"""
Upload class
"""
import logging, urllib
from galaxy import jobs, util, web
from galaxy.util import Params
from galaxy.util.hash_util import hmac_new
from galaxy.web.base.controller import BaseUIController
log = logging.getLogger( __name__ )
[docs]class ASync( BaseUIController ):
@web.expose
[docs] 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
[docs] 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 = 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.get_tool( 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, name=data.name, info=data.info, dbkey=data.dbkey, data_type=data.ext )
# 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)
else:
#
# no data_id must be parameter submission
#
if params.data_type:
GALAXY_TYPE = params.data_type
elif params.galaxyFileFormat == 'wig': #this is an undocumented legacy special case
GALAXY_TYPE = 'wig'
else:
GALAXY_TYPE = params.GALAXY_TYPE or tool.outputs.values()[0].format
GALAXY_NAME = params.name or params.GALAXY_NAME or '%s query' % tool.name
GALAXY_INFO = params.info or params.GALAXY_INFO or params.galaxyDescription or ''
GALAXY_BUILD = params.dbkey or params.GALAXY_BUILD or params.galaxyFreeze or '?'
#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={}, num_jobs=1, job_errors=[] )