mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-28 02:58:18 +08:00
Ramkrishna Chakrabarty
3d72267f44
- eliminated the transfer_datasets.ini config file - eliminated the data transfer user - now the admin user initiating the data transfer is used as the data transfer user. - the admin user is provided the add_library_item permission before data transfer if they dont have it - sample update & data transfer amqp messages now includes api_key
96 lines
3.3 KiB
Python
96 lines
3.3 KiB
Python
'''
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This script gets barcode data from a barcode scanner using serial communication
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and sends the state representated by the barcode scanner & the barcode string
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to the Galaxy LIMS RabbitMQ server. The message is sent in XML which has 2 tags,
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barcode & state. The state of the scanner should be set in the galaxy_amq.ini
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file as a configuration variable.
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'''
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from amqplib import client_0_8 as amqp
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import ConfigParser
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import sys, os
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import serial
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import array
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import time
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import optparse
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xml = \
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''' <sample>
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<barcode>%(BARCODE)s</barcode>
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<state>%(STATE)s</state>
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<api_key>%(API_KEY)s</api_key>
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</sample>'''
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def handle_scan(states, amqp_config, barcode):
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if states.get(barcode[:2], None):
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values = dict( BARCODE=barcode[2:],
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STATE=states.get(barcode[:2]),
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API_KEY=amqp_config['api_key'] )
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print values
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data = xml % values
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print data
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conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'],
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userid=amqp_config['userid'],
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password=amqp_config['password'],
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virtual_host=amqp_config['virtual_host'],
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insist=False)
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chan = conn.channel()
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msg = amqp.Message(data,
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content_type='text/plain',
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application_headers={'msg_type': 'sample_state_update'})
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msg.properties["delivery_mode"] = 2
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chan.basic_publish(msg,
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exchange=amqp_config['exchange'],
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routing_key=amqp_config['routing_key'])
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chan.close()
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conn.close()
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def recv_data(states, amqp_config, s):
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while True:
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bytes = s.inWaiting()
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if bytes:
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print '%i bytes recvd' % bytes
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msg = s.read(bytes)
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print msg
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handle_scan(states, amqp_config, msg.strip())
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def main():
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parser = optparse.OptionParser()
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parser.add_option('-c', '--config-file', help='config file with all the AMQP config parameters',
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dest='config_file', action='store')
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parser.add_option('-p', '--port', help='Name of the port where the scanner is connected',
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dest='port', action='store')
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(opts, args) = parser.parse_args()
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config = ConfigParser.ConfigParser()
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config.read(opts.config_file)
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amqp_config = {}
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states = {}
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for option in config.options("galaxy:amqp"):
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amqp_config[option] = config.get("galaxy:amqp", option)
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# abort if api_key is not set in the config file
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if not amqp_config['api_key']:
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print 'Error: Set the api_key config variable in the config file before starting the amqp_publisher script.'
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sys.exit( 1 )
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count = 1
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while True:
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section = 'scanner%i' % count
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if config.has_section(section):
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states[config.get(section, 'prefix')] = config.get(section, 'state')
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count = count + 1
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else:
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break
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print amqp_config
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print states
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s = serial.Serial(int(opts.port))
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print 'Port %s is open: %s' %( opts.port, s.isOpen())
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recv_data(states, amqp_config, s)
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s.close()
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print 'Port %s is open: %s' %( opts.port, s.isOpen())
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if __name__ == '__main__':
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main()
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