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)
# 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})
# Use provided URL or fallback to tool action
url = URL or tool.action
# Does url already have query params?
if '?' in url:
url_join_char = '&'
else:
url_join_char = '?'
url = "%s%s%s" % (url, url_join_char,
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()
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)
# redirect to main when getting no parameters
if not kwd:
return trans.response.send_redirect("/index")
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 + f'/async/{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
TOOL_OUTPUT_TYPE = None
for key, obj in tool.outputs.items():
try:
TOOL_OUTPUT_TYPE = obj.format
params[key] = data.id
break
except Exception:
# exclude outputs different from ToolOutput (e.g. collections) from the previous assumption
continue
if TOOL_OUTPUT_TYPE is None:
raise Exception("Error: ToolOutput object not found")
original_history = trans.sa_session.query(
trans.app.model.History).get(data.history_id)
tool.execute(trans, incoming=params, history=original_history)
else:
log.debug('async error -> %s' % STATUS)
trans.log_event('Async error -> %s' % STATUS)
data.state = data.blurb = "error"
data.info = "Error -> %s" % STATUS
trans.sa_session.flush()
return f"Data {data_id} with status {STATUS} received. OK"
else:
#
# no data_id must be parameter submission
#
GALAXY_TYPE = None
if params.data_type:
GALAXY_TYPE = params.data_type
elif params.galaxyFileFormat == 'wig': # this is an undocumented legacy special case
GALAXY_TYPE = 'wig'
elif params.GALAXY_TYPE:
GALAXY_TYPE = params.GALAXY_TYPE
else:
# Assume there is exactly one output
outputs_count = 0
for obj in tool.outputs.values():
try:
GALAXY_TYPE = obj.format
outputs_count += 1
except Exception:
# exclude outputs different from ToolOutput (e.g. collections) from the previous assumption
# a collection object does not have the 'format' attribute, so it will throw an exception
continue
if outputs_count > 1:
raise Exception(
"Error: the tool should have just one output")
if GALAXY_TYPE is None:
raise Exception("Error: ToolOutput object not found")
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
trans.history.add_dataset(data, genome_build=GALAXY_BUILD)
trans.sa_session.add(trans.history)
trans.sa_session.flush()
# Need to explicitly create the file
data.dataset.object_store.create(data)
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 + f'/async/{tool_id}/{data.id}/{key}'
params.update({'GALAXY_URL': galaxy_url})
params.update({'data_id': data.id})
# Use provided URL or fallback to tool action
url = URL or tool.action
# Does url already have query params?
if '?' in url:
url_join_char = '&'
else:
url_join_char = '?'
url = "{}{}{}".format(url, url_join_char,
urlencode(params.flatten()))
log.debug("connecting to -> %s" % url)
trans.log_event("Async connecting to -> %s" % url)
text = requests.get(url).text.strip()
if not text.endswith('OK'):
raise Exception(text)
data.state = data.blurb = data.states.RUNNING
except Exception as e:
data.info = unicodify(e)
data.state = data.blurb = data.states.ERROR
trans.sa_session.flush()
return trans.fill_template('root/tool_runner.mako',
out_data={},
num_jobs=1,
job_errors=[])
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()
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)
# redirect to main when getting no parameters
if not kwd:
return trans.response.send_redirect("/index")
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
TOOL_OUTPUT_TYPE = None
for key, obj in tool.outputs.items():
try:
TOOL_OUTPUT_TYPE = obj.format
params[key] = data.id
break
except Exception:
# exclude outputs different from ToolOutput (e.g. collections) from the previous assumption
continue
if TOOL_OUTPUT_TYPE is None:
raise Exception("Error: ToolOutput object not found")
original_history = trans.sa_session.query(trans.app.model.History).get(data.history_id)
tool.execute(trans, incoming=params, history=original_history)
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
#
GALAXY_TYPE = None
if params.data_type:
GALAXY_TYPE = params.data_type
elif params.galaxyFileFormat == 'wig': # this is an undocumented legacy special case
GALAXY_TYPE = 'wig'
elif params.GALAXY_TYPE:
GALAXY_TYPE = params.GALAXY_TYPE
else:
# Assume there is exactly one output
outputs_count = 0
for obj in tool.outputs.values():
try:
GALAXY_TYPE = obj.format
outputs_count += 1
except Exception:
# exclude outputs different from ToolOutput (e.g. collections) from the previous assumption
# a collection object does not have the 'format' attribute, so it will throw an exception
continue
if outputs_count > 1:
raise Exception("Error: the tool should have just one output")
if GALAXY_TYPE is None:
raise Exception("Error: ToolOutput object not found")
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})
# Use provided URL or fallback to tool action
url = URL or tool.action
# Does url already have query params?
if '?' in url:
url_join_char = '&'
else:
url_join_char = '?'
url = "%s%s%s" % (url, url_join_char, urlencode(params.flatten()))
log.debug("connecting to -> %s" % url)
trans.log_event("Async connecting to -> %s" % url)
text = requests.get(url).text.strip()
if not text.endswith('OK'):
raise Exception(text)
data.state = data.blurb = data.states.RUNNING
except Exception as e:
data.info = str(e)
data.state = data.blurb = data.states.ERROR
trans.sa_session.flush()
return trans.fill_template('root/tool_runner.mako', out_data={}, num_jobs=1, job_errors=[])