mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Ramkrishna Chakrabarty
6a9ab2813a
- added web api methods to update requests, samples using restful api - removed the old ad-doc web api - modified the data transfer code to use this api - code cleanup
168 lines
6.9 KiB
Python
168 lines
6.9 KiB
Python
#/usr/bin/python
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from datetime import datetime
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import sys
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import optparse
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import os
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import time
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import logging
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assert sys.version_info[:2] >= ( 2, 4 )
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new_path = [ os.path.join( os.getcwd(), "lib" ) ]
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new_path.extend( sys.path[1:] ) # remove scripts/ from the path
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sys.path = new_path
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from galaxy import eggs
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from galaxy.model.custom_types import *
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import pkg_resources
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pkg_resources.require( "psycopg2" )
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import psycopg2
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pkg_resources.require( "SQLAlchemy >= 0.4" )
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from sqlalchemy import *
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from sqlalchemy.orm import sessionmaker
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#logging.basicConfig(level=logging.DEBUG)
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#log = logging.getLogger( 'GalaxyDbInterface' )
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class GalaxyDbInterface(object):
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def __init__(self, dbstr):
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self.dbstr = dbstr
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self.db_engine = create_engine(self.dbstr)
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self.db_engine.echo = False
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self.metadata = MetaData(self.db_engine)
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self.session = sessionmaker(bind=self.db_engine)
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self.event_table = Table('sample_event', self.metadata, autoload=True )
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self.sample_table = Table('sample', self.metadata, autoload=True )
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self.sample_dataset_table = Table('sample_dataset', self.metadata, autoload=True )
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self.request_table = Table('request', self.metadata, autoload=True )
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self.request_event_table = Table('request_event', self.metadata, autoload=True )
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self.state_table = Table('sample_state', self.metadata, autoload=True )
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def get_sample_id(self, field_name='bar_code', value=None):
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if not value:
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return -1
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sample_id = -1
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if field_name =='name':
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stmt = select(columns=[self.sample_table.c.id],
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whereclause=self.sample_table.c.name==value)
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result = stmt.execute()
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sample_id = result.fetchone()[0]
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elif field_name == 'bar_code':
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stmt = select(columns=[self.sample_table.c.id],
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whereclause=self.sample_table.c.bar_code==value)
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result = stmt.execute()
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x = result.fetchone()
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if x:
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sample_id = x[0]
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#log.debug('Sample ID: %i' % sample_id)
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return sample_id
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return -1
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def get_request_id(self, sample_id):
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query = select(columns=[self.sample_table.c.request_id],
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whereclause=self.sample_table.c.id==sample_id)
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request_id = query.execute().fetchall()[0][0]
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return request_id
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def current_state(self, sample_id):
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'''
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This method returns the current state of the sample for the given sample_id
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'''
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stmt = select(columns=[self.event_table.c.sample_state_id],
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whereclause=self.event_table.c.sample_id==sample_id,
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order_by=self.event_table.c.update_time.desc())
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result = stmt.execute()
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all_states = result.fetchall()
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current_state_id = all_states[0][0]
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return current_state_id
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def all_possible_states(self, sample_id):
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subsubquery = select(columns=[self.sample_table.c.request_id],
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whereclause=self.sample_table.c.id==sample_id)
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self.request_id = subsubquery.execute().fetchall()[0][0]
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#log.debug('REQUESTID: %i' % self.request_id)
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subquery = select(columns=[self.request_table.c.request_type_id],
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whereclause=self.request_table.c.id==self.request_id)
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request_type_id = subquery.execute().fetchall()[0][0]
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#log.debug('REQUESTTYPEID: %i' % request_type_id)
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query = select(columns=[self.state_table.c.id, self.state_table.c.name],
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whereclause=self.state_table.c.request_type_id==request_type_id,
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order_by=self.state_table.c.id.asc())
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states = query.execute().fetchall()
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#log.debug('POSSIBLESTATES: '+ str(states))
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return states
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def change_state(self, sample_id, new_state=None):
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'''
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This method changes the state of the sample to the the 'new_state'
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'''
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if not new_state:
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return
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new_state_id = -1
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# find the state_id for this new state in the list of possible states
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possible_states = self.all_possible_states(sample_id)
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for state_id, state_name in possible_states:
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if new_state == state_name:
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new_state_id = state_id
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if new_state_id == -1:
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return
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#log.debug('Updating sample_id %i state to %s' % (sample_id, new_state))
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i = self.event_table.insert()
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i.execute(update_time=datetime.utcnow(),
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create_time=datetime.utcnow(),
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sample_id=sample_id,
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sample_state_id=int(new_state_id),
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comment='Update by barcode scan')
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# if all the samples for this request are in the final state
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# then change the request state to 'Complete'
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result = select(columns=[self.sample_table.c.id],
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whereclause=self.sample_table.c.request_id==self.request_id).execute()
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sample_id_list = result.fetchall()
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request_complete = True
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for sid in sample_id_list:
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current_state_id = self.current_state(sid[0])
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if current_state_id != possible_states[-1][0]:
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request_complete = False
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break
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if request_complete:
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request_state = 'Complete'
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#log.debug('Updating request_id %i state to "%s"' % (self.request_id, request_state))
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i = self.request_event_table.insert()
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i.execute(update_time=datetime.utcnow(),
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create_time=datetime.utcnow(),
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request_id=self.request_id,
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state=request_state,
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comment='All samples of this request have finished processing.')
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def set_sample_dataset_status(self, id, new_status, msg=None):
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u = self.sample_dataset_table.update(whereclause=self.sample_dataset_table.c.id==int(id))
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u.execute(status=new_status)
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if new_status == 'Error':
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u.execute(error_msg=msg)
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else:
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u.execute(error_msg='')
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return
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if __name__ == '__main__':
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print '''This file should not be run directly. To start the Galaxy AMQP Listener:
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%sh run_galaxy_listener.sh'''
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dbstr = 'postgres://postgres:postgres@localhost/g2'
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parser = optparse.OptionParser()
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parser.add_option('-n', '--name', help='name of the sample field', dest='name', \
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action='store', default='bar_code')
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parser.add_option('-v', '--value', help='value of the sample field', dest='value', \
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action='store')
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parser.add_option('-s', '--state', help='new state of the sample', dest='state', \
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action='store')
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(opts, args) = parser.parse_args()
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gs = GalaxyDbInterface(dbstr)
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sample_id = gs.get_sample_id(field_name=opts.name, value=opts.value)
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gs.change_state(sample_id, opts.state)
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