Some more info I got:
Error Traceback:
AttributeError: 'NoneType' object has no attribute 'id'
URL: http://machine/Galaxy/tool_runner/upload_async_create
Module weberror.evalexception.middleware:364 in respond view
<< try:
__traceback_supplement__ = errormiddleware.Supplement,
self, environ
app_iter = self.application(environ,
detect_start_response)
try:
return_iter = list(app_iter)>> app_iter =
self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__
environ {'CONTENT_LENGTH': '-1', 'CONTENT_TYPE':
'application/x-www-form-urlencoded; charset=UTF-8', 'HTTP_A ...
CCEPT': 'application/json, text/javascript, */*',
'HTTP_ACCEPT_CHARSET': 'ISO-8859-1,utf-8;q=0.7,*;q=0.7',
'HTTP_ACCEPT_ENCODING': 'gzip,deflate', 'HTTP_ACCEPT_LANGUAGE':
'en-us,en;q=0.5', 'HTTP_AUTHORIZATION': 'Basic YmJlYW46Sk5pSDRaMDQ0',
'HTTP_CACHE_CONTROL': 'no-cache', 'HTTP_CONNECTION': 'Keep-Alive',
'HTTP_COOKIE': 'galaxysession=33005c171a3e324bad0e3b40bdfd0bf581598cb7
a85d7060724c2e6830ea5edab1193453c8172c04;
galaxysession=33005c171a3e324bb73b0945c58c488314c73c2a4e579af333d4f87d
dcb166851b77c5f9669d5782;
CMAP_USER_PREF=highlight%3D%3Bpixel_height%3D%3Bfont_size%3Dsmall%3Bim
age_type%3Dpng%3Blabel_features%3Dall%3Bref_species_acc%3D%3Baggregate
%3D%3Bscale_maps%3D1%3Bcorrs_to_map%3D%3Bstack_maps%3D%3Bshow_intraslo
t_corr%3D%3Bsplit_agg_ev%3D%3Bcomp_menu_order%3Ddisplay_order%3Blink_g
roup%3DUnknown%20Group%3Bomit_area_boxes%3D%3Bdata_source%3D',
'HTTP_HOST': 'machine', 'HTTP_PRAGMA': 'no-cache', 'HTTP_REFERER':
'http://machine/Galaxy/', 'HTTP_REMOTE_USER': 'erick@machine.com',
'HTTP_USER_AGENT': 'Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US;
rv:1.9.1.8) Gecko/20100202 (CK-BBS) Firefox/3.5.8',
'HTTP_X_REQUESTED_WITH': 'XMLHttpRequest', 'PATH_INFO':
'/tool_runner/upload_async_create', 'QUERY_STRING': '', 'REMOTE_ADDR':
'10.3.154.134', 'REQUEST_METHOD': 'POST', 'SCRIPT_NAME': '/Galaxy',
'SERVER_NAME': 'machine', 'SERVER_PORT': '8080', 'SERVER_PROTOCOL':
'HTTP/1.1', 'paste.config': {'__file__': '/galaxy/universe_wsgi.ini',
'admin_users': 'erick@machine.com', 'apache_xsendfile': 'true',
'brand': 'GRID', 'bugs_email': 'mailto:erick.antezana@machine.com',
'bx_display_sites': 'main', 'cookie_path': '/Galaxy',
'database_connection': 'mysql://galaxy:test@mysql_DB/galaxygrid',
'database_engine_option_pool_recycle': '7200',
'datatype_converters_config_file': 'datatype_converters_conf.xml',
'datatype_converters_path': '/galaxy/lib/galaxy/datatypes/converters',
'datatype_indexers_path': '/galaxy/lib/galaxy/datatypes/indexers',
'debug': 'True', 'default_cluster_job_runner': 'sge:///',
'enable_tracks': 'True', 'error_email_to':
'erick.antezana@machine.com', 'file_path': 'database/files',
'gbrowse_display_sites': 'main,test,tair', 'here':
'/tools/bioinfo/shared/app/galaxy/dev', 'id_secret': 'test',
'job_queue_cleanup_interval': '30', 'job_scheduler_policy':
'galaxy.jobs.schedulingpolicy.roundrobin:UserRoundRobin',
'log_actions': 'True', 'log_events': 'True', 'log_level': 'DEBUG',
'log_memory_usage': 'False', 'logo_url': '/Galaxy', 'new_file_path':
'database/tmp', 'new_user_dataset_access_role_default_private':
'False', 'remote_user_logout_href': 'http://machine/',
'remote_user_maildomain': 'machine.com', 'require_login': 'True',
'sendmail_path': '/usr/sbin/sendmail', 'session_data_dir':
'/galaxy/database/beaker_sessions', 'session_key': 'galaxysessions',
'session_secret': 'test_grid', 'session_type': 'file',
'set_metadata_externally': 'False', 'start_job_runners': 'sge',
'static_cache_time': '360', 'static_dir': '/galaxy/static/',
'static_enabled': 'True', 'static_favicon_dir':
'/galaxy/static/favicon.ico', 'static_images_dir':
'/galaxy/static/images', 'static_scripts_dir':
'/galaxy/static/scripts/', 'static_style_dir':
'/galaxy/static/june_2007_style/blue', 'tool_config_file':
'tool_conf.xml', 'tool_data_path': 'tool-data', 'tool_path': 'tools',
'ucsc_display_sites': 'main,test,archaea,ucla', 'use_beaker_session':
'True', 'use_interactive': 'True', 'use_lint': 'False',
'use_new_layout': 'true', 'use_remote_user': 'True', 'wiki_url':
'http://machine/mediawiki/index.php/Galaxy_Install'}, 'paste.cookies':
(<simplecookie: cmap_user_pref="highlight%3D%3Bpixel_height%3D%3Bfont_size%3Dsmall%3Bi
mage_type%3Dpng%3Blabel_features%3Dall%3Bref_species_acc%3D%3Baggregat
e%3D%3Bscale_maps%3D1%3Bcorrs_to_map%3D%3Bstack_maps%3D%3Bshow_intrasl
ot_corr%3D%3Bsplit_agg_ev%3D%3Bcomp_menu_order%3Ddisplay_order%3Blink_
group%3DUnknown%20Group%3Bomit_area_boxes%3D%3Bdata_source%3D" galaxysession="33005c171a3e324bb73b0945c58c488314c73c2a4e579af333d4f87
ddcb166851b77c5f9669d5782">,
'galaxysession=33005c171a3e324bad0e3b40bdfd0bf581598cb7a85d7060724c2e6
830ea5edab1193453c8172c04;
galaxysession=33005c171a3e324bb73b0945c58c488314c73c2a4e579af333d4f87d
dcb166851b77c5f9669d5782;
CMAP_USER_PREF=highlight%3D%3Bpixel_height%3D%3Bfont_size%3Dsmall%3Bim
age_type%3Dpng%3Blabel_features%3Dall%3Bref_species_acc%3D%3Baggregate
%3D%3Bscale_maps%3D1%3Bcorrs_to_map%3D%3Bstack_maps%3D%3Bshow_intraslo
t_corr%3D%3Bsplit_agg_ev%3D%3Bcomp_menu_order%3Ddisplay_order%3Blink_g
roup%3DUnknown%20Group%3Bomit_area_boxes%3D%3Bdata_source%3D'),
'paste.evalexception':
<weberror.evalexception.middleware.evalexception object="" at="" 0x18e7d5d0="">, 'paste.evalexception.debug_count': 1273231204,
'paste.expected_exceptions': [<class 'paste.httpexceptions.httpexception'="">], 'paste.httpexceptions':
<paste.httpexceptions.httpexceptionhandler object="" at="" 0x18c4d250="">,
'paste.httpserver.thread_pool': <paste.httpserver.threadpool object="" at="" 0x15b953d0="">, 'paste.printdebug_listeners': [<cstringio.stringo object="" at="" 0x19223ab0="">, <paste.script.serve.lazywriter object="" at="" 0x15ade610="">],
'paste.recursive.forward': <paste.recursive.forwarder from="" galaxy="">,
'paste.recursive.include': <paste.recursive.includer from="" galaxy="">,
'paste.recursive.include_app_iter': <paste.recursive.includerappiter from="" galaxy="">, 'paste.recursive.script_name': '/Galaxy',
'paste.remove_printdebug': <function remove_printdebug="" at="" 0x197fd668="">,
'paste.throw_errors': True, 'weberror.evalexception':
<weberror.evalexception.middleware.evalexception object="" at="" 0x18e7d5d0="">, 'weberror.evalexception.debug_count': 1273231204,
'webob._parsed_post_vars': (MultiDict([('tool_id', 'upload1'),
('tool_state', '8002544b0200006464613837376461383730386161373764386439
61396230633436333936666536396432646636623a3762323236363639366336353733
3232336132303232356237623563323236363639366336353566363436313734363135
6332323361323036653735366336633263323035633232356635663639366536343635
3738356635663563323233613230333032633230356332323733373036313633363535
6637343666356637343631363235633232336132303665373536633663326332303563
3232373537323663356637303631373337343635356332323361323035633232346536
6636653635356332323764356432323263323032323566356637303631363736353566
3566323233613230333032633230323236363639366336353566373437393730363532
3233613230323235633232363137353734366635633232323232633230323236363639
3663363537333566366436353734363136343631373436313232336132303232376235
6332323636363936633635356637343739373036353563323233613230356332323631
3735373436663563323232633230356332323566356636333735373237323635366537
3435663633363137333635356635663563323233613230333233383764323232633230
3232363137333739366536333566363436313734363137333635373437333232336132
3032323563323234653666366536353563323232323263323032323634363236623635
3739323233613230323235623563323233663563323232633230356332323366356332
3235643232376471002e'),
('file_type', 'auto'), ('async_datasets', 'None'),
('files_0|file_data', 'Q68LV4.gff3'), ('files_0|url_paste', ''),
('dbkey', '?')]), <fakecgibody at="" 192fe710="" viewing="" multidict([('to...?')])="">), 'webob._parsed_query_vars': (MultiDict([]),
''), 'wsgi.errors': <paste.script.serve.lazywriter object="" at="" 0x15ade610="">, 'wsgi.input': <fakecgibody at="" 192fe710="" viewing="" multidict([('to...?')])="">, 'wsgi.multiprocess': False,
'wsgi.multithread': True, 'wsgi.run_once': False, 'wsgi.url_scheme':
'http', 'wsgi.version': (1, 0)}
listeners [<cstringio.stringo object="" at="" 0x19223ab0="">,
<paste.script.serve.lazywriter object="" at="" 0x15ade="" ...="" 610="">]
logged <cstringio.stringo object="" at="" 0x19223ab0="">
remove_printdebug <function remove_printdebug="" at="" 0x197fd668="">
removed []
replacement_stdout <paste.debug.prints.teefile object="" at="" 0x192fed10="">
self <paste.debug.prints.printdebugmiddleware object="" at="" 0x18c5b110="">
start_response <function detect_start_response="" at="" 0x193e86e0="">
view
<< try:
status, headers, body = wsgilib.intercept_output(
environ, self.app)
if status is None:
# Some error occurred>> environ, self.app)
Module paste.wsgilib:539 in intercept_output view
<< data.append(headers)
return output.write
app_iter = application(environ, replacement_start_response)
if data[0] is None:
return (None, None, app_iter)>> app_iter =
application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ view
<< environ['paste.recursive.script_name'] = my_script_name
try:
return self.application(environ, start_response)
except ForwardRequestException, e:
middleware = CheckForRecursionMiddleware(>> return
self.application(environ, start_response)
Module galaxy.web.framework.middleware.remoteuser:102 in __call__
view
<< """
return self.error( start_response, title,
message )
return self.app( environ, start_response )
else:
title = "Access to Galaxy is denied">> return
self.app( environ, start_response )
Module paste.httpexceptions:632 in __call__ view
<< []).append(HTTPException)
try:
return self.application(environ, start_response)
except HTTPException, exc:
return exc(environ, start_response)>> return
self.application(environ, start_response)
Module galaxy.web.framework.base:125 in __call__ view
<< kwargs.pop( '_', None )
try:
body = method( trans, **kwargs )
except Exception, e:
body = self.handle_controller_exception( e, trans,
**kwargs )>> body = method( trans, **kwargs )
Module galaxy.web.framework:62 in decorator view
<< def decorator( self, trans, *args, **kwargs ):
trans.response.set_content_type( "text/javascript" )
return simplejson.dumps( func( self, trans, *args,
**kwargs ) )
if not hasattr(func, '_orig'):
decorator._orig = func>> return simplejson.dumps( func(
self, trans, *args, **kwargs ) )
Module galaxy.web.controllers.tool_runner:186 in upload_async_create
view
<< else:
tool_state = tool.new_state( trans )
errors = tool.update_state( trans, tool.inputs,
tool_state.inputs, kwd, update_only = True )
datasets = []
dataset_upload_inputs = []>> errors = tool.update_state(
trans, tool.inputs, tool_state.inputs, kwd, update_only = True )
Module galaxy.tools:1070 in update_state view
<< else:
incoming_value = get_incoming_value( incoming,
key, None )
value, error = check_param( trans, input,
incoming_value, context )
# If a callback was provided, allow it to
process the value
if item_callback:>> value, error =
check_param( trans, input, incoming_value, context )
Module galaxy.tools.parameters:56 in check_param view
<< if value is not None or isinstance(param,
DataToolParameter):
# Convert value from HTML representation
value = param.from_html( value, trans, param_values )
# Allow the value to be converted if neccesary
filtered_value = param.filter_value( value, trans,
param_values )>> value = param.from_html( value, trans, param_values
)
Module galaxy.tools.parameters.basic:564 in from_html
context <galaxy.util.expressions.expressioncontext object="" at="" 0x19a54bd0="">
self <galaxy.tools.parameters.basic.genomebuildparameter object="" at="" 0x17eaad50="">
trans <galaxy.web.framework.universewebtransaction object="" at="" 0x193ee2d0="">
value u'?'
view
<< value = value.split( "\n" )
return UnvalidatedValue( value )
legal_values = self.get_legal_values( trans, context )
if isinstance( value, list ):
if not(self.repeat):>> legal_values =
self.get_legal_values( trans, context )
Module galaxy.tools.parameters.basic:734 in get_legal_values
other_values <galaxy.util.expressions.expressioncontext object="" at="" 0x19a54bd0="">
self <galaxy.tools.parameters.basic.genomebuildparameter object="" at="" 0x17eaad50="">
trans <galaxy.web.framework.universewebtransaction object="" at="" 0x193ee2d0="">
view
<< yield build_name, dbkey, ( dbkey == last_used_build )
def get_legal_values( self, trans, other_values ):
return set( dbkey for dbkey, _ in trans.db_builds )
class ColumnListParameter( SelectToolParameter ):>> return set(
dbkey for dbkey, _ in trans.db_builds )
Module galaxy.web.framework:659 in db_builds
dbnames []
self <galaxy.web.framework.universewebtransaction object="" at="" 0x193ee2d0="">
view
<< dbnames = list()
datasets = self.sa_session.query(
self.app.model.HistoryDatasetAssociation ) \
.filter_by( deleted=False,
history_id=self.history.id, extension="len" )
if datasets.count() > 0:
dbnames.append( (util.dbnames.default_value,
'--------- User Defined Builds ----------') )>> .filter_by(
deleted=False, history_id=self.history.id, extension="len" )
AttributeError: 'NoneType' object has no attribute 'id'
