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=33005c171a3e324bad0e3b40bdfd0bf581598cb7a85d7060724c2e6830ea5edab1193453c8172c04; galaxysession=33005c171a3e324bb73b0945c58c488314c73c2a4e579af333d4f87ddcb166851b77c5f9669d5782; CMAP_USER_PREF=highlight%3D%3Bpixel_height%3D%3Bfont_size%3Dsmall%3Bimage_type%3Dpng%3Blabel_features%3Dall%3Bref_species_acc%3D%3Baggregate%3D%3Bscale_maps%3D1%3Bcorrs_to_map%3D%3Bstack_maps%3D%3Bshow_intraslot_corr%3D%3Bsplit_agg_ev%3D%3Bcomp_menu_order%3Ddisplay_order%3Blink_group%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%3Bimage_type%3Dpng%3Blabel_features%3Dall%3Bref_species_acc%3D%3Baggregate%3D%3Bscale_maps%3D1%3Bcorrs_to_map%3D%3Bstack_maps%3D%3Bshow_intraslot_corr%3D%3Bsplit_agg_ev%3D%3Bcomp_menu_order%3Ddisplay_order%3Blink_group%3DUnknown%20Group%3Bomit_area_boxes%3D%3Bdata_source%3D' galaxysession='33005c171a3e324bb73b0945c58c488314c73c2a4e579af333d4f87ddcb166851b77c5f9669d5782'>, 'galaxysession=33005c171a3e324bad0e3b40bdfd0bf581598cb7a85d7060724c2e6830ea5edab1193453c8172c04; galaxysession=33005c171a3e324bb73b0945c58c488314c73c2a4e579af333d4f87ddcb166851b77c5f9669d5782; CMAP_USER_PREF=highlight%3D%3Bpixel_height%3D%3Bfont_size%3Dsmall%3Bimage_type%3Dpng%3Blabel_features%3Dall%3Bref_species_acc%3D%3Baggregate%3D%3Bscale_maps%3D1%3Bcorrs_to_map%3D%3Bstack_maps%3D%3Bshow_intraslot_corr%3D%3Bsplit_agg_ev%3D%3Bcomp_menu_order%3Ddisplay_order%3Blink_group%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', '8002544b020000646461383737646138373038616137376438643961396230633436333936666536396432646636623a37623232363636393663363537333232336132303232356237623563323236363639366336353566363436313734363135633232336132303665373536633663326332303563323235663566363936653634363537383566356635633232336132303330326332303563323237333730363136333635356637343666356637343631363235633232336132303665373536633663326332303563323237353732366335663730363137333734363535633232336132303563323234653666366536353563323237643564323232633230323235663566373036313637363535663566323233613230333032633230323236363639366336353566373437393730363532323361323032323563323236313735373436663563323232323263323032323636363936633635373335663664363537343631363436313734363132323361323032323762356332323636363936633635356637343739373036353563323233613230356332323631373537343666356332323263323035633232356635663633373537323732363536653734356636333631373336353566356635633232336132303332333837643232326332303232363137333739366536333566363436313734363137333635373437333232336132303232356332323465366636653635356332323232326332303232363436323662363537393232336132303232356235633232336635633232326332303563323233663563323235643232376471002e'), ('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' On 6 May 2010 17:22, Erick Antezana <erick.antezana@gmail.com> wrote:

Hi,

 I just installed and configured Galaxy to run on our SGE cluster.

 I tried to upload a file (fasta, ggff3, ...) without any success... it seems I missed something at the level of the config.

 the log shows the following message:

galaxy.web.framework DEBUG 2010-05-06 17:17:06,940 Error: this request returned None from get_history(): http://machine/Galaxy/tool_runner/upload_async_create galaxy.web.framework DEBUG 2010-05-06 17:17:06,940 Error: this request returned None from get_history(): http://machine/Galaxy/tool_runner/upload_async_create galaxy.web.framework DEBUG 2010-05-06 17:17:06,940 Error: this request returned None from get_history(): http://machine/Galaxy/tool_runner/upload_async_create galaxy.web.framework DEBUG 2010-05-06 17:17:06,940 Error: this request returned None from get_history(): http://machine/Galaxy/tool_runner/upload_async_create

any tip where to look at?

I am making use of the proxy config too (http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy)... which actually works very fine in our other instances that are running on local (not clustered).

thanks, Erick