mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Enable running the create_users and create_categories scripts via run_tool_shed.sh
This commit is contained in:
Dave Bouvier
@@ -0,0 +1,100 @@
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#!/bin/bash
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stop_err() {
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echo $1
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python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_bootstrap.pid --log-file=tool_shed_bootstrap.log --stop-daemon
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exit 1
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}
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tool_shed=`./lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh $@`
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if [ $? -ne 0 ] ; then
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exit 0
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fi
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log_file="lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap.log"
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database_result=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute check_db --config_file tool_shed_wsgi.ini`
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if [ $? -ne 0 ] ; then
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stop_err "Unable to bootstrap tool shed. $database_result"
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fi
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echo "Bootstrapping from tool shed at $tool_shed."
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echo -n "Creating database... "
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python scripts/create_db.py tool_shed
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if [ $? -eq 0 ] ; then
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echo "done."
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else
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stop_err "failed."
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fi
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if [ $? -eq 0 ] ; then
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user_auth=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute admin_user_info --config_file tool_shed_wsgi.ini`
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local_shed_url=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute get_url --config_file tool_shed_wsgi.ini`
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fi
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admin_user_name=`echo $user_auth | awk 'BEGIN { FS="__SEP__" } ; { print \$1 }'`
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admin_user_email=`echo $user_auth | awk 'BEGIN { FS="__SEP__" } ; { print \$2 }'`
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admin_user_password=`echo $user_auth | awk 'BEGIN { FS="__SEP__" } ; { print \$3 }'`
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echo -n "Creating user '$admin_user_name' with email address '$admin_user_email'..."
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python lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py tool_shed_wsgi.ini >> $log_file
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echo " done."
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sed -i "s/#admin_users = user1@example.org,user2@example.org/admin_users = $admin_user_email/" tool_shed_wsgi.ini
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echo -n "Starting tool shed in order to populate users and categories... "
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if [ -f tool_shed_bootstrap.pid ] ; then
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stop_err "A bootstrap process is already running."
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fi
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python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_bootstrap.pid --log-file=tool_shed_bootstrap.log --daemon > /dev/null
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shed_pid=`cat tool_shed_bootstrap.pid`
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while : ; do
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tail -n 1 tool_shed_bootstrap.log | grep -q "Removing PID file tool_shed_webapp.pid"
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if [ $? -eq 0 ] ; then
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echo "failed."
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echo "More information about this failure may be found in the following log snippet from tool_shed_bootstrap.log:"
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echo "========================================"
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tail -n 40 tool_shed_bootstrap.log
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echo "========================================"
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stop_err " "
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fi
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tail -n 2 tool_shed_bootstrap.log | grep -q "Starting server in PID $shed_pid"
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if [ $? -eq 0 ] ; then
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echo "done."
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break
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fi
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done
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echo -n "Retrieving admin user's API key..."
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api_key_json=`curl -s --user $admin_user_email:$admin_user_password $local_shed_url/api/authenticate/baseauth/`
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api_key=`echo $api_key_json | grep api_key | awk 'BEGIN { FS="\"" } ; { print \$4 }' | sed 's/\\s\+//'`
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if [[ -z $api_key && ${api_key+x} ]] ; then
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stop_err "Error getting API key for user $admin_user_email."
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fi
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echo " done."
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if [ $? -eq 0 ] ; then
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echo -n "Creating users... "
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python lib/tool_shed/scripts/api/create_users.py -a $api_key -f $tool_shed -t $local_shed_url >> $log_file
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echo "done."
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echo -n "Creating categories... "
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python lib/tool_shed/scripts/api/create_categories.py -a $api_key -f $tool_shed -t $local_shed_url >> $log_file
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echo "done."
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else
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stop_err "Error getting API key from local tool shed."
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fi
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echo "Bootstrap complete, shutting down temporary tool shed process. A log has been saved to tool_shed_bootstrap.log"
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python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_bootstrap.pid --log-file=tool_shed_bootstrap.log --stop-daemon
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exit 0
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+130
@@ -0,0 +1,130 @@
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#!/usr/bin/python
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import argparse
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import ConfigParser
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import os
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import sys
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new_path = [ os.path.join( os.getcwd(), "lib" ) ]
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new_path.extend( sys.path[1:] )
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sys.path = new_path
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from galaxy import eggs
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eggs.require( "SQLAlchemy >= 0.4" )
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import galaxy.webapps.tool_shed.model.mapping as tool_shed_model
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from sqlalchemy.exc import ProgrammingError
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from sqlalchemy.exc import OperationalError
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from tool_shed.util import xml_util
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def check_db( config_parser ):
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dburi = None
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if config_parser.has_option( 'app:main', 'database_connection' ):
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dburi = config_parser.get( 'app:main', 'database_connection' )
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elif config_parser.has_option( 'app:main', 'database_file' ):
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db_file = config_parser.get( 'app:main', 'database_file' )
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dburi = "sqlite:///%s?isolation_level=IMMEDIATE" % db_file
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else:
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print 'The database configuration setting is missing from the tool_shed_wsgi.ini file. Add this setting before attempting to bootstrap.'
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exit(1)
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sa_session = None
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database_exists_message = 'The database configured for this Tool Shed is not new, so bootstrapping is not allowed. '
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database_exists_message += 'Create a new database that has not been migrated before attempting to bootstrap.'
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try:
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model = tool_shed_model.init( config_parser.get( 'app:main', 'file_path' ), dburi, engine_options={}, create_tables=False )
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sa_session = model.context.current
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print database_exists_message
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exit(1)
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except ProgrammingError, e:
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pass
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except OperationalError, e:
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pass
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try:
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if sa_session is not None:
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result = sa_session.execute( 'SELECT version FROM migrate_version' ).first()
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if result[0] >= 2:
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print database_exists_message
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exit(1)
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else:
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pass
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except ProgrammingError, e:
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pass
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if config_parser.has_option( 'app:main', 'hgweb_config_dir' ):
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hgweb_config_parser = ConfigParser.ConfigParser()
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hgweb_dir = config_parser.get( 'app:main', 'hgweb_config_dir' )
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hgweb_config_file = os.path.join( hgweb_dir, 'hgweb.config' )
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if not os.path.exists( hgweb_config_file ):
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exit(0)
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hgweb_config_parser.read( hgweb_config_file )
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configured_repos = hgweb_config_parser.items( 'paths' )
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if len( configured_repos ) >= 1:
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message = "This Tool Shed's hgweb.config file contains entries, so bootstrapping is not allowed. Delete"
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message += " the current hgweb.config file along with all associated repositories in the configured "
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message += "location before attempting to boostrap."
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print
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exit(1)
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else:
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exit(0)
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else:
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exit(0)
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exit(0)
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def admin_user_info( config_parser ):
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user_info_config = os.path.abspath( os.path.join( os.getcwd(), 'lib/tool_shed/scripts/bootstrap_tool_shed', 'user_info.xml' ) )
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tree, error_message = xml_util.parse_xml( user_info_config )
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if tree is None:
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print "The XML file ", user_info_config, " seems to be invalid, using defaults."
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email = 'admin@test.org'
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password = 'testuser'
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username = 'admin'
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else:
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root = tree.getroot()
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for elem in root:
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if elem.tag == 'email':
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email = elem.text
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elif elem.tag == 'password':
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password = elem.text
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elif elem.tag == 'username':
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username = elem.text
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print '%s__SEP__%s__SEP__%s' % ( username, email, password )
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return 0
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def get_local_tool_shed_url( config_parser ):
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port = '9009'
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if config_parser.has_section( 'server:main' ):
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if config_parser.has_option( 'server:main', 'port' ):
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port = config_parser.get( 'server:main', 'port' )
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host = '127.0.0.1'
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print 'http://%s:%s' % ( host, port )
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return 0
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def main( args ):
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config_parser = ConfigParser.ConfigParser()
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if os.path.exists( args.config ):
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config_parser.read( args.config )
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else:
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return 1
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if args.method == 'check_db':
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return check_db( config_parser )
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elif args.method == 'admin_user_info':
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return admin_user_info( config_parser )
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elif args.method == 'get_url':
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return get_local_tool_shed_url( config_parser )
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else:
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return 1
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parser = argparse.ArgumentParser()
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parser.add_argument( '-c', '--config_file', dest='config', action='store', default='tool_shed_wsgi.ini' )
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parser.add_argument( '-e', '--execute', dest='method', action='store', default='check_db' )
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args = parser.parse_args()
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if __name__ == '__main__':
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exit( main( args ) )
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@@ -125,7 +125,7 @@ def validate_password( password ):
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return ''
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def validate_publicname( username ):
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"""""Validates the public username."""
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"""Validates the public username."""
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if len( username ) < 3:
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return "Public name must be at least 3 characters in length"
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if len( username ) > 255:
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@@ -154,5 +154,7 @@ if __name__ == "__main__":
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if user is not None:
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api_key = create_api_key( app, user )
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print "Created new user with public username '", user.username, ". An API key was also created and associated with the user."
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exit(0)
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else:
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print "Problem creating a new user and an associated API key."
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exit(1)
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@@ -0,0 +1,15 @@
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#!/bin/bash
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while (( $# )) ; do
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case "$1" in
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-bootstrap_from_tool_shed|--bootstrap_from_tool_shed)
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bootstrap="true"
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tool_shed=$2
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echo $tool_shed
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exit 0
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break
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;;
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esac
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shift 1
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done
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exit 1
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@@ -5,41 +5,7 @@ cd `dirname $0`
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python ./scripts/check_python.py
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[ $? -ne 0 ] && exit 1
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SAMPLES="
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community_wsgi.ini.sample
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datatypes_conf.xml.sample
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external_service_types_conf.xml.sample
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migrated_tools_conf.xml.sample
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reports_wsgi.ini.sample
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shed_tool_conf.xml.sample
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tool_conf.xml.sample
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shed_tool_data_table_conf.xml.sample
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tool_data_table_conf.xml.sample
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tool_sheds_conf.xml.sample
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data_manager_conf.xml.sample
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shed_data_manager_conf.xml.sample
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openid_conf.xml.sample
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job_metrics_conf.xml.sample
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universe_wsgi.ini.sample
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tool-data/shared/ncbi/builds.txt.sample
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tool-data/shared/ensembl/builds.txt.sample
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tool-data/shared/ucsc/builds.txt.sample
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tool-data/shared/ucsc/publicbuilds.txt.sample
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tool-data/shared/ucsc/ucsc_build_sites.txt.sample
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tool-data/shared/igv/igv_build_sites.txt.sample
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tool-data/shared/rviewer/rviewer_build_sites.txt.sample
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tool-data/*.sample
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static/welcome.html.sample
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"
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# Create any missing config/location files
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for sample in $SAMPLES; do
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file=`echo $sample | sed -e 's/\.sample$//'`
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if [ ! -f "$file" -a -f "$sample" ]; then
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echo "Initializing $file from `basename $sample`"
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cp $sample $file
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fi
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done
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./scripts/copy_sample_files.sh
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if [ -n "$GALAXY_UNIVERSE_CONFIG_DIR" ]; then
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python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR"
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+9
-32
@@ -2,37 +2,14 @@
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cd `dirname $0`
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SAMPLES="
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tool_shed_wsgi.ini.sample
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datatypes_conf.xml.sample
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external_service_types_conf.xml.sample
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migrated_tools_conf.xml.sample
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reports_wsgi.ini.sample
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shed_tool_conf.xml.sample
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tool_conf.xml.sample
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shed_tool_data_table_conf.xml.sample
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tool_data_table_conf.xml.sample
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tool_sheds_conf.xml.sample
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openid_conf.xml.sample
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universe_wsgi.ini.sample
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lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample
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tool-data/shared/ncbi/builds.txt.sample
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tool-data/shared/ensembl/builds.txt.sample
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tool-data/shared/ucsc/builds.txt.sample
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tool-data/shared/ucsc/publicbuilds.txt.sample
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tool-data/shared/igv/igv_build_sites.txt.sample
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tool-data/shared/rviewer/rviewer_build_sites.txt.sample
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tool-data/*.sample
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static/welcome.html.sample
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"
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./scripts/copy_sample_files.sh
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# Create any missing config/location files
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for sample in $SAMPLES; do
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file=`echo $sample | sed -e 's/\.sample$//'`
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if [ ! -f "$file" -a -f "$sample" ]; then
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echo "Initializing $file from `basename $sample`"
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cp $sample $file
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fi
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done
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tool_shed=`./lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh $@`
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args=$@
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python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_webapp.pid --log-file=tool_shed_webapp.log $@
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if [ $? -eq 0 ] ; then
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bash ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh $@
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args=`echo $@ | sed "s#-\?-bootstrap_from_tool_shed $tool_shed##"`
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fi
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python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_webapp.pid --log-file=tool_shed_webapp.log $args
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Executable
+39
@@ -0,0 +1,39 @@
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#!/bin/bash
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SAMPLES="
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tool_shed_wsgi.ini.sample
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datatypes_conf.xml.sample
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external_service_types_conf.xml.sample
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migrated_tools_conf.xml.sample
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reports_wsgi.ini.sample
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shed_tool_conf.xml.sample
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tool_conf.xml.sample
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shed_tool_data_table_conf.xml.sample
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tool_data_table_conf.xml.sample
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tool_sheds_conf.xml.sample
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data_manager_conf.xml.sample
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shed_data_manager_conf.xml.sample
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openid_conf.xml.sample
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job_metrics_conf.xml.sample
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universe_wsgi.ini.sample
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lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample
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tool-data/shared/ncbi/builds.txt.sample
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tool-data/shared/ensembl/builds.txt.sample
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tool-data/shared/ucsc/builds.txt.sample
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tool-data/shared/ucsc/publicbuilds.txt.sample
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tool-data/shared/ucsc/ucsc_build_sites.txt.sample
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tool-data/shared/igv/igv_build_sites.txt.sample
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tool-data/shared/rviewer/rviewer_build_sites.txt.sample
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tool-data/*.sample
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static/welcome.html.sample
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"
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# Create any missing config/location files
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for sample in $SAMPLES; do
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file=${sample%.sample}
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if [ ! -f "$file" -a -f "$sample" ]; then
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echo "Initializing $file from `basename $sample`"
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cp $sample $file
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fi
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done
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