_for( controller='users', + action='show', + id=trans.security.encode_id( user.id ) ) + return user_dict + + def __validate( self, trans, email, password, confirm, username ): + if not username: + return "A public user name is required in the Tool Shed." + if username in [ 'repos' ]: + 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 + message = validate_email( trans, email ) + if not message: + message = validate_password( trans, password, confirm ) + if not message and username: + message = validate_publicname( trans, username ) + return message

diff -r f6561aae5484240c8b76cc32a7b4b1f501b0e660 -r f337aefda5c6c709760c51019df777c083b036bb lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -107,6 +107,13 @@ name_prefix='repository_revision_', path_prefix='/api', parent_resources=dict( member_name='repository_revision', collection_name='repository_revisions' ) ) + webapp.mapper.resource( 'user', + 'users', + controller='users', + name_prefix='user_', + path_prefix='/api', + new={ 'create_user' : 'POST' }, + parent_resources=dict( member_name='user', collection_name='users' ) ) webapp.finalize_config() # Wrap the webapp in some useful middleware if kwargs.get( 'middleware', True ):

diff -r f6561aae5484240c8b76cc32a7b4b1f501b0e660 -r f337aefda5c6c709760c51019df777c083b036bb lib/galaxy/webapps/tool_shed/model/__init__.py --- a/lib/galaxy/webapps/tool_shed/model/__init__.py +++ b/lib/galaxy/webapps/tool_shed/model/__init__.py @@ -20,8 +20,8 @@

class User( object, Dictifiable ): - dict_collection_visible_keys = ( 'id', 'email' ) - dict_element_visible_keys = ( 'id', 'email', 'username' ) + dict_collection_visible_keys = ( 'id', 'username' ) + dict_element_visible_keys = ( 'id', 'username' )

def __init__( self, email=None, password=None ): self.email = email

diff -r f6561aae5484240c8b76cc32a7b4b1f501b0e660 -r f337aefda5c6c709760c51019df777c083b036bb lib/tool_shed/scripts/api/create_categories.py --- a/lib/tool_shed/scripts/api/create_categories.py +++ b/lib/tool_shed/scripts/api/create_categories.py @@ -9,10 +9,10 @@

This script is very useful for populating a new development Tool Shed with the set of categories that currently exist in either the test or main public Galaxy Tool Sheds. This will streamline building -new repository hierarchies in the development Tool Shed and exportin gthem into a capsule that can be +new repository hierarchies in the development Tool Shed and exporting them into a capsule that can be imported into one of the public Tool Sheds.

-Here is a working example of how to use this script to retrieve the current set of repositories that are +Here is a working example of how to use this script to retrieve the current set of categories that are available in the test public Tool Shed and create each of them in a local development Tool Shed.

./create_categories.py -a <api key> -f http://testtoolshed.g2.bx.psu.edu -t http://localhost:9009

diff -r f6561aae5484240c8b76cc32a7b4b1f501b0e660 -r f337aefda5c6c709760c51019df777c083b036bb lib/tool_shed/scripts/api/create_users.py --- /dev/null +++ b/lib/tool_shed/scripts/api/create_users.py @@ -0,0 +1,60 @@ +#!/usr/bin/env python +""" +This script will retrieve a list of dictionaries (one for each user) from the Tool Shed defined +by the --from_tool_shed parameter, which should be a base Tool Shed URL. It will retrieve the +username from each dictionary and create a new user with that username in the Tool Shed defined +by the --to_tool_shed parameter (a different base Tool Shed URL). An email and password value +will automatically be provided for each user. Email addresses will be <username>@test.org and +passwords will be testuser. Users that already exist with a specified username in the Tool Shed +in which the users are being created will not be affected. + +This script is very useful for populating a new development Tool Shed with the set of users that +currently exist in either the test or main public Galaxy Tool Sheds. This will streamline building +new repository hierarchies in the development Tool Shed and exporting them into a capsule that can +be imported into one of the public Tool Sheds. + +Here is a working example of how to use this script to retrieve the current set of users that +are available in the test public Tool Shed and create each of them in a local development Tool Shed. + +./create_users.py -a <api key> -f http://testtoolshed.g2.bx.psu.edu -t http://localhost:9009 +""" + +import os +import sys +import argparse +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import get +from common import submit + +def main( options ): + api_key = options.api + from_tool_shed = options.from_tool_shed.rstrip( '/' ) + to_tool_shed = options.to_tool_shed.rstrip( '/' ) + # Get the users from the specified Tool Shed. + url = '%s/api/users' % from_tool_shed + user_dicts = get( url ) + create_response_dicts = [] + for user_dict in user_dicts: + username = user_dict.get( 'username', None ) + if username is not None: + email = '%s@test.org' % username + password = 'testuser' + data = dict( email=email, + password=password, + username=username ) + url = '%s/api/users/new/create_user' % to_tool_shed + try: + response = submit( url, data, api_key ) + except Exception, e: + response = str( e ) + log.exception( str( e ) ) + create_response_dict = dict( response=response ) + create_response_dicts.append( create_response_dict ) + +if __name__ == '__main__': + parser = argparse.ArgumentParser( description='Retrieve a list of users from a Tool Shed and create them in another Tool Shed.' ) + parser.add_argument( "-a", "--api", dest="api", required=True, help="API Key for Tool Shed in which users will be created" ) + parser.add_argument( "-f", "--from_tool_shed", dest="from_tool_shed", required=True, help="URL of Tool Shed from which to retrieve the users" ) + parser.add_argument( "-t", "--to_tool_shed", dest="to_tool_shed", required=True, help="URL of Tool Shed in which to create the users" ) + options = parser.parse_args() + main( options )

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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