/lib/galaxy/web/controllers/async.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 138 lines · 90 code · 25 blank · 23 comment · 22 complexity · 8f31dd26033f301dc9a03d7aad7c601c MD5 · raw file
- """
- Upload class
- """
- from galaxy.web.base.controller import *
- from galaxy import jobs, util, datatypes, web
- import logging, urllib, sys
- from galaxy.util.hash_util import *
- log = logging.getLogger( __name__ )
- class ASync( BaseUIController ):
- @web.expose
- def default(self, trans, tool_id=None, data_id=None, data_secret=None, **kwd):
- """Catches the tool id and redirects as needed"""
- return self.index( trans, tool_id=tool_id, data_id=data_id, data_secret=data_secret, **kwd)
- @web.expose
- def index(self, trans, tool_id=None, data_secret=None, **kwd):
- """Manages ascynchronous connections"""
- if tool_id is None:
- return "tool_id argument is required"
- tool_id=str(tool_id)
- #log.debug('async params -> %s' % kwd)
- # redirect to main when getting no parameters
- if not kwd:
- return trans.response.send_redirect( "/index" )
- history = trans.get_history( create=True )
- params = util.Params(kwd, sanitize=False)
- STATUS = params.STATUS
- URL = params.URL
- data_id = params.data_id
- log.debug('async dataid -> %s' % data_id)
- trans.log_event( 'Async dataid -> %s' % str(data_id) )
- # initialize the tool
- toolbox = self.get_toolbox()
- tool = toolbox.tools_by_id.get(tool_id, '')
- if not tool:
- return "Tool with id %s not found" % tool_id
-
- #
- # we have an incoming data_id
- #
- if data_id:
- if not URL:
- return "No URL parameter was submitted for data %s" % data_id
- data = trans.sa_session.query( trans.model.HistoryDatasetAssociation ).get( data_id )
-
- if not data:
- return "Data %s does not exist or has already been deleted" % data_id
- if STATUS == 'OK':
- key = hmac_new( trans.app.config.tool_secret, "%d:%d" % ( data.id, data.history_id ) )
- if key != data_secret:
- return "You do not have permission to alter data %s." % data_id
- # push the job into the queue
- data.state = data.blurb = data.states.RUNNING
- log.debug('executing tool %s' % tool.id)
- trans.log_event( 'Async executing tool %s' % tool.id, tool_id=tool.id )
- galaxy_url = trans.request.base + '/async/%s/%s/%s' % ( tool_id, data.id, key )
- galaxy_url = params.get("GALAXY_URL",galaxy_url)
- params = dict( url=URL, GALAXY_URL=galaxy_url )
- # Assume there is exactly one output file possible
- params[tool.outputs.keys()[0]] = data.id
- tool.execute( trans, incoming=params )
- else:
- log.debug('async error -> %s' % STATUS)
- trans.log_event( 'Async error -> %s' % STATUS )
- data.state = data.blurb = jobs.JOB_ERROR
- data.info = "Error -> %s" % STATUS
-
- trans.sa_session.flush()
-
- return "Data %s with status %s received. OK" % (data_id, STATUS)
-
- #
- # no data_id must be parameter submission
- #
- if not data_id and len(params)>3:
-
- if params.galaxyFileFormat == 'wig':
- GALAXY_TYPE = 'wig'
- else:
- GALAXY_TYPE = params.GALAXY_TYPE or 'interval'
-
- GALAXY_NAME = params.GALAXY_NAME or '%s query' % tool.name
- GALAXY_INFO = params.GALAXY_INFO or params.galaxyDescription or ''
- GALAXY_BUILD = params.GALAXY_BUILD or params.galaxyFreeze or 'hg17'
-
- #data = datatypes.factory(ext=GALAXY_TYPE)()
- #data.ext = GALAXY_TYPE
- #data.name = GALAXY_NAME
- #data.info = GALAXY_INFO
- #data.dbkey = GALAXY_BUILD
- #data.state = jobs.JOB_OK
- #history.datasets.add_dataset( data )
-
- data = trans.app.model.HistoryDatasetAssociation( create_dataset=True, sa_session=trans.sa_session, extension=GALAXY_TYPE )
- trans.app.security_agent.set_all_dataset_permissions( data.dataset, trans.app.security_agent.history_get_default_permissions( trans.history ) )
- data.name = GALAXY_NAME
- data.dbkey = GALAXY_BUILD
- data.info = GALAXY_INFO
- trans.sa_session.add( data ) #Need to add data to session before setting state (setting state requires that the data object is in the session, but this may change)
- data.state = data.states.NEW
- open( data.file_name, 'wb' ).close() #create the file
- trans.history.add_dataset( data, genome_build=GALAXY_BUILD )
- trans.sa_session.add( trans.history )
- trans.sa_session.flush()
- trans.log_event( "Added dataset %d to history %d" %(data.id, trans.history.id ), tool_id=tool_id )
- try:
- key = hmac_new( trans.app.config.tool_secret, "%d:%d" % ( data.id, data.history_id ) )
- galaxy_url = trans.request.base + '/async/%s/%s/%s' % ( tool_id, data.id, key )
- params.update( { 'GALAXY_URL' :galaxy_url } )
- params.update( { 'data_id' :data.id } )
- url = tool.action + '?' + urllib.urlencode( params.flatten() )
- log.debug("connecting to -> %s" % url)
- trans.log_event( "Async connecting to -> %s" % url )
- text = urllib.urlopen(url).read(-1)
- text = text.strip()
- if not text.endswith('OK'):
- raise Exception, text
- data.state = data.blurb = data.states.RUNNING
- except Exception, e:
- data.info = str(e)
- data.state = data.blurb = data.states.ERROR
-
- trans.sa_session.flush()
- return trans.fill_template( 'tool_executed.mako', history=history, toolbox=toolbox, tool=tool, util=util, out_data={} )