1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/f61263482700/ Changeset: f61263482700 User: greg Date: 2014-05-16 23:14:24 Summary: Add a script for creating a new user and an associated API key to streamline the process of setting up a new local development tool shed. Affected #: 2 files

diff -r 9fbe2754793109a1680239131b5507614d431870 -r f61263482700499fd79238b6468c18e6915aaf08 lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py --- /dev/null +++ b/lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py @@ -0,0 +1,158 @@ +#!/usr/bin/env python + +import ConfigParser +import logging +import os +import re +import sys + +from optparse import OptionParser + +new_path = [ os.path.join( os.getcwd(), "lib" ) ] +new_path.extend( sys.path[1:] ) +sys.path = new_path + +from galaxy import eggs +eggs.require( "SQLAlchemy >= 0.4" ) +eggs.require( 'mercurial' ) + +from galaxy.web import security +import galaxy.webapps.tool_shed.config as tool_shed_config +from galaxy.webapps.tool_shed.model import mapping +from tool_shed.util import xml_util + +log = logging.getLogger( __name__ ) + + +VALID_PUBLICNAME_RE = re.compile( "^[a-z0-9-]+$" ) +VALID_EMAIL_RE = re.compile( "[^@]+@[^@]+.[^@]+" ) + + +class BootstrapApplication( object ): + """ + Creates a basic Tool Shed application in order to discover the database connection and use SQL + to create a user and API key. + """ + + def __init__( self, config ): + self.config = config + if not self.config.database_connection: + self.config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % str( config.database ) + print 'Using database connection: ', self.config.database_connection + # Setup the database engine and ORM + self.model = mapping.init( self.config.file_path, + self.config.database_connection, + engine_options={}, + create_tables=False ) + self.security = security.SecurityHelper( id_secret=self.config.id_secret ) + self.hgweb_config_manager = self.model.hgweb_config_manager + self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir + print 'Using hgweb.config file: ', self.hgweb_config_manager.hgweb_config + + @property + def sa_session( self ): + """Returns a SQLAlchemy session.""" + return self.model.context.current + + def shutdown( self ): + pass + +def create_api_key( app, user ): + api_key = app.security.get_new_guid() + new_key = app.model.APIKeys() + new_key.user_id = user.id + new_key.key = api_key + app.sa_session.add( new_key ) + app.sa_session.flush() + return api_key + +def create_user( app ): + user_info_config = os.path.abspath( os.path.join( app.config.root, 'lib/tool_shed/scripts/bootstrap_tool_shed', 'user_info.xml' ) ) + email = None + password = None + username = None + tree, error_message = xml_util.parse_xml( user_info_config ) + if tree is None: + print "The XML file ", user_info_config, " seems to be invalid, using defaults." + email = 'admin@test.org' + password = 'testuser' + username = 'admin' + else: + root = tree.getroot() + for elem in root: + if elem.tag == 'email': + email = elem.text + elif elem.tag == 'password': + password = elem.text + elif elem.tag == 'username': + username = elem.text + if email and password and username: + invalid_message = validate( email, password, username ) + if invalid_message: + print invalid_message + else: + user = app.model.User( email=email ) + user.set_password_cleartext( password ) + user.username = username + app.sa_session.add( user ) + app.sa_session.flush() + app.model.security_agent.create_private_user_role( user ) + return user + else: + print "Missing required values for email: ", email, ", password: ", password, ", username: ", username + return None + +def validate( email, password, username ): + message = validate_email( email ) + if not message: + message = validate_password( password ) + if not message: + message = validate_publicname( username ) + return message + +def validate_email( email ): + """Validates the email format.""" + message = '' + if not( VALID_EMAIL_RE.match( email ) ): + message = "Please enter a real email address." + elif len( email ) > 255: + message = "Email address exceeds maximum allowable length." + return message + +def validate_password( password ): + if len( password ) < 6: + return "Use a password of at least 6 characters" + return '' + +def validate_publicname( username ): + """""Validates the public username.""" + if len( username ) < 3: + return "Public name must be at least 3 characters in length" + if len( username ) > 255: + return "Public name cannot be more than 255 characters in length" + if not( VALID_PUBLICNAME_RE.match( username ) ): + return "Public name must contain only lower-case letters, numbers and '-'" + return '' + +if __name__ == "__main__": + parser = OptionParser() + ( options, args ) = parser.parse_args() + try: + ini_file = args[ 0 ] + except IndexError: + print "Usage: python %s <tool shed .ini file> [options]" % sys.argv[ 0 ] + exit( 127 ) + config_parser = ConfigParser.ConfigParser( { 'here':os.getcwd() } ) + print "Reading ini file: ", ini_file + config_parser.read( ini_file ) + config_dict = {} + for key, value in config_parser.items( "app:main" ): + config_dict[ key ] = value + config = tool_shed_config.Configuration( **config_dict ) + app = BootstrapApplication( config ) + user = create_user( app ) + if user is not None: + api_key = create_api_key( app, user ) + print "Created new user with public username '", user.username, ". An API key was also created and associated with the user." + else: + print "Problem creating a new user and an associated API key."

diff -r 9fbe2754793109a1680239131b5507614d431870 -r f61263482700499fd79238b6468c18e6915aaf08 lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml --- /dev/null +++ b/lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<user> + <email>admin@test.org</email> + <password>testuser</password> + <username>admin</username> +</user>

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

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