Ah, I thought this was fixed but it isn't. I can now share my workflow with other users and they can successfully run it, but when I share it via a link it still does not work and results in a server error.
I have logged in as another user and confirmed that I can both run the shared workflow and run the tools ad-hoc in sequence. Here is the stack trace from paster.log
Error - exceptions.KeyError: 'referenceGenome' URL: http://galaxy.glbrc.wisc.edu/u/branden-timm/w/huihuangs-workflow File '/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.4.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.4.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.4.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy_dist/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy_dist/lib/galaxy/web/controllers/workflow.py', line 186 in display_by_username_and_slug return trans.fill_template_mako( "workflow/display.mako", item=stored_workflow, item_data=stored_workflow.latest_workflow.steps ) File '/home/galaxy/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 653 in fill_template_mako return template.render( **data ) File '/home/galaxy/galaxy_dist/eggs/Mako-0.2.5-py2.4.egg/mako/template.py', line 133 in render return runtime._render(self, self.callable_, args, data) File '/home/galaxy/galaxy_dist/eggs/Mako-0.2.5-py2.4.egg/mako/runtime.py', line 364 in _render _render_context(template, callable_, context, *args, **_kwargs_for_callable(callable_, data)) File '/home/galaxy/galaxy_dist/eggs/Mako-0.2.5-py2.4.egg/mako/runtime.py', line 381 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/home/galaxy/galaxy_dist/eggs/Mako-0.2.5-py2.4.egg/mako/runtime.py', line 414 in _exec_template callable_(context, *args, **kwargs) File '/home/galaxy/galaxy_dist/database/compiled_templates/base_panels.mako.py', line 97 in render_body __M_writer(unicode(self.center_panel())) File '/home/galaxy/galaxy_dist/eggs/Mako-0.2.5-py2.4.egg/mako/runtime.py', line 255 in <lambda> return lambda *args, **kwargs:callable_(self.context, *args, **kwargs) File '/home/galaxy/galaxy_dist/database/compiled_templates/display_base.mako.py', line 217 in render_center_panel __M_writer(unicode(self.render_content())) File '/home/galaxy/galaxy_dist/eggs/Mako-0.2.5-py2.4.egg/mako/runtime.py', line 255 in <lambda> return lambda *args, **kwargs:callable_(self.context, *args, **kwargs) File '/home/galaxy/galaxy_dist/database/compiled_templates/display_base.mako.py', line 177 in render_render_content __M_writer(unicode(self.render_item( item, item_data ))) File '/home/galaxy/galaxy_dist/eggs/Mako-0.2.5-py2.4.egg/mako/runtime.py', line 255 in <lambda> return lambda *args, **kwargs:callable_(self.context, *args, **kwargs) File '/home/galaxy/galaxy_dist/database/compiled_templates/workflow/display.mako.py', line 111 in render_render_item __M_writer(unicode(do_inputs( tool.inputs, step.state.inputs, "", step ))) File '/home/galaxy/galaxy_dist/database/compiled_templates/workflow/display.mako.py', line 78 in do_inputs return render_do_inputs(context,inputs,values,prefix,step,other_values) File '/home/galaxy/galaxy_dist/database/compiled_templates/workflow/display.mako.py', line 209 in render_do_inputs __M_writer(unicode(do_inputs( input.cases[ current_case ].inputs, group_values, new_prefix, step, other_values ))) File '/home/galaxy/galaxy_dist/database/compiled_templates/workflow/display.mako.py', line 151 in do_inputs return render_do_inputs(context,inputs,values,prefix,step,other_values) File '/home/galaxy/galaxy_dist/database/compiled_templates/workflow/display.mako.py', line 215 in render_do_inputs __M_writer(unicode(row_for_param( input, values[ input.name ], other_values, prefix, step ))) File '/home/galaxy/galaxy_dist/database/compiled_templates/workflow/display.mako.py', line 149 in row_for_param return render_row_for_param(context,param,value,other_values,prefix,step) File '/home/galaxy/galaxy_dist/database/compiled_templates/workflow/display.mako.py', line 293 in render_row_for_param html_field = param.get_html_field( t, value, other_values ) File '/home/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py', line 1234 in get_html_field dataset_collector( history.active_datasets, None ) File '/home/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py', line 1224 in dataset_collector target_ext, converted_dataset = hda.find_conversion_destination( self.formats, converter_safe = self.converter_safe( other_values, trans ) ) File '/home/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py', line 1350 in converter_safe self.tool.visit_inputs( other_values, visitor ) File '/home/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py', line 795 in visit_inputs callback( "", input, value[input.name] ) KeyError: 'referenceGenome'
CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' 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_CONNECTION: 'Keep-Alive' HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a73ff5b9f4f415c4817e6947a58de1e3dc22da0226e65bb79eaf16daa9e2c1ce7' HTTP_HOST: 'galaxy.glbrc.wisc.edu' HTTP_REFERER: 'http://galaxy.glbrc.wisc.edu/workflow/sharing?id=ebfb8f50c6abde6d' HTTP_USER_AGENT: 'Mozilla/5.0 (X11; U; Linux i686 (x86_64); en-US; rv:1.9.2.9) Gecko/20100830 Red Hat/3.6-2.el5 Firefox/3.6.9' HTTP_X_FORWARDED_FOR: '128.104.79.82' HTTP_X_FORWARDED_HOST: 'galaxy.glbrc.wisc.edu' HTTP_X_FORWARDED_SERVER: 'galaxy.glbrc.wisc.edu' ORGINAL_HTTP_HOST: 'localhost:8080' ORGINAL_REMOTE_ADDR: '127.0.0.1' PATH_INFO: '/u/branden-timm/w/huihuangs-workflow' REMOTE_ADDR: '128.104.79.82' REQUEST_METHOD: 'GET' SERVER_NAME: '0.0.0.0' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.1'
Configuration ------------- __file__: '/home/galaxy/galaxy_dist/universe_wsgi.ini' admin_users: 'btimm@glbrc.wisc.edu,jmccurdy@glbrc.wisc.edu,ybukhman@glbrc.wisc.edu' apache_xsendfile: 'True' database_connection: 'mysql://galaxy:g@l@xy!!@mysqlprod.glbrc.wisc.edu/galaxy' debug: 'False' here: '/home/galaxy/galaxy_dist' static_cache_time: '360' static_dir: '/home/galaxy/galaxy_dist/static/' static_enabled: 'True' static_favicon_dir: '/home/galaxy/galaxy_dist/static/favicon.ico' static_images_dir: '/home/galaxy/galaxy_dist/static/images' static_scripts_dir: '/home/galaxy/galaxy_dist/static/scripts/' static_style_dir: '/home/galaxy/galaxy_dist/static/june_2007_style/blue' track_jobs_in_database: 'True' use_interactive: 'False'
WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0xe7e1c90> paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603a73ff5b9f4f415c4817e6947a58de1e3dc22da0226e65bb79eaf16daa9e2c1ce7'>, 'galaxysession=c6ca0ddb55be603a73ff5b9f4f415c4817e6947a58de1e3dc22da0226e65bb79eaf16daa9e2c1ce7') paste.expected_exceptions: [<class paste.httpexceptions.HTTPException at 0x2b05f3635ef0>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0xe7e17d0> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x2b05f2fe6550> paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True webob._parsed_query_vars: (MultiDict([]), '') wsgi process: 'Multithreaded' ------------------------------------------------------------
Cheers
-- Branden Timm btimm@glbrc.wisc.edu
Jeremy Goecks wrote:
Hi Brandon,
Answering a couple questions will help us diagnose the issue:
(a) where exactly are you seeing this error? when trying to view a shared workflow or someplace else?
(b) can users currently run your tool? (this will suggest or rule out a problem with your .loc)
Also, can you please provide the complete stack trace found in paster.
Thanks, J.
On Sep 14, 2010, at 12:41 PM, Branden Timm wrote:
Hello, I have a workflow that I've tried to share both with users and via link. Trying to use either of these methods to access the shared workflow results in a Server Error. paster.log reports:
File '/home/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py', line 795 in visit_inputs callback( "", input, value[input.name] ) KeyError: 'referenceGenome'
referenceGenome is a param from one of my tool's xml configuration file. Here is the relevant section:
<param name="referenceGenome" type="select" label="Reference Genome"> <options from_file="soap_indices.loc"> <column name="name" index="1"/> <column name="value" index="2"/> </options> </param>
soap_indices.loc only contains one line currently ecoliU00096 E. Coli U00096 /home/galaxy/galaxy_dist/soap_indices/ecoli_U00096.fasta.index
I'm confused as to why I am getting this KeyError, but I suspect that perhaps I have set up my .loc file incorrectly? Any help would be greatly appreciated. Cheers
-- Branden Timm Great Lakes Bioenergy Research Center btimm@glbrc.wisc.edu
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
J.