Hi Branden, Can you send me--and only me--your tool's XML file and the workflow that's failing? You can download the workflow by clicking on the workflow, selecting 'Download or Export' and clicking on the download link. I'll post back to the list when we've figured out what's going on. Thanks, J. On Sep 15, 2010, at 9:14 PM, Branden Timm wrote:
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
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