#!/usr/bin/env python
import sys
from deiis.rabbit import Message, MessageBus
destination = '/tmp/submission.json'
if len(sys.argv) > 1:
destination = sys.argv[1]
message = Message.Command('SAVE ' + destination, [])
bus = MessageBus()
bus.publish('results', message)
print 'Save command sent. Saving to ' + destination
import sys
from deiis.rabbit import Message, MessageBus
if __name__ == '__main__':
message = Message(body='start', route=sys.argv[1:])
bus = MessageBus()
bus.send(message)
print 'Processing ' + filename
fp = open(filename, 'r')
dataset = Serializer.parse(fp, DataSet)
fp.close()
# The list of services to send the questions to.
""" Kaichen Chen 0304 """
if not debug:
pipeline = ['mmr.core', 'tiler.concat', 'results']
else:
pipeline = ['splitter', 'mmr.core', 'tiler.concat', 'results']
""" kaichenc 0307 """
host = os.environ.get('HOST', 'localhost')
print "DEBUG: Current host of Message Bus: {}".format(host)
count=0
bus = MessageBus(host = host)
for index in range(0,10):
question = dataset.questions[index]
# for question in dataset.questions:
message = Message(body=question, route=pipeline)
bus.publish('expand.none', message)
# bus.publish('splitter', message)
count = count + 1
print 'Sent {} questions for ranking.'.format(count)
print 'Done.'
#!/usr/bin/env python
import sys
from deiis.rabbit import MessageBus, Message
# All the services that may be running.
all = ['splitter', 'mmr.hard', 'mmr.soft', 'mmr.core',
'expand.none', 'expand.snomed', 'expand.umls',
'tiler.concat',
'results'
]
# The shutdown message for the services.
die = Message.Command('DIE', [])
bus = MessageBus()
if len(sys.argv) > 1:
if sys.argv[1] == 'all':
services = all
else:
services = sys.argv[1:]
else:
services = all
# Send the shutdown message to each of the services.
for service in services:
print 'Terminating ' + service
bus.publish(service, die)
print 'Done.'
import os
print 'stop.py: called'
# All the services that may be running.
all = [
'mmr.hard', 'mmr.soft', 'mmr.core', 'expand.none', 'expand.snomed',
'expand.umls', 'tiler.concat', 'results', 'splitter'
]
# The shutdown message for the services.
die = Message.Command('DIE', [])
""" kaichenc 0307 """
host = os.environ.get('HOST', 'localhost')
print "DEBUG: Current host of Message Bus: {}".format(host)
bus = MessageBus(host=host)
if len(sys.argv) > 1:
if sys.argv[1] == 'all':
services = all
else:
services = sys.argv[1:]
else:
services = all
# Send the shutdown message to each of the services.
for service in services:
print 'Terminating ' + service
bus.publish(service, die)
print 'Done.'
from deiis.model import Serializer, DataSet, Question
if __name__ == '__main__':
if len(sys.argv) <= 2:
print 'Usage: python pipeline.py <data.json> <RabbitMQ_host>'
exit(1)
# filename = 'data/training.json'
filename = sys.argv[1]
print 'Processing ' + filename
fp = open(filename, 'r')
dataset = Serializer.parse(fp, DataSet)
fp.close()
# The list of services to send the questions to.
#pipeline = ['mmr.core', 'tiler.concat', 'results']
pipeline = ['mmr.core', 'tiler.concat', 'results']
#pipeline = ['splitter', 'mmr.core', 'tiler.concat', 'results']
count=0
bus = MessageBus()
for index in range(0,10):
question = dataset.questions[index]
# for question in dataset.questions:
message = Message(body=question, route=pipeline)
print(question.body)
bus.publish('expand.none', message)
count = count + 1
print 'Sent {} questions for ranking.'.format(count)
print 'Done.'
#!/usr/bin/env python
import sys
from deiis.rabbit import Message, MessageBus
""" kaichenc 0307 """
import os
print 'save.py: called'
destination = '/tmp/submission.json'
if len(sys.argv) > 1:
destination = sys.argv[1]
message = Message.Command('SAVE ' + destination, [])
""" kaichenc 0307 """
host = os.environ.get('HOST', 'localhost')
print "DEBUG: Current host of Message Bus: {}".format(host)
bus = MessageBus(host=host)
bus.publish('results', message)
# print 'Save command sent. Saving to ' + destination
print 'DEBUG: Save command sent.'
print 'kaichenc: please refer to ResultsCollector for final destination'
print 'kaichenc: default /tmp/submission.json in linux'
print 'kaichenc: if path invalid, always save to ./tmp/submission.json'
#!/usr/bin/env python
import sys
from deiis.rabbit import Message, MessageBus
from deiis.model import Serializer, DataSet, Question
host = os.environ.get('RABBITMQ_HOST')
if __name__ == '__main__':
if len(sys.argv) == 1:
print 'Usage: python pipeline.py <data.json>'
exit(1)
filename = sys.argv[1]
print 'Processing ' + filename
fp = open(filename, 'r')
dataset = Serializer.parse(fp, DataSet)
fp.close()
pipeline = ['expand.none', 'mmr.core', 'tiler.concat', 'results']
count = 0
bus = MessageBus(host=host)
for index in range(0, 10):
question = dataset.questions[index]
message = Message(body=question, route=pipeline)
bus.publish("splitter", message)
count = count + 1
print 'Sent {} questions for ranking.'.format(count)
print 'Done.'
u'The increased odds ratios with African Americans was retained in post-menopausal women, while the protective odds ratios for pregnancy, smoking and oral contraceptives (OCs) became stronger in pre-menopausal women. The pattern by duration and timing of use does not suggest an etiologic role for OCs or hormone replacement therapy. ',
u'beginSection': u'abstract',
u'document': u'http://www.ncbi.nlm.nih.gov/pubmed/16570277',
u'endSection': u'abstract'
}, {
u'offsetInBeginSection': 1044,
u'offsetInEndSection': 1221,
u'text':
u'The use of hormone replacement therapy in symptomatic postmenopausal women either with previously treated disease or with dormant tumors is discussed, but remains controversial.',
u'beginSection': u'abstract',
u'document': u'http://www.ncbi.nlm.nih.gov/pubmed/15006250',
u'endSection': u'abstract'
}]
}
logger = logging.getLogger('main')
message = Message(route=['tiler.concat', 'results'], body=input)
json = Serializer.to_pretty_json(message)
logger.info('publishing question')
bus = MessageBus()
bus.publish('mmr.core', json)
# bus.publish('mmr.soft', json)
# bus.publish('mmr.hard', json)
# logger.info('Waiting for the thread to stop')
# results.wait_for()
#
# logger.info('Killing the ranker services')
# message = Message.Command('DIE', route=['mmr.hard', 'mmr.core'])
# bus.publish('mmr.soft', Serializer.to_json(message))
logger.info('Done')
for token in sentence:
print token
print ''
if __name__ == '__main__':
splitter = Splitter()
tokenizer = Tokenizer()
printer = Printer()
services = (splitter, tokenizer, printer)
for service in services:
print 'Staring service ' + str(type(service))
service.start()
print 'Sending the message to the splitter'
message = Message(body="Goodbye cruel world. I am leaving you today.",
route=['tokenizer', 'printer'])
bus = MessageBus()
bus.publish('splitter', message)
print 'Sleeping...'
time.sleep(1)
print 'Stopping all the services'
for service in services:
service.stop()
print 'Done.'